diff options
279 files changed, 252 insertions, 20097 deletions
diff --git a/README.md b/README.md index 01f3c655..292c849a 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ This contains the code for the Bayesian Network Webserver (BNW). -The master branch will be the stable version of the code for running with GeneNetwork. The original BNW website is compbio.uthsc.edu/BNW, which currently redirects to BNW_1.3. +The master branch will be the stable version of the code for running with GeneNetwork. The BNW website is compbio.uthsc.edu/BNW; the GeneNetwork version is at: bnw.genenetwork.org. There are a couple of files in the info_files directory that provide descriptions of the BNW code and other information. @@ -15,5 +15,10 @@ There are five branches. 4) genenet6_final_1.3: This is the final version of BNW on the GENENET6 server. -5) genenet8_initial_1.3: This is the working version of BNW on GENENET8 when we transitioned to that server. +5) genenet8_initial_1.3: This is the working version of BNW on GENENET8 when we transitioned to that server. + A couple of notes about this version. + - This version writes files created by users running BNW to /var/lib/genenet/bnw. + - The structure learning package needs to be installed in /var/lib/genenet/bnw. The files in var_lib_genenet_bnw need to be copied to /var/lib/genenet/bnw and build.sh should be run there. + - There is a python environment on GENENET8 that is used by BNW. This is in bnw-env, but I am not sure how well this will transition to other servers. + diff --git a/info_files/BNW_data_flow.txt b/info_files/BNW_data_flow.txt index 0c9dabc4..faff6476 100644 --- a/info_files/BNW_data_flow.txt +++ b/info_files/BNW_data_flow.txt @@ -1,5 +1,5 @@ This file will provide an overview of data flow within BNW and describe the output files that are created for the network. -These files are written to the /sourcecodes/data/ directory. +Files created by BNW are now written to /var/lib/genenet/bnw. This discusses what happens after clicking on "Learn network model from data" on homepage (home.php) and focuses on the core functions of BNW. Step 1: Upload data @@ -15,7 +15,7 @@ One additional note: BNW assigns each network a randomly generated 3 letter prefix when the file is uploaded. I will use ??? to signify this prefix. -The following 13 files are written to /sourcecodes/data directory during this step: +This writes many files to /var/lib/genenet/bnw directory during this step: 1) ???continuous_input_orig.txt: This is an exact copy of the input file uploaded by the user. 2) ???continuous_input.txt: Input file after processing by prepareInput.m. -A couple of notable changes are made that differentiate input.txt from input_orig.txt. @@ -49,7 +49,7 @@ This is a link to executionprogress.php which just displays a "progress bar" and To start structure learning, it runs execute_bn_gom.php. execute_bn_gom.php starts structure learning using run.sh and, then, run_octave in the run_scripts directory discussed in Step 3. -Output files from structure learning that are written to /sourcecodes/data: +Output files from structure learning that are written to /var/lib/genenet/bnw: 1) ???structure_input.txt: The structure matrix, containing the edges included in the network model. The format of this file is a header line containing the variable names. The rest is the strucure matrix where 1 indicates an edge is included in the network and a 2 is not. @@ -66,14 +66,15 @@ Before the process described in Step 2a, additional constraints or changes to de can be added using the structural constraint interface. This can be accessed by clicking on "Go to structure learning settings and the BNW - structural constraint interface" which links to create_tiers_gom.php + structural constraint interface" which links to create_tiers_gom_part1.php -The top section of create_tiers_gom.php is "Global structure learning settings" - Modifying this section will change the values in ???parent.txt, ???k.txt, and ???thr.txt. +This page allows for modifying "Global structure learning settings" + This will change the values in ???parent.txt, ???k.txt, and ???thr.txt. -The remaining sections will modify the ???ban.txt and ???white.txt files. +Clicking "Continue assign variables to tiers" will go to create_tiers_gom_part2.php. + This page will modify the ???ban.txt and ???white.txt files. -Clicking on "Perform Bayesian network modeling" goes to executionprogress.php and Step 2a is followed. +Clicking on "Click here to perform Bayesian network modeling after creating tiers" goes to tier_description_processing_gom.php and Step 2a is followed. Step 3: Parameter learning of the original network. diff --git a/info_files/BNW_file_overview.txt b/info_files/BNW_file_overview.txt index a3c2fad7..b2d191f2 100644 --- a/info_files/BNW_file_overview.txt +++ b/info_files/BNW_file_overview.txt @@ -1,18 +1,17 @@ -This file will provide an overview of the BNW code. +This file will provide an overview of the BNW code. It is not completely up to date. The information should be correct, but some files might be missing. At this point, BNW requires three packages that are not currently included in the BNW directory. These are dot/graphviz; octave; and plotly. The BNW code assumes: a) dot can be executed using /usr/bin/dot b) octave can be executed using /usr/bin/octave c) plotly: - The version of python on the current server is too old for plotly. I installed an newer version of python in my home directory: - python2.7 is currently installed in /home/jziebart/python/Python-2.7.15/python - Then, to use plotly, I modified files.py in: - /home/jziebart/python/lib/python2.7/site-packages/plotly to use absolute paths for PLOTLY_DIR and TEST_DIR - The files that need plotly are: cv_plotly.py, kfold_plotly.py, and ts_plotly.py + Plotly runs through a python environment for BNW. The python version is 3.6.8 and the plotly version is 4.13.0. + The python environment files are in bnw-env. -BNW is currently located at /var/www/html/compbio/BNW_x.xx -(The current development version is BNW_1.22). + The files that need plotly are: cv_plotly.py, kfold_plotly.py, ts_plotly.py, violin_plotly.py, violin_ev_plotly.py, and violin_int_plotly.py. + +BNW is currently located at /var/www/html/compbio/BNW_x.x +(The current development version is BNW_1.3). The main BNW directory contains two basic files (index.html and home.php) and two directories. A couple of lines in home.php should be modified/updated to point to the correct BNW directory. @@ -22,6 +21,8 @@ downloads: This contains the downloadable version of the BNW structure learning sourcecodes: This contains the files and codes that are used by the webserver. The main purpose of this file is to provide a brief overview of the files that are contained in 'sourcecodes'. +bnw-env: The python environment for BNW. + 1. Directories within sourcecodes: a) bnt-master: This contains the code for BayesNetToolbox which is used in parameter learning in BNW. It has been slightly modified to work with Octave instead of MATLAB. @@ -30,19 +31,19 @@ a) bnt-master: This contains the code for BayesNetToolbox which is used in param b) parameter_learning: This contains the MATLAB/Octave code that we have written for parameter_learning. It also prepares data that has been uploaded to BNW for use with the structure learning code. -c) k-best and localscore: These two directories contains the C code used for structure learning. +c) BNW_workflow_test_files, example_datasets, and examples: These three directories contain files that are used by the tutorials and examples on the BNW homepage. -d) BNW_workflow_test_files, example_datasets, and examples: These three directories contain files that are used by the tutorials and examples on the BNW homepage. +d) data: The data for files generated by using BNW is written to this directory. It also contains several sub-directories that contain example data and networks. -e) data: The data for files generated by using BNW is written to this directory. It also contains several sub-directories that contain example data and networks. +e) run_scripts: Scripts that run Octave calculations. -f) run_scripts: Scripts that run Octave calculations. +f) scripts: Javascript libraries and associated files. 2. Files within sourcecodes: a) Major BNW php files: Many of these will be described in BNW_data_flow.txt. bn_file_load_gom.php: Used in uploading data to be used for structure learning. -create_tiers_gom.php: Structural constraint interface. +create_tiers_gom_part1.php and create_tiers_gom_part2.php: Structural constraint interface. home_upload.php: Used in uploading a data file and a structure file when the structure is known. layout_example.php: Main php file for displaying/making predictions with network using example data. layout.php: Main php file for displaying/making predictions with network using user uploaded data. @@ -64,9 +65,7 @@ structure run.sh c) Files related to home page, help files, example data sets, and tutorials: -BNW_overview.png -BNW_workflow_1.htm -BNW_workflow_2.htm +BNW_overview_new.png BNW_workflow_net1.htm BNW_workflow_sci.htm index.html @@ -83,18 +82,12 @@ sf-homepage.css graph-creator.css graph-creator.js -e) PHP files that support layout.php or layout_example.php: -add_evd_example.php +e) PHP files that support layout.php: add_evd.php -add_inv_example.php add_inv.php -network_layout_evd_2_example.php network_layout_evd_2.php -network_layout_evd_example.php network_layout_evd.php -network_layout_inv_2_example.php network_layout_inv_2.php -network_layout_inv_example.php network_layout_inv.php f) Files used for cross-validation/making predictions using a test set: diff --git a/info_files/server_change_notes.txt b/info_files/old_server_change_notes.txt index 849d6f84..e3638b60 100644 --- a/info_files/server_change_notes.txt +++ b/info_files/old_server_change_notes.txt @@ -1,3 +1,5 @@ +This is out of date, but I will leave it here until I can update it. + This file will contain notes about changes that might need to be made on a new server: Required software: diff --git a/sourcecodes/bn_genenet.php b/sourcecodes/bn_genenet.php index de33e952..8fd5aea7 100644 --- a/sourcecodes/bn_genenet.php +++ b/sourcecodes/bn_genenet.php @@ -8,14 +8,9 @@ function genenetwork_data() { with(window.document.key_search) { - //searchkey.value="<?php echo $_POST['My_Genenet'] ?>"; genenet_str = "<?php echo $_POST['My_Genenet'] ?>"; - //genenet_str = genenet_str.slice(0,-1); - //console.log(genenet_str); genenet_str = genenet_str.replace(/,/g, '\t'); genenet_str = genenet_str.replace(/;/g,'\n'); - //console.log(genenet_str); - //genenet_str = genenet_str + "\n\n"; searchkey.value=genenet_str; } } diff --git a/sourcecodes/data/example1/Bqxban.txt b/sourcecodes/data/example1/Bqxban.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example1/Bqxban.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example1/Bqxcontinuous_input.txt b/sourcecodes/data/example1/Bqxcontinuous_input.txt deleted file mode 100644 index 5e296c45..00000000 --- a/sourcecodes/data/example1/Bqxcontinuous_input.txt +++ /dev/null @@ -1,203 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -2 2 1 1 1 1 1 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-0.48699 -0.10105 -1 1 -1.0408 -0.99866 2.0799 1.1634 0.092516 0.30401 -1 1 -0.87125 -0.88987 1.0278 1.0157 -0.23725 1.2377 -1 2 -0.020591 -0.03398 -0.024834 -1.3588 -0.045961 -0.89693 -1 1 0.9213 -0.57037 1.044 1.2994 0.046517 0.66563 -1 2 -0.87288 -0.96382 -0.704 -1.2184 0.046903 -0.30008 -1 2 0.77586 -0.34168 -0.09867 -0.37744 -0.24309 -0.13441 -2 1 0.19521 0.67595 1.4533 1.5115 0.19553 0.79596 -2 1 -1.3273 1.0891 1.2544 0.98928 0.045725 0.54963 -2 2 0.59176 0.65915 -0.84578 -0.080229 -0.26961 0.24045 -1 2 -0.66958 -1.042 -1.2138 -0.7612 -0.22775 -0.40062 -1 2 1.1154 -0.57069 -0.6592 -2.1961 -0.013175 0.46007 -1 2 -0.5254 0.0031225 -0.77758 0.8169 0.13224 -0.65572 -2 1 0.24551 1.5078 0.10719 1.1454 0.70578 0.59051 -1 2 0.29875 -0.11455 -1.0497 -0.77881 0.080708 -0.48337 -1 1 -0.1047 0.011628 1.2504 0.41776 -0.20102 1.2252 -1 2 0.44808 -0.8165 -0.080134 -0.49618 0.051011 -0.71722 -2 1 2.0365 1.5592 1.3257 1.2472 -0.47899 0.10943 -1 1 -0.16507 -0.66011 0.98739 0.58519 0.245 -0.43277 -1 2 -0.028366 -0.16961 -1.3266 0.14248 -0.24634 -1.1154 -2 1 0.92842 1.8842 1.3169 1.0358 -0.20988 0.88021 -2 2 0.33158 0.32463 -0.50924 0.40233 0.54391 -0.24309 -1 2 1.2555 0.1928 -0.487 0.048779 -0.23483 -1.477 -2 1 0.75021 0.85943 -0.2323 0.10748 -0.68906 0.84276 -2 2 0.6297 1.7397 -1.6136 -0.43268 -0.21442 -0.77462 -2 1 0.53168 1.0807 1.0853 0.62304 0.44036 0.48087 -1 2 -0.31256 -0.69771 -0.88556 -1.333 0.038614 -1.5744 -1 2 -0.039695 -0.52447 0.91401 -0.93272 0.53434 -0.080746 -2 1 -0.16596 0.56821 0.76008 0.45442 0.10286 0.6539 -1 2 -0.4331 -0.89669 -1.3097 -1.2157 0.1065 -0.8512 -1 2 -0.34708 -0.51457 -1.012 -0.39437 -0.55374 -1.144 -2 2 0.024082 0.7128 -1.3702 -1.4492 -0.10228 -0.59071 -1 2 -0.0037109 -0.68845 -0.649 -0.91581 0.066805 -0.98583 -2 1 0.68706 0.067424 0.87139 0.7938 -0.099645 1.529 -2 2 -0.31183 0.57814 -0.80815 -0.66724 -0.31919 -0.61319 -1 2 -0.11153 -0.6246 -0.27979 -0.18363 0.83639 0.014919 -2 2 0.20406 1.5838 -0.96334 -1.1228 -0.17808 -1.2123 -2 2 -0.1134 0.63358 -0.53321 -0.84276 -0.27657 -0.36992 -1 2 0.25517 0.67006 -0.1349 0.18275 0.40982 -0.62487 -1 1 -1.2684 0.31042 0.91155 0.66143 0.2483 -0.12434 -1 1 -0.97542 -0.85419 0.7663 0.16362 -0.18737 0.67266 -1 2 -0.043882 -0.62746 -0.82816 -0.40626 -0.051048 -0.61297 -1 1 0.59605 -0.45852 1.2962 0.78156 -0.48154 0.17778 -2 2 -0.06266 1.1144 -0.80524 -0.3189 -0.16038 -0.96372 -1 2 -1.1821 1.0798 -1.3407 -0.52643 0.12458 -0.7871 -2 2 0.59446 0.89186 -0.97856 -0.64658 0.2712 -1.5538 -1 2 0.15067 0.41827 -1.0487 -1.0551 0.19143 -1.4537 -1 2 -1.073 0.022587 -1.7088 -1.3777 0.1964 -0.84025 -2 1 0.20928 1.8026 1.2073 2.78 0.15131 0.3448 -1 2 -1.1317 -0.6359 -0.70457 -1.676 -0.22886 -0.58769 -1 1 -0.039428 -0.58746 0.56 0.7896 -0.052581 0.99511 -1 2 0.55023 -0.20403 0.138 -0.70518 0.66927 -0.28861 -2 2 0.57423 1.1886 0.092876 0.025677 -0.41099 -1.2858 -2 2 -0.14179 1.5827 -0.94328 0.7703 -0.43967 -0.50448 -2 2 0.14666 1.0492 -0.0030259 -0.62418 -0.087515 -0.048386 - diff --git a/sourcecodes/data/example1/Bqxgraphviz.txt b/sourcecodes/data/example1/Bqxgraphviz.txt deleted file mode 100644 index 498a5fd8..00000000 --- a/sourcecodes/data/example1/Bqxgraphviz.txt +++ /dev/null @@ -1,12 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Geno1 -> Trait2; -Geno2 -> Trait3; -Geno2 -> Trait4; -Geno2 -> Trait6; -Trait2 -> Trait1; -Trait2 -> Trait4; -Trait3 -> Trait4; -Trait6 -> Trait3; -} \ No newline at end of file diff --git a/sourcecodes/data/example1/Bqxk.txt b/sourcecodes/data/example1/Bqxk.txt deleted file mode 100644 index d00491fd..00000000 --- a/sourcecodes/data/example1/Bqxk.txt +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/sourcecodes/data/example1/Bqxmap.txt b/sourcecodes/data/example1/Bqxmap.txt deleted file mode 100644 index dc9ba9be..00000000 --- a/sourcecodes/data/example1/Bqxmap.txt +++ /dev/null @@ -1,8 +0,0 @@ -Geno1 0.473175 1.335000 -Geno2 0.496318 1.570000 -Trait1 0.668009 -0.023903 -Trait2 0.796873 0.038552 -Trait3 1.036694 0.068708 -Trait4 0.984008 -0.010125 -Trait5 0.316471 0.008911 -Trait6 0.904542 -0.114267 diff --git a/sourcecodes/data/example1/Bqxmapdata.txt b/sourcecodes/data/example1/Bqxmapdata.txt deleted file mode 100644 index 42b2fd9c..00000000 --- a/sourcecodes/data/example1/Bqxmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 diff --git a/sourcecodes/data/example1/Bqxname.txt b/sourcecodes/data/example1/Bqxname.txt deleted file mode 100644 index 8f42b468..00000000 --- a/sourcecodes/data/example1/Bqxname.txt +++ /dev/null @@ -1 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 diff --git a/sourcecodes/data/example1/Bqxnet_figure.txt b/sourcecodes/data/example1/Bqxnet_figure.txt deleted file mode 100644 index 11113895..00000000 --- a/sourcecodes/data/example1/Bqxnet_figure.txt +++ /dev/null @@ -1,652 +0,0 @@ -8 -1200 1200 -Trait5 0 0 -Geno2 300 0 -Trait6 220 240 -Trait3 100 480 -Geno1 600 0 -Trait2 620 240 -Trait4 420 720 -Trait1 500 480 -Trait5 1 -250 150 -0 -0 --3.2055 0.0025 --3.1368 0.0030 --3.0681 0.0038 --2.9994 0.0046 --2.9308 0.0057 --2.8621 0.0069 --2.7934 0.0083 --2.7247 0.0101 --2.6561 0.0121 --2.5874 0.0144 --2.5187 0.0172 --2.4500 0.0203 --2.3813 0.0240 --2.3127 0.0281 --2.2440 0.0328 --2.1753 0.0381 --2.1066 0.0441 --2.0379 0.0508 --1.9693 0.0582 --1.9006 0.0664 --1.8319 0.0754 --1.7632 0.0852 --1.6945 0.0958 --1.6259 0.1073 --1.5572 0.1195 --1.4885 0.1326 --1.4198 0.1463 --1.3511 0.1608 --1.2825 0.1758 --1.2138 0.1914 --1.1451 0.2074 --1.0764 0.2237 --1.0078 0.2401 --0.9391 0.2565 --0.8704 0.2728 --0.8017 0.2888 --0.7330 0.3042 --0.6644 0.3190 --0.5957 0.3330 --0.5270 0.3460 --0.4583 0.3578 --0.3896 0.3682 --0.3210 0.3772 --0.2523 0.3846 --0.1836 0.3904 --0.1149 0.3944 --0.0462 0.3965 -0.0224 0.3969 -0.0911 0.3953 -0.1598 0.3920 -0.2285 0.3868 -0.2971 0.3800 -0.3658 0.3715 -0.4345 0.3615 -0.5032 0.3502 -0.5719 0.3376 -0.6405 0.3240 -0.7092 0.3095 -0.7779 0.2942 -0.8466 0.2784 -0.9153 0.2622 -0.9839 0.2458 -1.0526 0.2294 -1.1213 0.2130 -1.1900 0.1969 -1.2587 0.1812 -1.3273 0.1659 -1.3960 0.1513 -1.4647 0.1373 -1.5334 0.1240 -1.6021 0.1114 -1.6707 0.0997 -1.7394 0.0888 -1.8081 0.0787 -1.8768 0.0694 -1.9454 0.0610 -2.0141 0.0533 -2.0828 0.0464 -2.1515 0.0401 -2.2202 0.0346 -2.2888 0.0297 -2.3575 0.0253 -2.4262 0.0215 -2.4949 0.0182 -2.5636 0.0153 -2.6322 0.0129 -2.7009 0.0107 -2.7696 0.0089 -2.8383 0.0074 -2.9070 0.0061 -2.9756 0.0050 -3.0443 0.0040 -3.1130 0.0033 -3.1817 0.0026 -3.2503 0.0021 -3.3190 0.0017 -3.3877 0.0014 -3.4564 0.0011 -3.5251 0.0008 -3.5937 0.0007 -3.6624 0.0005 -Geno2 2 -250 150 -0 -3 3 4 7 -1 0.4300 -2 0.5700 -Trait6 1 -250 150 -1 2 -1 4 --3.6825 0.0005 --3.6140 0.0006 --3.5455 0.0008 --3.4769 0.0010 --3.4084 0.0013 --3.3399 0.0016 --3.2713 0.0020 --3.2028 0.0025 --3.1343 0.0031 --3.0658 0.0038 --2.9972 0.0046 --2.9287 0.0057 --2.8602 0.0069 --2.7917 0.0084 --2.7231 0.0101 --2.6546 0.0121 --2.5861 0.0145 --2.5176 0.0172 --2.4490 0.0204 --2.3805 0.0240 --2.3120 0.0282 --2.2435 0.0329 --2.1749 0.0382 --2.1064 0.0441 --2.0379 0.0508 --1.9694 0.0582 --1.9008 0.0664 --1.8323 0.0753 --1.7638 0.0851 --1.6953 0.0957 --1.6267 0.1071 --1.5582 0.1193 --1.4897 0.1323 --1.4212 0.1461 --1.3526 0.1605 --1.2841 0.1755 --1.2156 0.1910 --1.1471 0.2069 --1.0785 0.2232 --1.0100 0.2396 --0.9415 0.2560 --0.8730 0.2722 --0.8044 0.2881 --0.7359 0.3036 --0.6674 0.3184 --0.5989 0.3324 --0.5303 0.3454 --0.4618 0.3572 --0.3933 0.3677 --0.3248 0.3768 --0.2562 0.3843 --0.1877 0.3901 --0.1192 0.3942 --0.0507 0.3965 -0.0179 0.3969 -0.0864 0.3955 -0.1549 0.3923 -0.2234 0.3873 -0.2920 0.3806 -0.3605 0.3722 -0.4290 0.3624 -0.4975 0.3512 -0.5661 0.3387 -0.6346 0.3252 -0.7031 0.3108 -0.7716 0.2956 -0.8402 0.2799 -0.9087 0.2638 -0.9772 0.2474 -1.0457 0.2310 -1.1143 0.2147 -1.1828 0.1986 -1.2513 0.1829 -1.3198 0.1676 -1.3884 0.1529 -1.4569 0.1388 -1.5254 0.1255 -1.5939 0.1129 -1.6625 0.1011 -1.7310 0.0901 -1.7995 0.0799 -1.8680 0.0706 -1.9366 0.0620 -2.0051 0.0542 -2.0736 0.0472 -2.1421 0.0409 -2.2107 0.0353 -2.2792 0.0303 -2.3477 0.0259 -2.4162 0.0221 -2.4848 0.0187 -2.5533 0.0157 -2.6218 0.0132 -2.6903 0.0110 -2.7589 0.0092 -2.8274 0.0076 -2.8959 0.0062 -2.9644 0.0051 -3.0330 0.0042 -3.1015 0.0034 -3.1700 0.0027 -Trait3 1 -250 150 -2 2 3 -1 7 --2.7825 0.0086 --2.7216 0.0101 --2.6608 0.0119 --2.5999 0.0140 --2.5390 0.0163 --2.4782 0.0190 --2.4173 0.0220 --2.3565 0.0254 --2.2956 0.0292 --2.2347 0.0335 --2.1739 0.0383 --2.1130 0.0435 --2.0521 0.0494 --1.9913 0.0558 --1.9304 0.0628 --1.8695 0.0704 --1.8087 0.0786 --1.7478 0.0875 --1.6870 0.0970 --1.6261 0.1072 --1.5652 0.1181 --1.5044 0.1295 --1.4435 0.1415 --1.3826 0.1541 --1.3218 0.1672 --1.2609 0.1807 --1.2000 0.1946 --1.1392 0.2088 --1.0783 0.2232 --1.0175 0.2378 --0.9566 0.2524 --0.8957 0.2668 --0.8349 0.2811 --0.7740 0.2951 --0.7131 0.3086 --0.6523 0.3216 --0.5914 0.3338 --0.5305 0.3453 --0.4697 0.3559 --0.4088 0.3654 --0.3480 0.3738 --0.2871 0.3811 --0.2262 0.3870 --0.1654 0.3916 --0.1045 0.3948 --0.0436 0.3966 -0.0172 0.3969 -0.0781 0.3957 -0.1389 0.3932 -0.1998 0.3892 -0.2607 0.3838 -0.3215 0.3771 -0.3824 0.3692 -0.4433 0.3601 -0.5041 0.3500 -0.5650 0.3389 -0.6259 0.3270 -0.6867 0.3143 -0.7476 0.3010 -0.8084 0.2872 -0.8693 0.2731 -0.9302 0.2587 -0.9910 0.2441 -1.0519 0.2295 -1.1128 0.2150 -1.1736 0.2007 -1.2345 0.1867 -1.2954 0.1730 -1.3562 0.1597 -1.4171 0.1469 -1.4779 0.1346 -1.5388 0.1229 -1.5997 0.1119 -1.6605 0.1014 -1.7214 0.0916 -1.7823 0.0824 -1.8431 0.0739 -1.9040 0.0660 -1.9649 0.0587 -2.0257 0.0521 -2.0866 0.0460 -2.1474 0.0405 -2.2083 0.0355 -2.2692 0.0310 -2.3300 0.0270 -2.3909 0.0234 -2.4518 0.0203 -2.5126 0.0174 -2.5735 0.0150 -2.6344 0.0128 -2.6952 0.0109 -2.7561 0.0092 -2.8169 0.0078 -2.8778 0.0066 -2.9387 0.0055 -2.9995 0.0046 -3.0604 0.0038 -3.1213 0.0032 -3.1821 0.0026 -3.2430 0.0022 -3.3039 0.0018 -Geno1 2 -250 150 -0 -1 6 -1 0.6650 -2 0.3350 -Trait2 1 -250 150 -1 5 -2 7 8 --3.0753 0.0037 --3.0078 0.0045 --2.9403 0.0055 --2.8728 0.0067 --2.8053 0.0081 --2.7378 0.0097 --2.6702 0.0116 --2.6027 0.0139 --2.5352 0.0165 --2.4677 0.0195 --2.4002 0.0229 --2.3327 0.0268 --2.2652 0.0313 --2.1977 0.0363 --2.1302 0.0420 --2.0627 0.0483 --1.9951 0.0553 --1.9276 0.0631 --1.8601 0.0716 --1.7926 0.0809 --1.7251 0.0910 --1.6576 0.1019 --1.5901 0.1135 --1.5226 0.1260 --1.4551 0.1392 --1.3876 0.1530 --1.3201 0.1675 --1.2525 0.1826 --1.1850 0.1981 --1.1175 0.2139 --1.0500 0.2300 --0.9825 0.2462 --0.9150 0.2623 --0.8475 0.2782 --0.7800 0.2937 --0.7125 0.3088 --0.6450 0.3231 --0.5775 0.3366 --0.5099 0.3490 --0.4424 0.3603 --0.3749 0.3703 --0.3074 0.3788 --0.2399 0.3858 --0.1724 0.3912 --0.1049 0.3948 --0.0374 0.3967 -0.0301 0.3968 -0.0976 0.3951 -0.1652 0.3916 -0.2327 0.3865 -0.3002 0.3796 -0.3677 0.3713 -0.4352 0.3614 -0.5027 0.3503 -0.5702 0.3379 -0.6377 0.3246 -0.7052 0.3103 -0.7727 0.2954 -0.8402 0.2799 -0.9078 0.2640 -0.9753 0.2479 -1.0428 0.2317 -1.1103 0.2156 -1.1778 0.1998 -1.2453 0.1842 -1.3128 0.1691 -1.3803 0.1546 -1.4478 0.1406 -1.5153 0.1274 -1.5829 0.1148 -1.6504 0.1031 -1.7179 0.0921 -1.7854 0.0819 -1.8529 0.0725 -1.9204 0.0640 -1.9879 0.0561 -2.0554 0.0490 -2.1229 0.0426 -2.1904 0.0369 -2.2579 0.0318 -2.3255 0.0273 -2.3930 0.0233 -2.4605 0.0198 -2.5280 0.0168 -2.5955 0.0141 -2.6630 0.0119 -2.7305 0.0099 -2.7980 0.0082 -2.8655 0.0068 -2.9330 0.0056 -3.0005 0.0046 -3.0681 0.0038 -3.1356 0.0031 -3.2031 0.0025 -3.2706 0.0020 -3.3381 0.0016 -3.4056 0.0013 -3.4731 0.0010 -3.5406 0.0008 -3.6081 0.0006 -3.6756 0.0005 -Trait4 1 -250 150 -3 2 4 6 -0 --3.2636 0.0025 --3.1926 0.0031 --3.1216 0.0039 --3.0506 0.0048 --2.9796 0.0059 --2.9086 0.0071 --2.8376 0.0086 --2.7666 0.0104 --2.6957 0.0125 --2.6247 0.0150 --2.5537 0.0178 --2.4827 0.0211 --2.4117 0.0248 --2.3407 0.0291 --2.2697 0.0340 --2.1987 0.0395 --2.1277 0.0456 --2.0567 0.0525 --1.9857 0.0601 --1.9148 0.0685 --1.8438 0.0777 --1.7728 0.0877 --1.7018 0.0986 --1.6308 0.1102 --1.5598 0.1226 --1.4888 0.1358 --1.4178 0.1497 --1.3468 0.1643 --1.2758 0.1794 --1.2049 0.1949 --1.1339 0.2108 --1.0629 0.2270 --0.9919 0.2432 --0.9209 0.2593 --0.8499 0.2751 --0.7789 0.2906 --0.7079 0.3055 --0.6369 0.3196 --0.5659 0.3328 --0.4949 0.3448 --0.4240 0.3557 --0.3530 0.3651 --0.2820 0.3730 --0.2110 0.3792 --0.1400 0.3838 --0.0690 0.3865 -0.0020 0.3874 -0.0730 0.3865 -0.1440 0.3838 -0.2150 0.3792 -0.2859 0.3730 -0.3569 0.3651 -0.4279 0.3557 -0.4989 0.3448 -0.5699 0.3328 -0.6409 0.3196 -0.7119 0.3055 -0.7829 0.2906 -0.8539 0.2752 -0.9249 0.2593 -0.9959 0.2432 -1.0668 0.2270 -1.1378 0.2109 -1.2088 0.1950 -1.2798 0.1794 -1.3508 0.1643 -1.4218 0.1498 -1.4928 0.1359 -1.5638 0.1227 -1.6348 0.1102 -1.7058 0.0986 -1.7767 0.0877 -1.8477 0.0777 -1.9187 0.0685 -1.9897 0.0601 -2.0607 0.0525 -2.1317 0.0456 -2.2027 0.0395 -2.2737 0.0340 -2.3447 0.0291 -2.4157 0.0248 -2.4867 0.0211 -2.5576 0.0178 -2.6286 0.0150 -2.6996 0.0125 -2.7706 0.0104 -2.8416 0.0086 -2.9126 0.0071 -2.9836 0.0059 -3.0546 0.0048 -3.1256 0.0039 -3.1966 0.0031 -3.2675 0.0025 -3.3385 0.0020 -3.4095 0.0016 -3.4805 0.0013 -3.5515 0.0010 -3.6225 0.0008 -3.6935 0.0006 -3.7645 0.0005 -3.8355 0.0004 -Trait1 1 -250 150 -1 6 -0 --3.6875 0.0005 --3.6097 0.0006 --3.5318 0.0008 --3.4540 0.0011 --3.3761 0.0014 --3.2983 0.0018 --3.2204 0.0024 --3.1425 0.0030 --3.0647 0.0038 --2.9868 0.0048 --2.9090 0.0061 --2.8311 0.0076 --2.7533 0.0094 --2.6754 0.0115 --2.5976 0.0141 --2.5197 0.0172 --2.4418 0.0208 --2.3640 0.0251 --2.2861 0.0300 --2.2083 0.0356 --2.1304 0.0421 --2.0526 0.0495 --1.9747 0.0577 --1.8969 0.0670 --1.8190 0.0773 --1.7411 0.0887 --1.6633 0.1011 --1.5854 0.1145 --1.5076 0.1290 --1.4297 0.1444 --1.3519 0.1608 --1.2740 0.1778 --1.1962 0.1956 --1.1183 0.2138 --1.0404 0.2323 --0.9626 0.2509 --0.8847 0.2694 --0.8069 0.2875 --0.7290 0.3050 --0.6512 0.3216 --0.5733 0.3371 --0.4955 0.3513 --0.4176 0.3639 --0.3397 0.3746 --0.2619 0.3834 --0.1840 0.3900 --0.1062 0.3944 --0.0283 0.3964 -0.0495 0.3961 -0.1274 0.3934 -0.2052 0.3884 -0.2831 0.3812 -0.3610 0.3719 -0.4388 0.3606 -0.5167 0.3476 -0.5945 0.3330 -0.6724 0.3172 -0.7502 0.3003 -0.8281 0.2826 -0.9059 0.2644 -0.9838 0.2458 -1.0617 0.2272 -1.1395 0.2088 -1.2174 0.1907 -1.2952 0.1731 -1.3731 0.1562 -1.4509 0.1401 -1.5288 0.1250 -1.6066 0.1108 -1.6845 0.0976 -1.7624 0.0855 -1.8402 0.0744 -1.9181 0.0644 -1.9959 0.0554 -2.0738 0.0474 -2.1516 0.0403 -2.2295 0.0340 -2.3073 0.0286 -2.3852 0.0238 -2.4631 0.0198 -2.5409 0.0163 -2.6188 0.0134 -2.6966 0.0109 -2.7745 0.0088 -2.8523 0.0071 -2.9302 0.0057 -3.0080 0.0045 -3.0859 0.0036 -3.1638 0.0028 -3.2416 0.0022 -3.3195 0.0017 -3.3973 0.0013 -3.4752 0.0010 -3.5530 0.0008 -3.6309 0.0006 -3.7087 0.0004 -3.7866 0.0003 -3.8645 0.0002 -3.9423 0.0002 -4.0202 0.0001 -4.0980 0.0001 diff --git a/sourcecodes/data/example1/Bqxnlevels.txt b/sourcecodes/data/example1/Bqxnlevels.txt deleted file mode 100644 index 32457058..00000000 --- a/sourcecodes/data/example1/Bqxnlevels.txt +++ /dev/null @@ -1,4 +0,0 @@ -Geno1 1 2 -Geno2 1 2 - - diff --git a/sourcecodes/data/example1/Bqxnnode.txt b/sourcecodes/data/example1/Bqxnnode.txt deleted file mode 100644 index 45a4fb75..00000000 --- a/sourcecodes/data/example1/Bqxnnode.txt +++ /dev/null @@ -1 +0,0 @@ -8 diff --git a/sourcecodes/data/example1/Bqxnrows.txt b/sourcecodes/data/example1/Bqxnrows.txt deleted file mode 100644 index 3bc92d44..00000000 --- a/sourcecodes/data/example1/Bqxnrows.txt +++ /dev/null @@ -1 +0,0 @@ -201 diff --git a/sourcecodes/data/example1/Bqxparameters.txt b/sourcecodes/data/example1/Bqxparameters.txt deleted file mode 100644 index d1345709..00000000 --- a/sourcecodes/data/example1/Bqxparameters.txt +++ /dev/null @@ -1,34 +0,0 @@ -Geno1 -Discrete node with 2 states -1 0.6650 -2 0.3350 - -Geno2 -Discrete node with 2 states -1 0.4300 -2 0.5700 - -Trait1 -Continuous node --0.0239 0.6720 - -Trait2 -Continuous node -0.0386 0.8009 - -Trait3 -Continuous node -0.0687 1.0420 - -Trait4 -Continuous node --0.0081 1.0133 - -Trait5 -Continuous node -0.0089 0.3181 - -Trait6 -Continuous node --0.1143 0.9091 - diff --git a/sourcecodes/data/example1/Bqxparent.txt b/sourcecodes/data/example1/Bqxparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example1/Bqxparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example1/Bqxstructure_old.txt b/sourcecodes/data/example1/Bqxstructure_old.txt deleted file mode 100644 index 7749d17e..00000000 --- a/sourcecodes/data/example1/Bqxstructure_old.txt +++ /dev/null @@ -1,7 +0,0 @@ -Geno1 0.6650 0.3350 -Trait2 0.0037 0.0045 0.0055 0.0067 0.0081 0.0097 0.0116 0.0139 0.0165 0.0195 0.0229 0.0268 0.0313 0.0363 0.0420 0.0483 0.0553 0.0631 0.0716 0.0809 0.0910 0.1019 0.1135 0.1260 0.1392 0.1530 0.1675 0.1826 0.1981 0.2139 0.2300 0.2462 0.2623 0.2782 0.2937 0.3088 0.3231 0.3366 0.3490 0.3603 0.3703 0.3788 0.3858 0.3912 0.3948 0.3967 0.3968 0.3951 0.3916 0.3865 0.3796 0.3713 0.3614 0.3503 0.3379 0.3246 0.3103 0.2954 0.2799 0.2640 0.2479 0.2317 0.2156 0.1998 0.1842 0.1691 0.1546 0.1406 0.1274 0.1148 0.1031 0.0921 0.0819 0.0725 0.0640 0.0561 0.0490 0.0426 0.0369 0.0318 0.0273 0.0233 0.0198 0.0168 0.0141 0.0119 0.0099 0.0082 0.0068 0.0056 0.0046 0.0038 0.0031 0.0025 0.0020 0.0016 0.0013 0.0010 0.0008 0.0006 0.0005 -Geno2 0.4300 0.5700 -Trait3 0.0086 0.0101 0.0119 0.0140 0.0163 0.0190 0.0220 0.0254 0.0292 0.0335 0.0383 0.0435 0.0494 0.0558 0.0628 0.0704 0.0786 0.0875 0.0970 0.1072 0.1181 0.1295 0.1415 0.1541 0.1672 0.1807 0.1946 0.2088 0.2232 0.2378 0.2524 0.2668 0.2811 0.2951 0.3086 0.3216 0.3338 0.3453 0.3559 0.3654 0.3738 0.3811 0.3870 0.3916 0.3948 0.3966 0.3969 0.3957 0.3932 0.3892 0.3838 0.3771 0.3692 0.3601 0.3500 0.3389 0.3270 0.3143 0.3010 0.2872 0.2731 0.2587 0.2441 0.2295 0.2150 0.2007 0.1867 0.1730 0.1597 0.1469 0.1346 0.1229 0.1119 0.1014 0.0916 0.0824 0.0739 0.0660 0.0587 0.0521 0.0460 0.0405 0.0355 0.0310 0.0270 0.0234 0.0203 0.0174 0.0150 0.0128 0.0109 0.0092 0.0078 0.0066 0.0055 0.0046 0.0038 0.0032 0.0026 0.0022 0.0018 -Trait4 0.0025 0.0031 0.0039 0.0048 0.0059 0.0071 0.0086 0.0104 0.0125 0.0150 0.0178 0.0211 0.0248 0.0291 0.0340 0.0395 0.0456 0.0525 0.0601 0.0685 0.0777 0.0877 0.0986 0.1102 0.1226 0.1358 0.1497 0.1643 0.1794 0.1949 0.2108 0.2270 0.2432 0.2593 0.2751 0.2906 0.3055 0.3196 0.3328 0.3448 0.3557 0.3651 0.3730 0.3792 0.3838 0.3865 0.3874 0.3865 0.3838 0.3792 0.3730 0.3651 0.3557 0.3448 0.3328 0.3196 0.3055 0.2906 0.2752 0.2593 0.2432 0.2270 0.2109 0.1950 0.1794 0.1643 0.1498 0.1359 0.1227 0.1102 0.0986 0.0877 0.0777 0.0685 0.0601 0.0525 0.0456 0.0395 0.0340 0.0291 0.0248 0.0211 0.0178 0.0150 0.0125 0.0104 0.0086 0.0071 0.0059 0.0048 0.0039 0.0031 0.0025 0.0020 0.0016 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004 -Trait6 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0020 0.0025 0.0031 0.0038 0.0046 0.0057 0.0069 0.0084 0.0101 0.0121 0.0145 0.0172 0.0204 0.0240 0.0282 0.0329 0.0382 0.0441 0.0508 0.0582 0.0664 0.0753 0.0851 0.0957 0.1071 0.1193 0.1323 0.1461 0.1605 0.1755 0.1910 0.2069 0.2232 0.2396 0.2560 0.2722 0.2881 0.3036 0.3184 0.3324 0.3454 0.3572 0.3677 0.3768 0.3843 0.3901 0.3942 0.3965 0.3969 0.3955 0.3923 0.3873 0.3806 0.3722 0.3624 0.3512 0.3387 0.3252 0.3108 0.2956 0.2799 0.2638 0.2474 0.2310 0.2147 0.1986 0.1829 0.1676 0.1529 0.1388 0.1255 0.1129 0.1011 0.0901 0.0799 0.0706 0.0620 0.0542 0.0472 0.0409 0.0353 0.0303 0.0259 0.0221 0.0187 0.0157 0.0132 0.0110 0.0092 0.0076 0.0062 0.0051 0.0042 0.0034 0.0027 -Trait1 0.0005 0.0006 0.0008 0.0011 0.0014 0.0018 0.0024 0.0030 0.0038 0.0048 0.0061 0.0076 0.0094 0.0115 0.0141 0.0172 0.0208 0.0251 0.0300 0.0356 0.0421 0.0495 0.0577 0.0670 0.0773 0.0887 0.1011 0.1145 0.1290 0.1444 0.1608 0.1778 0.1956 0.2138 0.2323 0.2509 0.2694 0.2875 0.3050 0.3216 0.3371 0.3513 0.3639 0.3746 0.3834 0.3900 0.3944 0.3964 0.3961 0.3934 0.3884 0.3812 0.3719 0.3606 0.3476 0.3330 0.3172 0.3003 0.2826 0.2644 0.2458 0.2272 0.2088 0.1907 0.1731 0.1562 0.1401 0.1250 0.1108 0.0976 0.0855 0.0744 0.0644 0.0554 0.0474 0.0403 0.0340 0.0286 0.0238 0.0198 0.0163 0.0134 0.0109 0.0088 0.0071 0.0057 0.0045 0.0036 0.0028 0.0022 0.0017 0.0013 0.0010 0.0008 0.0006 0.0004 0.0003 0.0002 0.0002 0.0001 0.0001 diff --git a/sourcecodes/data/example1/Bqxthr.txt b/sourcecodes/data/example1/Bqxthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example1/Bqxthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example1/Bqxtier.txt b/sourcecodes/data/example1/Bqxtier.txt deleted file mode 100644 index bc94239b..00000000 --- a/sourcecodes/data/example1/Bqxtier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,0,Tier2,0,Tier3,0, \ No newline at end of file diff --git a/sourcecodes/data/example1/Bqxtype.txt b/sourcecodes/data/example1/Bqxtype.txt deleted file mode 100644 index 285a68af..00000000 --- a/sourcecodes/data/example1/Bqxtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -2 2 1 1 1 1 1 1 diff --git a/sourcecodes/data/example1/Bqxwhite.txt b/sourcecodes/data/example1/Bqxwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example1/Bqxwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example1/old/Bqxrun_initialstructure.sh b/sourcecodes/data/example1/old/Bqxrun_initialstructure.sh deleted file mode 100644 index a8a8ebe0..00000000 --- a/sourcecodes/data/example1/old/Bqxrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Bqx -fi -exit diff --git a/sourcecodes/data/example1/standardized_data.txt b/sourcecodes/data/example1/standardized_data.txt deleted file mode 100644 index 743e8b02..00000000 --- a/sourcecodes/data/example1/standardized_data.txt +++ /dev/null @@ -1,201 +0,0 @@ -Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 -1.8453 2 -0.70749 -1.3361 2 1.5443 -0.43784 0.72827 -0.9605 1 0.85158 1.5164 1 -1.1632 1.0263 -0.11408 --0.63336 1 0.53936 1.1602 1 -0.74229 1.4011 -1.541 -1.3355 2 -1.7216 -0.76715 1 0.12195 -0.66179 0.099211 -0.36111 2 -0.74876 -0.98283 1 -2.0753 -1.2335 -0.99244 --1.177 1 0.51257 0.84261 1 0.065663 1.2658 -0.64654 -0.076305 1 1.5888 1.7606 1 -0.66331 1.4736 0.39057 --0.53841 2 0.11031 -1.5038 1 0.23456 -0.060179 0.14097 --0.59968 1 0.48834 1.0431 1 -0.59377 0.22579 -0.99932 -0.37839 1 1.293 0.49142 1 -1.2855 0.37537 0.50786 --0.98262 1 1.6051 0.57702 2 0.44497 0.92494 1.9396 --0.32154 1 1.0249 0.77512 1 -0.62075 0.32547 1.8129 -0.094471 1 1.0318 1.5671 2 -0.60413 0.75183 -1.4864 --0.2677 2 -1.3762 -0.039045 2 0.61004 -0.20296 -0.34315 -1.45 2 0.22686 -0.18131 1 -0.5462 -0.61255 -0.83409 --0.94296 2 -1.0223 -1.1896 1 -0.4021 -1.2644 -1.2822 --0.65504 2 -2.6825 -1.035 1 0.25776 -1.4615 0.84597 -1.3635 1 1.5647 0.59499 2 1.372 1.0621 0.74498 -0.60321 1 0.68692 1.4714 2 0.81867 1.711 0.90082 --0.5142 2 -1.0962 -1.5522 1 -0.04535 -1.2401 -0.62273 --1.2303 1 0.82027 1.0532 2 -0.12811 1.344 0.60516 -0.84008 2 -0.7159 -0.44987 1 -0.56344 -1.5572 1.0854 -0.47761 1 1.5622 1.2168 1 -0.30596 1.1251 -1.3723 --1.3546 2 -0.7484 -0.096654 1 0.03293 0.23078 0.81604 --0.32954 2 -1.6183 -0.57119 1 -0.9399 -1.5734 -0.76341 -0.57841 1 0.24378 0.681 1 -0.7778 1.305 0.77773 -0.11524 2 -0.85367 0.35424 2 2.3096 0.75697 1.7572 -1.1463 2 0.0096586 -0.25741 1 -0.52081 -1.5513 0.64513 --1.3926 2 -0.88863 -0.68795 2 0.0060478 -0.43763 0.97179 --0.34841 1 1.0004 0.23941 1 -0.83161 0.87503 -0.88918 -0.79176 1 0.59541 1.0092 1 -1.9591 0.77295 0.31259 --1.7691 2 0.055429 -1.1837 2 1.1172 -0.091192 1.3241 -0.23812 2 -0.13588 -0.98943 1 -0.041159 -0.43704 -0.39754 -1.4262 1 0.46298 1.327 1 0.15808 1.1741 -0.073642 -1.3584 1 1.5511 0.49802 1 -0.96618 -0.037384 0.26987 --0.45407 2 -0.11918 -0.20984 1 -0.84764 0.68704 0.15725 -1.3502 1 1.1228 1.7003 1 -0.34181 1.3601 0.19859 -0.51265 2 0.059243 -0.61724 1 -1.2675 -1.2719 -1.5483 -1.6144 2 -1.6767 -0.4403 2 -0.7614 0.046076 -0.6741 --0.99883 2 -0.76648 0.33667 2 0.97148 -1.1389 -0.11754 -0.24789 1 0.4729 1.0484 1 -0.62124 0.34555 -0.08916 -1.6957 2 0.014711 -1.3474 1 -0.026706 -1.4606 -1.4336 --0.54533 1 0.88108 1.3793 1 -0.29202 1.3706 -1.1708 --1.7381 1 0.16189 0.96739 1 -0.77438 0.96572 1.2346 --0.844 2 -1.0713 -0.50552 2 1.1809 -0.13536 3.098 --1.8946 1 0.83747 0.55294 1 0.21042 0.78685 -0.41553 --1.2313 1 0.77672 1.7131 1 -0.38666 1.694 -0.79692 --0.7674 2 -1.151 -0.091205 1 0.9644 -0.57897 0.21389 -0.72057 2 -0.34897 -0.95934 1 -1.3832 -0.57841 -0.10718 -1.2095 2 0.5788 -0.77644 2 0.86817 -0.56945 0.13481 -0.09126 1 1.0274 0.59902 1 0.094442 0.30723 1.2562 --1.7398 1 0.67041 0.82202 1 -0.30164 0.94827 -0.94259 --0.66818 1 0.49087 1.2694 1 -0.18615 0.78217 -1.3239 --0.2258 2 -1.4193 -1.44 1 -1.5421 -1.6216 -0.34851 -1.4939 2 0.12307 -0.97417 2 -1.9058 -1.6405 -2.6645 -0.59683 2 -0.27561 -1.5921 1 -0.012339 -1.033 0.22517 -0.32502 1 1.8115 0.59888 1 -0.78178 0.37072 -1.5597 -0.33627 2 -0.54037 -0.092937 1 -0.23801 -0.28432 0.25627 --0.71947 2 -0.96292 -0.87226 2 1.0454 -1.1866 -1.1152 -0.7723 2 -0.74389 -0.31293 2 0.56738 -1.597 0.21919 -1.1117 1 0.22881 0.53378 1 0.28362 0.62928 -0.56731 --0.37072 1 1.1896 1.2033 2 1.7889 1.9867 -1.1364 -1.9537 2 -1.2797 -1.1399 1 -0.45995 -1.6282 -0.33873 --1.1043 1 1.0871 2.3039 2 -0.27611 0.615 0.27237 --1.3202 1 0.86019 1.2914 2 0.27461 0.94779 -0.83546 --0.46478 1 1.29 0.43419 1 0.6874 1.6104 -0.36581 --1.1858 2 -1.2069 -0.56475 1 0.18024 -0.54017 0.23717 -0.32802 1 0.87458 1.8613 2 0.40544 1.1088 1.7576 -1.1735 2 -0.66747 -1.6202 1 0.53589 -0.9149 0.45212 --1.16 1 1.0838 0.61868 2 0.72867 1.3378 0.2647 -1.462 2 0.19509 -1.4192 1 0.56635 -0.85302 0.33371 -1.0695 1 0.21919 1.322 2 1.3441 1.1727 0.76002 --0.22703 1 1.1363 0.54703 1 -0.48891 1.2236 -0.91644 -1.3458 2 -0.6068 -1.7825 1 -0.68775 -0.89217 0.99689 --0.091249 1 0.68469 0.60839 1 -0.6527 0.58896 -0.24017 -0.67203 1 0.72395 1.1051 1 -1.4197 0.29802 0.188 -0.34537 1 1.2845 1.4258 1 -0.6173 1.0233 -0.24233 --1.0761 2 -1.2815 -0.94371 1 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--0.53493 2 -0.9391 -0.84301 2 1.3501 -0.31379 -0.058019 -0.3655 2 -0.74384 -1.3595 1 1.3067 -0.5247 -1.7338 -0.82879 2 -1.5915 -1.0102 2 1.0708 -0.6468 0.92568 -0.57673 2 -1.4808 -1.0779 1 0.47651 -1.062 0.26133 -0.59244 2 -0.8026 -1.7146 1 -0.020034 -1.3898 -1.5705 -0.44996 1 0.50751 1.0983 2 2.2137 2.8355 0.34907 --0.75132 2 -0.52338 -0.74591 1 -0.84637 -1.6929 -1.6584 --0.1943 1 1.2265 0.4739 1 -0.78558 0.81272 -0.023241 -2.0866 2 -0.19274 0.066839 1 -0.30442 -0.70635 0.85947 --1.3268 2 -1.2952 0.023312 2 1.4432 0.036383 0.8954 --1.4174 2 -0.43139 -0.97617 2 1.9378 0.79311 -0.17648 --0.30469 2 0.072833 -0.069195 2 1.2683 -0.62404 0.25533 diff --git a/sourcecodes/data/example2/hQGban.txt b/sourcecodes/data/example2/hQGban.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example2/hQGban.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example2/hQGcontinuous_input.txt b/sourcecodes/data/example2/hQGcontinuous_input.txt deleted file mode 100644 index 5e296c45..00000000 --- a/sourcecodes/data/example2/hQGcontinuous_input.txt +++ /dev/null @@ -1,203 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -2 2 1 1 1 1 1 1 -2 2 0.46259 1.2692 -1.3164 -0.44096 0.5929 -0.75422 -1 1 -0.10011 -0.88834 1.6407 0.99972 0.31288 0.65602 -1 1 -1.0533 -0.55296 1.2715 1.3686 -0.19153 0.37361 -1 2 0.042371 0.13573 -0.72659 -0.66133 0.43157 -1.6715 -1 2 -0.68686 -1.6152 -0.95019 -1.2239 0.12319 -0.79155 -1 1 -0.4558 0.090877 0.94224 1.2354 -0.36356 0.34937 -1 1 0.237 -0.49002 1.8939 1.4399 0.033059 1.3229 -1 2 0.070265 0.22547 -1.4903 -0.069341 -0.16148 -0.01449 -1 1 -0.69146 -0.43461 1.1501 0.21205 -0.18087 0.32746 -1 1 0.31535 -0.9858 0.57816 0.35924 0.12866 1.0553 -2 1 1.2718 0.39314 0.6669 0.90002 -0.30206 1.3376 -1 1 1.1871 -0.45611 0.87227 0.31014 -0.092846 0.81278 -2 1 -1.0168 -0.44286 1.6933 0.72968 0.038808 0.81906 -2 2 -0.25313 0.52468 0.02823 -0.20984 -0.075809 -1.3591 -1 2 -0.58108 -0.3967 -0.11925 -0.61288 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2 0.57423 1.1886 0.092876 0.025677 -0.41099 -1.2858 -2 2 -0.14179 1.5827 -0.94328 0.7703 -0.43967 -0.50448 -2 2 0.14666 1.0492 -0.0030259 -0.62418 -0.087515 -0.048386 - diff --git a/sourcecodes/data/example2/hQGgraphviz.txt b/sourcecodes/data/example2/hQGgraphviz.txt deleted file mode 100644 index 7f279843..00000000 --- a/sourcecodes/data/example2/hQGgraphviz.txt +++ /dev/null @@ -1,11 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Geno1 -> Trait2; -Geno2 -> Trait3; -Geno2 -> Trait4; -Geno2 -> Trait6; -Trait2 -> Trait1; -Trait2 -> Trait4; -Trait3 -> Trait4; -} \ No newline at end of file diff --git a/sourcecodes/data/example2/hQGk.txt b/sourcecodes/data/example2/hQGk.txt deleted file mode 100644 index 29d6383b..00000000 --- a/sourcecodes/data/example2/hQGk.txt +++ /dev/null @@ -1 +0,0 @@ -100 diff --git a/sourcecodes/data/example2/hQGmap.txt b/sourcecodes/data/example2/hQGmap.txt deleted file mode 100644 index dc9ba9be..00000000 --- a/sourcecodes/data/example2/hQGmap.txt +++ /dev/null @@ -1,8 +0,0 @@ -Geno1 0.473175 1.335000 -Geno2 0.496318 1.570000 -Trait1 0.668009 -0.023903 -Trait2 0.796873 0.038552 -Trait3 1.036694 0.068708 -Trait4 0.984008 -0.010125 -Trait5 0.316471 0.008911 -Trait6 0.904542 -0.114267 diff --git a/sourcecodes/data/example2/hQGmapdata.txt b/sourcecodes/data/example2/hQGmapdata.txt deleted file mode 100644 index 42b2fd9c..00000000 --- a/sourcecodes/data/example2/hQGmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 diff --git a/sourcecodes/data/example2/hQGname.txt b/sourcecodes/data/example2/hQGname.txt deleted file mode 100644 index 8f42b468..00000000 --- a/sourcecodes/data/example2/hQGname.txt +++ /dev/null @@ -1 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 diff --git a/sourcecodes/data/example2/hQGnet_figure.txt b/sourcecodes/data/example2/hQGnet_figure.txt deleted file mode 100644 index 893f9f14..00000000 --- a/sourcecodes/data/example2/hQGnet_figure.txt +++ /dev/null @@ -1,652 +0,0 @@ -8 -1200 1200 -Trait5 0 0 -Geno2 300 0 -Trait6 120 300 -Trait3 420 300 -Geno1 600 0 -Trait2 720 300 -Trait4 100 600 -Trait1 500 600 -Trait5 1 -250 150 -0 -0 --3.2055 0.0025 --3.1368 0.0030 --3.0681 0.0038 --2.9994 0.0046 --2.9308 0.0057 --2.8621 0.0069 --2.7934 0.0083 --2.7247 0.0101 --2.6561 0.0121 --2.5874 0.0144 --2.5187 0.0172 --2.4500 0.0203 --2.3813 0.0240 --2.3127 0.0281 --2.2440 0.0328 --2.1753 0.0381 --2.1066 0.0441 --2.0379 0.0508 --1.9693 0.0582 --1.9006 0.0664 --1.8319 0.0754 --1.7632 0.0852 --1.6945 0.0958 --1.6259 0.1073 --1.5572 0.1195 --1.4885 0.1326 --1.4198 0.1463 --1.3511 0.1608 --1.2825 0.1758 --1.2138 0.1914 --1.1451 0.2074 --1.0764 0.2237 --1.0078 0.2401 --0.9391 0.2565 --0.8704 0.2728 --0.8017 0.2888 --0.7330 0.3042 --0.6644 0.3190 --0.5957 0.3330 --0.5270 0.3460 --0.4583 0.3578 --0.3896 0.3682 --0.3210 0.3772 --0.2523 0.3846 --0.1836 0.3904 --0.1149 0.3944 --0.0462 0.3965 -0.0224 0.3969 -0.0911 0.3953 -0.1598 0.3920 -0.2285 0.3868 -0.2971 0.3800 -0.3658 0.3715 -0.4345 0.3615 -0.5032 0.3502 -0.5719 0.3376 -0.6405 0.3240 -0.7092 0.3095 -0.7779 0.2942 -0.8466 0.2784 -0.9153 0.2622 -0.9839 0.2458 -1.0526 0.2294 -1.1213 0.2130 -1.1900 0.1969 -1.2587 0.1812 -1.3273 0.1659 -1.3960 0.1513 -1.4647 0.1373 -1.5334 0.1240 -1.6021 0.1114 -1.6707 0.0997 -1.7394 0.0888 -1.8081 0.0787 -1.8768 0.0694 -1.9454 0.0610 -2.0141 0.0533 -2.0828 0.0464 -2.1515 0.0401 -2.2202 0.0346 -2.2888 0.0297 -2.3575 0.0253 -2.4262 0.0215 -2.4949 0.0182 -2.5636 0.0153 -2.6322 0.0129 -2.7009 0.0107 -2.7696 0.0089 -2.8383 0.0074 -2.9070 0.0061 -2.9756 0.0050 -3.0443 0.0040 -3.1130 0.0033 -3.1817 0.0026 -3.2503 0.0021 -3.3190 0.0017 -3.3877 0.0014 -3.4564 0.0011 -3.5251 0.0008 -3.5937 0.0007 -3.6624 0.0005 -Geno2 2 -250 150 -0 -3 3 4 7 -1 0.4300 -2 0.5700 -Trait6 1 -250 150 -1 2 -0 --3.6825 0.0005 --3.6140 0.0006 --3.5455 0.0008 --3.4769 0.0010 --3.4084 0.0013 --3.3399 0.0016 --3.2713 0.0020 --3.2028 0.0025 --3.1343 0.0031 --3.0658 0.0038 --2.9972 0.0046 --2.9287 0.0057 --2.8602 0.0069 --2.7917 0.0084 --2.7231 0.0101 --2.6546 0.0121 --2.5861 0.0145 --2.5176 0.0172 --2.4490 0.0204 --2.3805 0.0240 --2.3120 0.0282 --2.2435 0.0329 --2.1749 0.0382 --2.1064 0.0441 --2.0379 0.0508 --1.9694 0.0582 --1.9008 0.0664 --1.8323 0.0753 --1.7638 0.0851 --1.6953 0.0957 --1.6267 0.1071 --1.5582 0.1193 --1.4897 0.1323 --1.4212 0.1461 --1.3526 0.1605 --1.2841 0.1755 --1.2156 0.1910 --1.1471 0.2069 --1.0785 0.2232 --1.0100 0.2396 --0.9415 0.2560 --0.8730 0.2722 --0.8044 0.2881 --0.7359 0.3036 --0.6674 0.3184 --0.5989 0.3324 --0.5303 0.3454 --0.4618 0.3572 --0.3933 0.3677 --0.3248 0.3768 --0.2562 0.3843 --0.1877 0.3901 --0.1192 0.3942 --0.0507 0.3965 -0.0179 0.3969 -0.0864 0.3955 -0.1549 0.3923 -0.2234 0.3873 -0.2920 0.3806 -0.3605 0.3722 -0.4290 0.3624 -0.4975 0.3512 -0.5661 0.3387 -0.6346 0.3252 -0.7031 0.3108 -0.7716 0.2956 -0.8402 0.2799 -0.9087 0.2638 -0.9772 0.2474 -1.0457 0.2310 -1.1143 0.2147 -1.1828 0.1986 -1.2513 0.1829 -1.3198 0.1676 -1.3884 0.1529 -1.4569 0.1388 -1.5254 0.1255 -1.5939 0.1129 -1.6625 0.1011 -1.7310 0.0901 -1.7995 0.0799 -1.8680 0.0706 -1.9366 0.0620 -2.0051 0.0542 -2.0736 0.0472 -2.1421 0.0409 -2.2107 0.0353 -2.2792 0.0303 -2.3477 0.0259 -2.4162 0.0221 -2.4848 0.0187 -2.5533 0.0157 -2.6218 0.0132 -2.6903 0.0110 -2.7589 0.0092 -2.8274 0.0076 -2.8959 0.0062 -2.9644 0.0051 -3.0330 0.0042 -3.1015 0.0034 -3.1700 0.0027 -Trait3 1 -250 150 -1 2 -1 7 --2.7825 0.0086 --2.7216 0.0101 --2.6608 0.0119 --2.5999 0.0140 --2.5390 0.0163 --2.4782 0.0190 --2.4173 0.0220 --2.3565 0.0254 --2.2956 0.0292 --2.2347 0.0335 --2.1739 0.0383 --2.1130 0.0435 --2.0521 0.0494 --1.9913 0.0558 --1.9304 0.0627 --1.8695 0.0704 --1.8087 0.0786 --1.7478 0.0875 --1.6870 0.0970 --1.6261 0.1072 --1.5652 0.1180 --1.5044 0.1295 --1.4435 0.1415 --1.3826 0.1541 --1.3218 0.1672 --1.2609 0.1807 --1.2000 0.1946 --1.1392 0.2088 --1.0783 0.2232 --1.0175 0.2378 --0.9566 0.2524 --0.8957 0.2668 --0.8349 0.2811 --0.7740 0.2951 --0.7131 0.3086 --0.6523 0.3216 --0.5914 0.3338 --0.5305 0.3453 --0.4697 0.3559 --0.4088 0.3654 --0.3480 0.3739 --0.2871 0.3811 --0.2262 0.3870 --0.1654 0.3916 --0.1045 0.3948 --0.0436 0.3966 -0.0172 0.3969 -0.0781 0.3958 -0.1389 0.3932 -0.1998 0.3892 -0.2607 0.3838 -0.3215 0.3772 -0.3824 0.3692 -0.4433 0.3602 -0.5041 0.3500 -0.5650 0.3389 -0.6259 0.3270 -0.6867 0.3143 -0.7476 0.3010 -0.8084 0.2872 -0.8693 0.2731 -0.9302 0.2587 -0.9910 0.2441 -1.0519 0.2295 -1.1128 0.2150 -1.1736 0.2007 -1.2345 0.1867 -1.2954 0.1730 -1.3562 0.1597 -1.4171 0.1469 -1.4779 0.1346 -1.5388 0.1229 -1.5997 0.1118 -1.6605 0.1014 -1.7214 0.0916 -1.7823 0.0824 -1.8431 0.0739 -1.9040 0.0660 -1.9649 0.0587 -2.0257 0.0521 -2.0866 0.0460 -2.1474 0.0405 -2.2083 0.0355 -2.2692 0.0310 -2.3300 0.0270 -2.3909 0.0234 -2.4518 0.0202 -2.5126 0.0174 -2.5735 0.0150 -2.6344 0.0128 -2.6952 0.0109 -2.7561 0.0092 -2.8169 0.0078 -2.8778 0.0066 -2.9387 0.0055 -2.9995 0.0046 -3.0604 0.0038 -3.1213 0.0032 -3.1821 0.0026 -3.2430 0.0022 -3.3039 0.0018 -Geno1 2 -250 150 -0 -1 6 -1 0.6650 -2 0.3350 -Trait2 1 -250 150 -1 5 -2 7 8 --3.0753 0.0037 --3.0078 0.0045 --2.9403 0.0055 --2.8728 0.0067 --2.8053 0.0081 --2.7378 0.0097 --2.6702 0.0116 --2.6027 0.0139 --2.5352 0.0165 --2.4677 0.0195 --2.4002 0.0229 --2.3327 0.0268 --2.2652 0.0313 --2.1977 0.0363 --2.1302 0.0420 --2.0627 0.0483 --1.9951 0.0553 --1.9276 0.0631 --1.8601 0.0716 --1.7926 0.0809 --1.7251 0.0910 --1.6576 0.1019 --1.5901 0.1135 --1.5226 0.1260 --1.4551 0.1392 --1.3876 0.1530 --1.3201 0.1675 --1.2525 0.1826 --1.1850 0.1981 --1.1175 0.2139 --1.0500 0.2300 --0.9825 0.2462 --0.9150 0.2623 --0.8475 0.2782 --0.7800 0.2937 --0.7125 0.3088 --0.6450 0.3231 --0.5775 0.3366 --0.5099 0.3490 --0.4424 0.3603 --0.3749 0.3703 --0.3074 0.3788 --0.2399 0.3858 --0.1724 0.3912 --0.1049 0.3948 --0.0374 0.3967 -0.0301 0.3968 -0.0976 0.3951 -0.1652 0.3916 -0.2327 0.3865 -0.3002 0.3796 -0.3677 0.3713 -0.4352 0.3614 -0.5027 0.3503 -0.5702 0.3379 -0.6377 0.3246 -0.7052 0.3103 -0.7727 0.2954 -0.8402 0.2799 -0.9078 0.2640 -0.9753 0.2479 -1.0428 0.2317 -1.1103 0.2156 -1.1778 0.1998 -1.2453 0.1842 -1.3128 0.1691 -1.3803 0.1546 -1.4478 0.1406 -1.5153 0.1274 -1.5829 0.1148 -1.6504 0.1031 -1.7179 0.0921 -1.7854 0.0819 -1.8529 0.0725 -1.9204 0.0640 -1.9879 0.0561 -2.0554 0.0490 -2.1229 0.0426 -2.1904 0.0369 -2.2579 0.0318 -2.3255 0.0273 -2.3930 0.0233 -2.4605 0.0198 -2.5280 0.0168 -2.5955 0.0141 -2.6630 0.0119 -2.7305 0.0099 -2.7980 0.0082 -2.8655 0.0068 -2.9330 0.0056 -3.0005 0.0046 -3.0681 0.0038 -3.1356 0.0031 -3.2031 0.0025 -3.2706 0.0020 -3.3381 0.0016 -3.4056 0.0013 -3.4731 0.0010 -3.5406 0.0008 -3.6081 0.0006 -3.6756 0.0005 -Trait4 1 -250 150 -3 2 4 6 -0 --3.2636 0.0025 --3.1926 0.0031 --3.1216 0.0039 --3.0506 0.0048 --2.9796 0.0059 --2.9086 0.0071 --2.8376 0.0086 --2.7666 0.0104 --2.6957 0.0125 --2.6247 0.0150 --2.5537 0.0178 --2.4827 0.0211 --2.4117 0.0248 --2.3407 0.0291 --2.2697 0.0340 --2.1987 0.0395 --2.1277 0.0456 --2.0567 0.0525 --1.9857 0.0601 --1.9148 0.0685 --1.8438 0.0777 --1.7728 0.0877 --1.7018 0.0986 --1.6308 0.1102 --1.5598 0.1226 --1.4888 0.1358 --1.4178 0.1497 --1.3468 0.1643 --1.2758 0.1794 --1.2049 0.1949 --1.1339 0.2108 --1.0629 0.2270 --0.9919 0.2432 --0.9209 0.2593 --0.8499 0.2751 --0.7789 0.2906 --0.7079 0.3055 --0.6369 0.3196 --0.5659 0.3328 --0.4949 0.3448 --0.4240 0.3557 --0.3530 0.3651 --0.2820 0.3730 --0.2110 0.3792 --0.1400 0.3838 --0.0690 0.3865 -0.0020 0.3874 -0.0730 0.3865 -0.1440 0.3838 -0.2150 0.3792 -0.2859 0.3730 -0.3569 0.3651 -0.4279 0.3557 -0.4989 0.3448 -0.5699 0.3328 -0.6409 0.3196 -0.7119 0.3055 -0.7829 0.2906 -0.8539 0.2752 -0.9249 0.2593 -0.9959 0.2432 -1.0668 0.2270 -1.1378 0.2109 -1.2088 0.1950 -1.2798 0.1794 -1.3508 0.1643 -1.4218 0.1498 -1.4928 0.1358 -1.5638 0.1227 -1.6348 0.1102 -1.7058 0.0986 -1.7767 0.0877 -1.8477 0.0777 -1.9187 0.0685 -1.9897 0.0601 -2.0607 0.0525 -2.1317 0.0456 -2.2027 0.0395 -2.2737 0.0340 -2.3447 0.0291 -2.4157 0.0248 -2.4867 0.0211 -2.5576 0.0178 -2.6286 0.0150 -2.6996 0.0125 -2.7706 0.0104 -2.8416 0.0086 -2.9126 0.0071 -2.9836 0.0059 -3.0546 0.0048 -3.1256 0.0039 -3.1966 0.0031 -3.2675 0.0025 -3.3385 0.0020 -3.4095 0.0016 -3.4805 0.0013 -3.5515 0.0010 -3.6225 0.0008 -3.6935 0.0006 -3.7645 0.0005 -3.8355 0.0004 -Trait1 1 -250 150 -1 6 -0 --3.6875 0.0005 --3.6097 0.0006 --3.5318 0.0008 --3.4540 0.0011 --3.3761 0.0014 --3.2983 0.0018 --3.2204 0.0024 --3.1425 0.0030 --3.0647 0.0038 --2.9868 0.0048 --2.9090 0.0061 --2.8311 0.0076 --2.7533 0.0094 --2.6754 0.0115 --2.5976 0.0141 --2.5197 0.0172 --2.4418 0.0208 --2.3640 0.0251 --2.2861 0.0300 --2.2083 0.0356 --2.1304 0.0421 --2.0526 0.0495 --1.9747 0.0577 --1.8969 0.0670 --1.8190 0.0773 --1.7411 0.0887 --1.6633 0.1011 --1.5854 0.1145 --1.5076 0.1290 --1.4297 0.1444 --1.3519 0.1608 --1.2740 0.1778 --1.1962 0.1956 --1.1183 0.2138 --1.0404 0.2323 --0.9626 0.2509 --0.8847 0.2694 --0.8069 0.2875 --0.7290 0.3050 --0.6512 0.3216 --0.5733 0.3371 --0.4955 0.3513 --0.4176 0.3639 --0.3397 0.3746 --0.2619 0.3834 --0.1840 0.3900 --0.1062 0.3944 --0.0283 0.3964 -0.0495 0.3961 -0.1274 0.3934 -0.2052 0.3884 -0.2831 0.3812 -0.3610 0.3719 -0.4388 0.3606 -0.5167 0.3476 -0.5945 0.3330 -0.6724 0.3172 -0.7502 0.3003 -0.8281 0.2826 -0.9059 0.2644 -0.9838 0.2458 -1.0617 0.2272 -1.1395 0.2088 -1.2174 0.1907 -1.2952 0.1731 -1.3731 0.1562 -1.4509 0.1401 -1.5288 0.1250 -1.6066 0.1108 -1.6845 0.0976 -1.7624 0.0855 -1.8402 0.0744 -1.9181 0.0644 -1.9959 0.0554 -2.0738 0.0474 -2.1516 0.0403 -2.2295 0.0340 -2.3073 0.0286 -2.3852 0.0238 -2.4631 0.0198 -2.5409 0.0163 -2.6188 0.0134 -2.6966 0.0109 -2.7745 0.0088 -2.8523 0.0071 -2.9302 0.0057 -3.0080 0.0045 -3.0859 0.0036 -3.1638 0.0028 -3.2416 0.0022 -3.3195 0.0017 -3.3973 0.0013 -3.4752 0.0010 -3.5530 0.0008 -3.6309 0.0006 -3.7087 0.0004 -3.7866 0.0003 -3.8645 0.0002 -3.9423 0.0002 -4.0202 0.0001 -4.0980 0.0001 diff --git a/sourcecodes/data/example2/hQGnlevels.txt b/sourcecodes/data/example2/hQGnlevels.txt deleted file mode 100644 index 32457058..00000000 --- a/sourcecodes/data/example2/hQGnlevels.txt +++ /dev/null @@ -1,4 +0,0 @@ -Geno1 1 2 -Geno2 1 2 - - diff --git a/sourcecodes/data/example2/hQGnnode.txt b/sourcecodes/data/example2/hQGnnode.txt deleted file mode 100644 index 45a4fb75..00000000 --- a/sourcecodes/data/example2/hQGnnode.txt +++ /dev/null @@ -1 +0,0 @@ -8 diff --git a/sourcecodes/data/example2/hQGnrows.txt b/sourcecodes/data/example2/hQGnrows.txt deleted file mode 100644 index 3bc92d44..00000000 --- a/sourcecodes/data/example2/hQGnrows.txt +++ /dev/null @@ -1 +0,0 @@ -201 diff --git a/sourcecodes/data/example2/hQGparameters.txt b/sourcecodes/data/example2/hQGparameters.txt deleted file mode 100644 index 4cffac4a..00000000 --- a/sourcecodes/data/example2/hQGparameters.txt +++ /dev/null @@ -1,34 +0,0 @@ -Geno1 -Discrete node with 2 states -1 0.6650 -2 0.3350 - -Geno2 -Discrete node with 2 states -1 0.4300 -2 0.5700 - -Trait1 -Continuous node --0.0239 0.6720 - -Trait2 -Continuous node -0.0386 0.8009 - -Trait3 -Continuous node -0.0687 1.0419 - -Trait4 -Continuous node --0.0081 1.0133 - -Trait5 -Continuous node -0.0089 0.3181 - -Trait6 -Continuous node --0.1143 0.9091 - diff --git a/sourcecodes/data/example2/hQGparent.txt b/sourcecodes/data/example2/hQGparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example2/hQGparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example2/hQGstructure_old.txt b/sourcecodes/data/example2/hQGstructure_old.txt deleted file mode 100644 index f979ea93..00000000 --- a/sourcecodes/data/example2/hQGstructure_old.txt +++ /dev/null @@ -1,7 +0,0 @@ -Geno1 0.6650 0.3350 -Trait2 0.0037 0.0045 0.0055 0.0067 0.0081 0.0097 0.0116 0.0139 0.0165 0.0195 0.0229 0.0268 0.0313 0.0363 0.0420 0.0483 0.0553 0.0631 0.0716 0.0809 0.0910 0.1019 0.1135 0.1260 0.1392 0.1530 0.1675 0.1826 0.1981 0.2139 0.2300 0.2462 0.2623 0.2782 0.2937 0.3088 0.3231 0.3366 0.3490 0.3603 0.3703 0.3788 0.3858 0.3912 0.3948 0.3967 0.3968 0.3951 0.3916 0.3865 0.3796 0.3713 0.3614 0.3503 0.3379 0.3246 0.3103 0.2954 0.2799 0.2640 0.2479 0.2317 0.2156 0.1998 0.1842 0.1691 0.1546 0.1406 0.1274 0.1148 0.1031 0.0921 0.0819 0.0725 0.0640 0.0561 0.0490 0.0426 0.0369 0.0318 0.0273 0.0233 0.0198 0.0168 0.0141 0.0119 0.0099 0.0082 0.0068 0.0056 0.0046 0.0038 0.0031 0.0025 0.0020 0.0016 0.0013 0.0010 0.0008 0.0006 0.0005 -Geno2 0.4300 0.5700 -Trait3 0.0086 0.0101 0.0119 0.0140 0.0163 0.0190 0.0220 0.0254 0.0292 0.0335 0.0383 0.0435 0.0494 0.0558 0.0627 0.0704 0.0786 0.0875 0.0970 0.1072 0.1180 0.1295 0.1415 0.1541 0.1672 0.1807 0.1946 0.2088 0.2232 0.2378 0.2524 0.2668 0.2811 0.2951 0.3086 0.3216 0.3338 0.3453 0.3559 0.3654 0.3739 0.3811 0.3870 0.3916 0.3948 0.3966 0.3969 0.3958 0.3932 0.3892 0.3838 0.3772 0.3692 0.3602 0.3500 0.3389 0.3270 0.3143 0.3010 0.2872 0.2731 0.2587 0.2441 0.2295 0.2150 0.2007 0.1867 0.1730 0.1597 0.1469 0.1346 0.1229 0.1118 0.1014 0.0916 0.0824 0.0739 0.0660 0.0587 0.0521 0.0460 0.0405 0.0355 0.0310 0.0270 0.0234 0.0202 0.0174 0.0150 0.0128 0.0109 0.0092 0.0078 0.0066 0.0055 0.0046 0.0038 0.0032 0.0026 0.0022 0.0018 -Trait4 0.0025 0.0031 0.0039 0.0048 0.0059 0.0071 0.0086 0.0104 0.0125 0.0150 0.0178 0.0211 0.0248 0.0291 0.0340 0.0395 0.0456 0.0525 0.0601 0.0685 0.0777 0.0877 0.0986 0.1102 0.1226 0.1358 0.1497 0.1643 0.1794 0.1949 0.2108 0.2270 0.2432 0.2593 0.2751 0.2906 0.3055 0.3196 0.3328 0.3448 0.3557 0.3651 0.3730 0.3792 0.3838 0.3865 0.3874 0.3865 0.3838 0.3792 0.3730 0.3651 0.3557 0.3448 0.3328 0.3196 0.3055 0.2906 0.2752 0.2593 0.2432 0.2270 0.2109 0.1950 0.1794 0.1643 0.1498 0.1358 0.1227 0.1102 0.0986 0.0877 0.0777 0.0685 0.0601 0.0525 0.0456 0.0395 0.0340 0.0291 0.0248 0.0211 0.0178 0.0150 0.0125 0.0104 0.0086 0.0071 0.0059 0.0048 0.0039 0.0031 0.0025 0.0020 0.0016 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004 -Trait6 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0020 0.0025 0.0031 0.0038 0.0046 0.0057 0.0069 0.0084 0.0101 0.0121 0.0145 0.0172 0.0204 0.0240 0.0282 0.0329 0.0382 0.0441 0.0508 0.0582 0.0664 0.0753 0.0851 0.0957 0.1071 0.1193 0.1323 0.1461 0.1605 0.1755 0.1910 0.2069 0.2232 0.2396 0.2560 0.2722 0.2881 0.3036 0.3184 0.3324 0.3454 0.3572 0.3677 0.3768 0.3843 0.3901 0.3942 0.3965 0.3969 0.3955 0.3923 0.3873 0.3806 0.3722 0.3624 0.3512 0.3387 0.3252 0.3108 0.2956 0.2799 0.2638 0.2474 0.2310 0.2147 0.1986 0.1829 0.1676 0.1529 0.1388 0.1255 0.1129 0.1011 0.0901 0.0799 0.0706 0.0620 0.0542 0.0472 0.0409 0.0353 0.0303 0.0259 0.0221 0.0187 0.0157 0.0132 0.0110 0.0092 0.0076 0.0062 0.0051 0.0042 0.0034 0.0027 -Trait1 0.0005 0.0006 0.0008 0.0011 0.0014 0.0018 0.0024 0.0030 0.0038 0.0048 0.0061 0.0076 0.0094 0.0115 0.0141 0.0172 0.0208 0.0251 0.0300 0.0356 0.0421 0.0495 0.0577 0.0670 0.0773 0.0887 0.1011 0.1145 0.1290 0.1444 0.1608 0.1778 0.1956 0.2138 0.2323 0.2509 0.2694 0.2875 0.3050 0.3216 0.3371 0.3513 0.3639 0.3746 0.3834 0.3900 0.3944 0.3964 0.3961 0.3934 0.3884 0.3812 0.3719 0.3606 0.3476 0.3330 0.3172 0.3003 0.2826 0.2644 0.2458 0.2272 0.2088 0.1907 0.1731 0.1562 0.1401 0.1250 0.1108 0.0976 0.0855 0.0744 0.0644 0.0554 0.0474 0.0403 0.0340 0.0286 0.0238 0.0198 0.0163 0.0134 0.0109 0.0088 0.0071 0.0057 0.0045 0.0036 0.0028 0.0022 0.0017 0.0013 0.0010 0.0008 0.0006 0.0004 0.0003 0.0002 0.0002 0.0001 0.0001 diff --git a/sourcecodes/data/example2/hQGthr.txt b/sourcecodes/data/example2/hQGthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example2/hQGthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example2/hQGtier.txt b/sourcecodes/data/example2/hQGtier.txt deleted file mode 100644 index bc94239b..00000000 --- a/sourcecodes/data/example2/hQGtier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,0,Tier2,0,Tier3,0, \ No newline at end of file diff --git a/sourcecodes/data/example2/hQGtype.txt b/sourcecodes/data/example2/hQGtype.txt deleted file mode 100644 index 285a68af..00000000 --- a/sourcecodes/data/example2/hQGtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -2 2 1 1 1 1 1 1 diff --git a/sourcecodes/data/example2/hQGwhite.txt b/sourcecodes/data/example2/hQGwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example2/hQGwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example2/old/hQGrun_initialstructure.sh b/sourcecodes/data/example2/old/hQGrun_initialstructure.sh deleted file mode 100644 index 7d4cbfea..00000000 --- a/sourcecodes/data/example2/old/hQGrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure hQG -fi -exit diff --git a/sourcecodes/data/example2/standardized_data.txt b/sourcecodes/data/example2/standardized_data.txt deleted file mode 100644 index 743e8b02..00000000 --- a/sourcecodes/data/example2/standardized_data.txt +++ /dev/null @@ -1,201 +0,0 @@ -Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 -1.8453 2 -0.70749 -1.3361 2 1.5443 -0.43784 0.72827 -0.9605 1 0.85158 1.5164 1 -1.1632 1.0263 -0.11408 --0.63336 1 0.53936 1.1602 1 -0.74229 1.4011 -1.541 -1.3355 2 -1.7216 -0.76715 1 0.12195 -0.66179 0.099211 -0.36111 2 -0.74876 -0.98283 1 -2.0753 -1.2335 -0.99244 --1.177 1 0.51257 0.84261 1 0.065663 1.2658 -0.64654 -0.076305 1 1.5888 1.7606 1 -0.66331 1.4736 0.39057 --0.53841 2 0.11031 -1.5038 1 0.23456 -0.060179 0.14097 --0.59968 1 0.48834 1.0431 1 -0.59377 0.22579 -0.99932 -0.37839 1 1.293 0.49142 1 -1.2855 0.37537 0.50786 --0.98262 1 1.6051 0.57702 2 0.44497 0.92494 1.9396 --0.32154 1 1.0249 0.77512 1 -0.62075 0.32547 1.8129 -0.094471 1 1.0318 1.5671 2 -0.60413 0.75183 -1.4864 --0.2677 2 -1.3762 -0.039045 2 0.61004 -0.20296 -0.34315 -1.45 2 0.22686 -0.18131 1 -0.5462 -0.61255 -0.83409 --0.94296 2 -1.0223 -1.1896 1 -0.4021 -1.2644 -1.2822 --0.65504 2 -2.6825 -1.035 1 0.25776 -1.4615 0.84597 -1.3635 1 1.5647 0.59499 2 1.372 1.0621 0.74498 -0.60321 1 0.68692 1.4714 2 0.81867 1.711 0.90082 --0.5142 2 -1.0962 -1.5522 1 -0.04535 -1.2401 -0.62273 --1.2303 1 0.82027 1.0532 2 -0.12811 1.344 0.60516 -0.84008 2 -0.7159 -0.44987 1 -0.56344 -1.5572 1.0854 -0.47761 1 1.5622 1.2168 1 -0.30596 1.1251 -1.3723 --1.3546 2 -0.7484 -0.096654 1 0.03293 0.23078 0.81604 --0.32954 2 -1.6183 -0.57119 1 -0.9399 -1.5734 -0.76341 -0.57841 1 0.24378 0.681 1 -0.7778 1.305 0.77773 -0.11524 2 -0.85367 0.35424 2 2.3096 0.75697 1.7572 -1.1463 2 0.0096586 -0.25741 1 -0.52081 -1.5513 0.64513 --1.3926 2 -0.88863 -0.68795 2 0.0060478 -0.43763 0.97179 --0.34841 1 1.0004 0.23941 1 -0.83161 0.87503 -0.88918 -0.79176 1 0.59541 1.0092 1 -1.9591 0.77295 0.31259 --1.7691 2 0.055429 -1.1837 2 1.1172 -0.091192 1.3241 -0.23812 2 -0.13588 -0.98943 1 -0.041159 -0.43704 -0.39754 -1.4262 1 0.46298 1.327 1 0.15808 1.1741 -0.073642 -1.3584 1 1.5511 0.49802 1 -0.96618 -0.037384 0.26987 --0.45407 2 -0.11918 -0.20984 1 -0.84764 0.68704 0.15725 -1.3502 1 1.1228 1.7003 1 -0.34181 1.3601 0.19859 -0.51265 2 0.059243 -0.61724 1 -1.2675 -1.2719 -1.5483 -1.6144 2 -1.6767 -0.4403 2 -0.7614 0.046076 -0.6741 --0.99883 2 -0.76648 0.33667 2 0.97148 -1.1389 -0.11754 -0.24789 1 0.4729 1.0484 1 -0.62124 0.34555 -0.08916 -1.6957 2 0.014711 -1.3474 1 -0.026706 -1.4606 -1.4336 --0.54533 1 0.88108 1.3793 1 -0.29202 1.3706 -1.1708 --1.7381 1 0.16189 0.96739 1 -0.77438 0.96572 1.2346 --0.844 2 -1.0713 -0.50552 2 1.1809 -0.13536 3.098 --1.8946 1 0.83747 0.55294 1 0.21042 0.78685 -0.41553 --1.2313 1 0.77672 1.7131 1 -0.38666 1.694 -0.79692 --0.7674 2 -1.151 -0.091205 1 0.9644 -0.57897 0.21389 -0.72057 2 -0.34897 -0.95934 1 -1.3832 -0.57841 -0.10718 -1.2095 2 0.5788 -0.77644 2 0.86817 -0.56945 0.13481 -0.09126 1 1.0274 0.59902 1 0.094442 0.30723 1.2562 --1.7398 1 0.67041 0.82202 1 -0.30164 0.94827 -0.94259 --0.66818 1 0.49087 1.2694 1 -0.18615 0.78217 -1.3239 --0.2258 2 -1.4193 -1.44 1 -1.5421 -1.6216 -0.34851 -1.4939 2 0.12307 -0.97417 2 -1.9058 -1.6405 -2.6645 -0.59683 2 -0.27561 -1.5921 1 -0.012339 -1.033 0.22517 -0.32502 1 1.8115 0.59888 1 -0.78178 0.37072 -1.5597 -0.33627 2 -0.54037 -0.092937 1 -0.23801 -0.28432 0.25627 --0.71947 2 -0.96292 -0.87226 2 1.0454 -1.1866 -1.1152 -0.7723 2 -0.74389 -0.31293 2 0.56738 -1.597 0.21919 -1.1117 1 0.22881 0.53378 1 0.28362 0.62928 -0.56731 --0.37072 1 1.1896 1.2033 2 1.7889 1.9867 -1.1364 -1.9537 2 -1.2797 -1.1399 1 -0.45995 -1.6282 -0.33873 --1.1043 1 1.0871 2.3039 2 -0.27611 0.615 0.27237 --1.3202 1 0.86019 1.2914 2 0.27461 0.94779 -0.83546 --0.46478 1 1.29 0.43419 1 0.6874 1.6104 -0.36581 --1.1858 2 -1.2069 -0.56475 1 0.18024 -0.54017 0.23717 -0.32802 1 0.87458 1.8613 2 0.40544 1.1088 1.7576 -1.1735 2 -0.66747 -1.6202 1 0.53589 -0.9149 0.45212 --1.16 1 1.0838 0.61868 2 0.72867 1.3378 0.2647 -1.462 2 0.19509 -1.4192 1 0.56635 -0.85302 0.33371 -1.0695 1 0.21919 1.322 2 1.3441 1.1727 0.76002 --0.22703 1 1.1363 0.54703 1 -0.48891 1.2236 -0.91644 -1.3458 2 -0.6068 -1.7825 1 -0.68775 -0.89217 0.99689 --0.091249 1 0.68469 0.60839 1 -0.6527 0.58896 -0.24017 -0.67203 1 0.72395 1.1051 1 -1.4197 0.29802 0.188 -0.34537 1 1.2845 1.4258 1 -0.6173 1.0233 -0.24233 --1.0761 2 -1.2815 -0.94371 1 -1.4633 -0.69107 -0.8715 --0.20711 1 1.0174 0.69566 1 -0.58432 0.15352 -0.49345 -0.59929 1 1.5069 1.8419 1 -1.4583 -0.031663 0.0055113 --0.11492 1 1.2367 1.2191 1 -0.51421 1.1523 1.884 -1.2751 2 -0.52411 -0.64346 2 2.0614 -0.0023541 -0.77991 -0.90981 1 1.1284 1.2152 2 2.6756 1.2409 -0.0084945 --1.9542 2 -1.221 -1.4163 2 1.2826 -0.010965 1.0953 -1.7193 1 0.30492 1.2836 2 0.61499 0.56464 0.15443 --0.53199 1 0.23732 0.77552 1 -1.2032 -0.66655 0.09844 -0.036699 2 -1.0483 -1.779 1 0.3525 -0.60395 0.30022 --0.64389 1 -0.082056 0.48348 1 -0.86546 -0.4081 -0.099303 -0.7892 2 0.063117 -0.73251 1 -0.64062 -0.4066 0.12435 --0.92679 2 -1.4966 0.012855 1 0.79099 -0.55856 0.19256 -0.75147 1 0.0035339 0.026413 1 -0.50794 0.29651 -0.27764 -0.21172 2 -1.3492 -0.47335 1 0.23233 -0.70213 -1.8621 --0.97409 2 -0.629 -0.4728 1 0.091744 -0.086481 -0.49515 --1.0464 2 -1.6692 -0.8497 2 1.5077 0.095689 1.3063 --0.078054 1 1.7703 0.87897 2 1.6091 1.3305 -0.65192 -1.6149 2 -0.75709 -0.63085 1 -0.77532 -2.2636 -0.59675 --1.1678 1 0.0899 0.58095 2 -0.22151 0.26068 0.51619 --0.098842 2 -0.30237 -0.04093 1 -1.2385 -0.37569 -1.8217 --0.55001 2 -1.0301 -1.7087 2 2.6454 -1.328 0.34954 -1.0482 2 -0.26461 -1.3201 2 1.68 -0.0041651 -0.12113 -0.5008 2 -0.85959 -0.66514 1 -1.6141 0.29161 -0.95504 -0.309 1 1.0744 1.269 1 -0.96467 1.5905 -1.42 --0.03887 1 1.0667 1.0095 1 -0.089407 0.99929 1.152 --0.50172 2 -0.99479 -0.54327 2 -0.16208 -1.0551 0.47476 --0.094959 1 2.17 1.7212 2 0.51568 0.53768 -1.2639 --0.5209 2 -1.431 -0.70798 1 -0.4217 0.23091 0.57769 -0.6976 2 -1.2512 -0.50443 1 0.40922 -1.2722 -0.22881 --0.15737 2 -1.3037 -1.2446 1 -0.25 -1.3128 -0.48267 -1.7004 2 -0.093222 0.18072 1 -0.77286 -1.1751 0.70356 --0.34711 2 -0.40996 -0.38877 1 -0.74126 -0.076517 0.71538 -0.63301 2 -1.3066 -1.061 1 -0.020245 -0.47474 0.22151 -0.45593 1 0.98475 1.1245 1 -1.5284 0.87162 -1.1116 --0.074398 2 0.086143 -0.71909 1 -0.72312 -0.58633 -0.11884 -0.5737 1 1.3999 0.41267 1 0.14453 0.30696 0.39177 -0.50652 2 -0.76797 -0.93352 1 -0.537 -0.41761 0.072615 --1.6019 2 0.65979 -0.97526 1 0.28122 -0.88937 0.46709 -0.74414 1 1.6353 1.382 1 0.099487 1.2686 1.3095 --1.3504 2 -1.1309 -0.53372 2 0.13853 -1.3604 1.3258 --0.32328 2 -1.4115 -0.55521 1 -0.39333 -0.7941 1.0533 --0.74323 1 1.7072 0.49329 1 -0.87786 0.48373 -1.3411 -0.8876 2 -1.0691 -0.47533 1 -0.65919 -1.2867 1.3563 --0.26121 1 1.3665 1.3315 2 0.59812 1.5342 -0.51186 --0.52176 1 1.5091 0.71759 1 -0.79433 0.67907 -0.77268 --0.51351 2 -0.99866 -0.96005 2 -0.064251 -0.82275 1.8509 --0.17328 2 0.54034 -1.7709 1 0.38529 -1.362 0.6719 -0.15516 1 1.1328 -0.19576 1 -1.135 1.0527 0.29172 -0.45546 1 0.45829 1.7196 2 0.62149 2.3385 -2.0495 -2.0143 1 1.7214 1.3935 1 -1.973 1.0241 -0.84073 -0.017525 2 -1.3151 -0.89644 1 -0.75598 -1.0529 0.10505 --0.041089 2 -0.071698 -0.33496 1 -0.25915 -0.26742 0.55872 --0.072325 1 0.14302 1.099 1 0.45095 0.51954 -1.5618 -0.9507 2 -0.99789 -1.1502 1 -0.63471 0.61259 0.50063 --1.8153 2 -0.51697 -0.18793 1 -0.58518 -0.41489 -0.79261 --0.37059 2 -0.18087 -0.77008 2 0.14794 -0.66655 0.62335 --0.24334 2 0.033188 -0.22919 1 -1.8202 -0.18936 -0.69045 --0.83923 2 -0.41353 -1.3264 2 1.8901 -1.3452 0.28566 --1.5292 2 -0.28479 -0.49856 1 0.34714 -1.4144 -0.50451 --1.1641 1 0.77391 1.0241 1 -0.77302 0.27655 -2.6875 -2.6624 1 1.7387 1.374 1 0.041422 2.3695 -0.062096 -2.3682 1 1.907 0.94637 2 0.8413 0.76571 -1.6393 -0.31396 2 -1.292 -0.78457 2 -0.31227 -0.84139 -0.22892 --0.87392 2 0.53494 0.55115 1 -0.15179 -0.83441 1.0812 --1.1022 2 -0.57856 -0.21265 2 1.4486 0.11044 -0.38736 -0.42993 2 -1.5502 -0.063309 2 2.2649 -0.59644 2.3365 --1.5011 2 -2.2926 -0.96909 1 -0.40571 -1.1012 0.56007 --1.567 1 0.014611 -0.069863 2 1.3161 0.89287 0.96852 -0.26418 1 0.46242 1.94 1 -1.3016 1.1926 -1.5223 --0.77783 1 1.4946 0.92514 1 -1.1651 1.0425 -1.2685 --0.17339 2 -0.86526 -0.090231 1 -0.09102 -1.3706 0.0049574 -0.11883 1 0.8622 0.94077 1 -0.76414 1.3308 1.415 -0.12005 2 -0.20542 -0.74536 1 -1.2579 -1.2279 -1.2709 --0.79628 2 -0.022269 -0.16145 1 -0.47715 -0.37329 1.1972 -0.58969 1 1.0063 1.3356 2 0.79987 1.5464 0.32801 -0.11633 1 0.73396 1.1437 2 1.3183 1.0156 -1.9512 --0.88008 2 0.39215 -0.88212 2 0.77879 -0.071244 0.92164 --0.74781 2 -0.31657 -1.2371 1 -1.356 -0.76328 -0.96657 --0.069788 2 0.63495 -0.70214 1 -0.76454 -2.2215 1.7055 -0.3897 2 -0.59859 -0.81633 1 -0.04446 0.84047 -0.75073 -2.202 1 0.77915 0.03712 2 1.8438 1.1743 0.40331 -0.22687 2 -0.40806 -1.0788 1 -0.19213 -0.78118 0.48301 --0.66335 1 1.4808 1.1399 1 -0.033787 0.43484 -0.12095 -0.13303 2 -0.66658 -0.14357 1 -1.073 -0.49395 0.70655 --1.5417 1 0.2473 1.2125 2 1.9083 1.2778 3.0844 -0.74601 1 -0.35212 0.88616 1 -0.87675 0.60499 -0.21133 --0.80655 2 -1.1068 -1.3459 1 -0.26122 0.15508 -0.0066816 --0.69135 1 1.0994 1.204 2 2.3161 1.0629 1.4256 -1.6905 2 -0.14242 -0.55749 2 0.359 0.41916 0.53215 --0.77018 2 -1.5065 -0.53604 1 0.19357 0.059861 1.9152 --2.2055 1 1.058 -0.29035 2 1.0301 0.11952 1.1588 --0.70569 2 -0.73004 -1.6228 2 2.1348 -0.42942 0.97843 -1.3633 1 0.65794 0.98061 2 1.3078 0.64345 0.8317 -0.093858 2 -1.6142 -0.92049 1 -0.92394 -1.3444 -0.43212 -1.6603 2 0.037058 0.81538 1 -0.70654 -0.93759 -0.023641 -0.29687 1 0.84923 0.6669 2 0.66467 0.47209 -0.21266 -0.30837 2 -0.8147 -1.3296 1 -1.1736 -1.2252 -0.61256 --1.7779 2 -1.1384 -1.0425 1 -0.69411 -0.39049 -0.48379 --0.35135 2 -0.52672 -1.388 2 0.84612 -1.4625 0.071832 -0.18294 2 -0.96354 -0.6923 1 -0.91232 -0.9204 0.030227 --0.34302 1 1.8167 0.77427 2 0.036232 0.81699 1.0643 --1.0367 2 -0.55158 -0.84582 2 0.67713 -0.66779 -0.43102 -2.6147 2 0.14282 -0.33616 1 -0.83219 -0.17633 -0.13118 --0.59086 2 -1.2139 -0.99552 2 1.9391 -1.1308 0.34126 --0.90208 2 -0.28263 -0.58061 2 0.7467 -0.84617 -0.13398 -1.2668 2 -0.56449 -0.1964 1 0.79248 0.19601 0.41777 -0.75643 1 -0.011136 0.81301 1 0.34117 0.68247 -1.863 --0.62022 1 0.86997 0.6729 1 -1.1203 0.17657 -1.4244 --0.18946 2 -0.55133 -0.86512 1 -0.83578 -0.40257 -0.029909 --1.5498 1 0.32287 1.184 1 -0.62378 0.80455 0.92806 --0.53493 2 -0.9391 -0.84301 2 1.3501 -0.31379 -0.058019 -0.3655 2 -0.74384 -1.3595 1 1.3067 -0.5247 -1.7338 -0.82879 2 -1.5915 -1.0102 2 1.0708 -0.6468 0.92568 -0.57673 2 -1.4808 -1.0779 1 0.47651 -1.062 0.26133 -0.59244 2 -0.8026 -1.7146 1 -0.020034 -1.3898 -1.5705 -0.44996 1 0.50751 1.0983 2 2.2137 2.8355 0.34907 --0.75132 2 -0.52338 -0.74591 1 -0.84637 -1.6929 -1.6584 --0.1943 1 1.2265 0.4739 1 -0.78558 0.81272 -0.023241 -2.0866 2 -0.19274 0.066839 1 -0.30442 -0.70635 0.85947 --1.3268 2 -1.2952 0.023312 2 1.4432 0.036383 0.8954 --1.4174 2 -0.43139 -0.97617 2 1.9378 0.79311 -0.17648 --0.30469 2 0.072833 -0.069195 2 1.2683 -0.62404 0.25533 diff --git a/sourcecodes/data/example2_test/exAban.txt b/sourcecodes/data/example2_test/exAban.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example2_test/exAban.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example2_test/exAcontinuous_input.txt b/sourcecodes/data/example2_test/exAcontinuous_input.txt deleted file mode 100644 index 5e296c45..00000000 --- a/sourcecodes/data/example2_test/exAcontinuous_input.txt +++ /dev/null @@ -1,203 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -2 2 1 1 1 1 1 1 -2 2 0.46259 1.2692 -1.3164 -0.44096 0.5929 -0.75422 -1 1 -0.10011 -0.88834 1.6407 0.99972 0.31288 0.65602 -1 1 -1.0533 -0.55296 1.2715 1.3686 -0.19153 0.37361 -1 2 0.042371 0.13573 -0.72659 -0.66133 0.43157 -1.6715 -1 2 -0.68686 -1.6152 -0.95019 -1.2239 0.12319 -0.79155 -1 1 -0.4558 0.090877 0.94224 1.2354 -0.36356 0.34937 -1 1 0.237 -0.49002 1.8939 1.4399 0.033059 1.3229 -1 2 0.070265 0.22547 -1.4903 -0.069341 -0.16148 -0.01449 -1 1 -0.69146 -0.43461 1.1501 0.21205 -0.18087 0.32746 -1 1 0.31535 -0.9858 0.57816 0.35924 0.12866 1.0553 -2 1 1.2718 0.39314 0.6669 0.90002 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1.2962 0.78156 -0.48154 0.17778 -2 2 -0.06266 1.1144 -0.80524 -0.3189 -0.16038 -0.96372 -1 2 -1.1821 1.0798 -1.3407 -0.52643 0.12458 -0.7871 -2 2 0.59446 0.89186 -0.97856 -0.64658 0.2712 -1.5538 -1 2 0.15067 0.41827 -1.0487 -1.0551 0.19143 -1.4537 -1 2 -1.073 0.022587 -1.7088 -1.3777 0.1964 -0.84025 -2 1 0.20928 1.8026 1.2073 2.78 0.15131 0.3448 -1 2 -1.1317 -0.6359 -0.70457 -1.676 -0.22886 -0.58769 -1 1 -0.039428 -0.58746 0.56 0.7896 -0.052581 0.99511 -1 2 0.55023 -0.20403 0.138 -0.70518 0.66927 -0.28861 -2 2 0.57423 1.1886 0.092876 0.025677 -0.41099 -1.2858 -2 2 -0.14179 1.5827 -0.94328 0.7703 -0.43967 -0.50448 -2 2 0.14666 1.0492 -0.0030259 -0.62418 -0.087515 -0.048386 diff --git a/sourcecodes/data/example2_test/exAk.txt b/sourcecodes/data/example2_test/exAk.txt deleted file mode 100644 index 29d6383b..00000000 --- a/sourcecodes/data/example2_test/exAk.txt +++ /dev/null @@ -1 +0,0 @@ -100 diff --git a/sourcecodes/data/example2_test/exAparent.txt b/sourcecodes/data/example2_test/exAparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example2_test/exAparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example2_test/exAstructure_input.txt b/sourcecodes/data/example2_test/exAstructure_input.txt deleted file mode 100644 index 410c0fa4..00000000 --- a/sourcecodes/data/example2_test/exAstructure_input.txt +++ /dev/null @@ -1,9 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -0 0 0 1 0 0 0 0 -0 0 0 0 1 1 0 1 -0 0 0 0 0 0 0 0 -0 0 1 0 0 1 0 0 -0 0 0 0 0 1 0 0 -0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 diff --git a/sourcecodes/data/example2_test/exAstructure_input_temp.txt b/sourcecodes/data/example2_test/exAstructure_input_temp.txt deleted file mode 100644 index 27bddc96..00000000 --- a/sourcecodes/data/example2_test/exAstructure_input_temp.txt +++ /dev/null @@ -1,9 +0,0 @@ -Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 -0.000000 0.030654 0.000000 1.000000 0.000000 0.000000 0.350069 0.000000 -0.030654 0.000000 0.049399 0.000000 1.000000 1.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 0.000000 0.025163 0.000000 0.123845 0.000000 -0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.053585 0.000000 -0.000000 0.000000 0.013273 0.108604 0.000000 1.000000 0.010570 0.391609 -0.000000 0.000000 0.013713 0.000000 0.000000 0.000000 0.011282 0.026127 -0.000000 0.000000 0.028672 0.000000 0.000000 0.000000 0.000000 0.137567 -0.000000 0.000000 0.136004 0.056792 0.457123 0.029978 0.069699 0.000000 diff --git a/sourcecodes/data/example2_test/exAthr.txt b/sourcecodes/data/example2_test/exAthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example2_test/exAthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example2_test/exAwhite.txt b/sourcecodes/data/example2_test/exAwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example2_test/exAwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example_chl/old/bWRrun_evidencemodified.sh b/sourcecodes/data/example_chl/old/bWRrun_evidencemodified.sh deleted file mode 100644 index 763a268b..00000000 --- a/sourcecodes/data/example_chl/old/bWRrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified bWR -fi -exit diff --git a/sourcecodes/data/example_chl/old/bWRrun_initialstructure.sh b/sourcecodes/data/example_chl/old/bWRrun_initialstructure.sh deleted file mode 100644 index 3725f758..00000000 --- a/sourcecodes/data/example_chl/old/bWRrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure bWR -fi -exit diff --git a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt deleted file mode 100644 index cf674ffd..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt +++ /dev/null @@ -1,44 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight -2 1 1 1 1 -2 0.969230769 3 3.252367514 1 -2 0.925170068 1.6 2.46322088 1.033472803 -1 0.427272727 33.8 4.206610024 0.831372549 -2 0.877835951 8.3 3.764250875 0.967153285 -2 0.914862915 4.4 3.691700208 1.046025105 -2 0.560334528 4.9 2.604550033 0.98046875 -1 0.383073497 13.1 4.273556814 0.812316716 -1 0.101010101 18.6 5.089640217 0.771929825 -1 0.106719368 18.9 4.915125346 0.80994152 -2 0.894736842 2.5 2.691700208 0.995515695 -1 0.067226891 19.8 4.878194228 0.846153846 -2 0.921022067 2.9 4.127428778 1.03875969 -2 0.938701923 0.7 4.366310867 0.984732824 -1 0.658008658 15.7 4.531121115 0.884210526 -2 0.9 4.8 2.604550033 0.913194444 -2 0.790923825 10.4 2.390670213 0.892857143 -1 0.295539033 8.6 4.24137213 0.85840708 -2 0.317757009 12.2 4.449648073 0.889830508 -1 0.032418953 20.2 5.053428044 0.811320755 -1 0.603960396 23.4 4.283775979 0.805460751 -2 0.939351199 3.6 2.349277527 0.952380952 -1 0.978448276 0.4 3.495405563 0.8875 -1 0.1 23.2 4.675613388 0.766101695 -1 0.036363636 32.6 4.938109253 0.828125 -1 0.660247593 9.2 3.826398782 0.921052632 -1 0.078651685 35.8 4.513630383 0.852112676 -1 0.186915888 20.7 5.048247532 0.779761905 -1 0.071578947 35.6 4.574586809 0.797356828 -1 0.239520958 15.4 4.331548761 0.941176471 -1 0.205741627 24.5 5.058547488 0.774193548 -1 0.062300319 13.4 4.594790195 0.832236842 -2 0.599675851 5 4.18178644 0.969348659 -1 0.324246772 13.5 4.252367514 0.858585859 -1 0.87628866 14.2 2.929061124 0.869863014 -1 0.146103896 15.6 4.579726449 0.9 -1 0.257383966 22.5 5.210214148 0.75 -1 0.033333333 31.1 4.632578756 0.718644068 -1 0.29739777 36.1 3.880756445 0.798353909 -2 0.872979215 4.2 4.097465554 0.856756757 -2 0.909221902 4.3 3.650307523 0.976 -1 0.10041841 28.3 4.46322088 0.757462687 - diff --git a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt deleted file mode 100644 index 62705bb9..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt +++ /dev/null @@ -1,42 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight -2 0.969230769 3 3.252367514 1 -2 0.925170068 1.6 2.46322088 1.033472803 -1 0.427272727 33.8 4.206610024 0.831372549 -2 0.877835951 8.3 3.764250875 0.967153285 -2 0.914862915 4.4 3.691700208 1.046025105 -2 0.560334528 4.9 2.604550033 0.98046875 -1 0.383073497 13.1 4.273556814 0.812316716 -1 0.101010101 18.6 5.089640217 0.771929825 -1 0.106719368 18.9 4.915125346 0.80994152 -2 0.894736842 2.5 2.691700208 0.995515695 -1 0.067226891 19.8 4.878194228 0.846153846 -2 0.921022067 2.9 4.127428778 1.03875969 -2 0.938701923 0.7 4.366310867 0.984732824 -1 0.658008658 15.7 4.531121115 0.884210526 -2 0.9 4.8 2.604550033 0.913194444 -2 0.790923825 10.4 2.390670213 0.892857143 -1 0.295539033 8.6 4.24137213 0.85840708 -2 0.317757009 12.2 4.449648073 0.889830508 -1 0.032418953 20.2 5.053428044 0.811320755 -1 0.603960396 23.4 4.283775979 0.805460751 -2 0.939351199 3.6 2.349277527 0.952380952 -1 0.978448276 0.4 3.495405563 0.8875 -1 0.1 23.2 4.675613388 0.766101695 -1 0.036363636 32.6 4.938109253 0.828125 -1 0.660247593 9.2 3.826398782 0.921052632 -1 0.078651685 35.8 4.513630383 0.852112676 -1 0.186915888 20.7 5.048247532 0.779761905 -1 0.071578947 35.6 4.574586809 0.797356828 -1 0.239520958 15.4 4.331548761 0.941176471 -1 0.205741627 24.5 5.058547488 0.774193548 -1 0.062300319 13.4 4.594790195 0.832236842 -2 0.599675851 5 4.18178644 0.969348659 -1 0.324246772 13.5 4.252367514 0.858585859 -1 0.87628866 14.2 2.929061124 0.869863014 -1 0.146103896 15.6 4.579726449 0.9 -1 0.257383966 22.5 5.210214148 0.75 -1 0.033333333 31.1 4.632578756 0.718644068 -1 0.29739777 36.1 3.880756445 0.798353909 -2 0.872979215 4.2 4.097465554 0.856756757 -2 0.909221902 4.3 3.650307523 0.976 -1 0.10041841 28.3 4.46322088 0.757462687 diff --git a/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt b/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt deleted file mode 100644 index 2cd4e8cd..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt +++ /dev/null @@ -1,11 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Ctrq3 -> MAS; -Ctrq3 -> Neutrophil; -Ctrq3 -> Load; -Ctrq3 -> Weight; -MAS -> Neutrophil; -MAS -> Load; -Neutrophil -> Weight; -} \ No newline at end of file diff --git a/sourcecodes/data/example_chl/old_gn/bWRmap.txt b/sourcecodes/data/example_chl/old_gn/bWRmap.txt deleted file mode 100644 index b24eae2f..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRmap.txt +++ /dev/null @@ -1,5 +0,0 @@ -Ctrq3 0.487652 1.365854 -MAS 0.355012 0.479560 -Neutrophil 10.929756 15.048780 -Load 0.825354 4.077143 -Weight 0.088036 0.877077 diff --git a/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt b/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt deleted file mode 100644 index ce5416ce..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Ctrq3 MAS Load Neutrophil Weight diff --git a/sourcecodes/data/example_chl/old_gn/bWRname.txt b/sourcecodes/data/example_chl/old_gn/bWRname.txt deleted file mode 100644 index 48018335..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRname.txt +++ /dev/null @@ -1 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight diff --git a/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt b/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt deleted file mode 100644 index 6a3a1dbc..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt +++ /dev/null @@ -1,433 +0,0 @@ -5 -1200 1200 -Ctrq3 200 0 -MAS 320 240 -Load 0 480 -Neutrophil 400 480 -Weight 320 720 -Ctrq3 2 -250 150 -0 -4 2 3 4 5 -1 0.6341 -2 0.3659 -MAS 1 -250 150 -1 1 -2 3 4 --0.3226 0.0292 --0.3060 0.0326 --0.2895 0.0362 --0.2729 0.0401 --0.2564 0.0443 --0.2398 0.0489 --0.2232 0.0539 --0.2067 0.0592 --0.1901 0.0648 --0.1735 0.0709 --0.1570 0.0774 --0.1404 0.0842 --0.1239 0.0915 --0.1073 0.0992 --0.0907 0.1072 --0.0742 0.1157 --0.0576 0.1246 --0.0411 0.1338 --0.0245 0.1434 --0.0079 0.1534 -0.0086 0.1636 -0.0252 0.1742 -0.0417 0.1850 -0.0583 0.1961 -0.0749 0.2074 -0.0914 0.2188 -0.1080 0.2303 -0.1245 0.2419 -0.1411 0.2535 -0.1577 0.2651 -0.1742 0.2766 -0.1908 0.2879 -0.2073 0.2991 -0.2239 0.3099 -0.2405 0.3205 -0.2570 0.3307 -0.2736 0.3404 -0.2901 0.3496 -0.3067 0.3583 -0.3233 0.3663 -0.3398 0.3737 -0.3564 0.3804 -0.3729 0.3864 -0.3895 0.3916 -0.4061 0.3959 -0.4226 0.3994 -0.4392 0.4021 -0.4558 0.4038 -0.4723 0.4047 -0.4889 0.4046 -0.5054 0.4037 -0.5220 0.4018 -0.5386 0.3991 -0.5551 0.3954 -0.5717 0.3910 -0.5882 0.3857 -0.6048 0.3797 -0.6214 0.3729 -0.6379 0.3654 -0.6545 0.3572 -0.6710 0.3485 -0.6876 0.3392 -0.7042 0.3294 -0.7207 0.3192 -0.7373 0.3086 -0.7538 0.2977 -0.7704 0.2865 -0.7870 0.2752 -0.8035 0.2637 -0.8201 0.2521 -0.8366 0.2405 -0.8532 0.2289 -0.8698 0.2173 -0.8863 0.2059 -0.9029 0.1947 -0.9194 0.1837 -0.9360 0.1729 -0.9526 0.1623 -0.9691 0.1521 -0.9857 0.1422 -1.0022 0.1326 -1.0188 0.1234 -1.0354 0.1146 -1.0519 0.1062 -1.0685 0.0982 -1.0851 0.0906 -1.1016 0.0834 -1.1182 0.0765 -1.1347 0.0701 -1.1513 0.0641 -1.1679 0.0585 -1.1844 0.0532 -1.2010 0.0483 -1.2175 0.0438 -1.2341 0.0396 -1.2507 0.0357 -1.2672 0.0321 -1.2838 0.0288 -1.3003 0.0258 -1.3169 0.0231 -1.3335 0.0206 -Load 1 -250 150 -2 1 2 -0 -1.5239 0.0030 -1.5690 0.0036 -1.6142 0.0043 -1.6593 0.0050 -1.7044 0.0059 -1.7495 0.0069 -1.7946 0.0081 -1.8397 0.0094 -1.8849 0.0110 -1.9300 0.0127 -1.9751 0.0147 -2.0202 0.0169 -2.0653 0.0194 -2.1104 0.0222 -2.1556 0.0253 -2.2007 0.0287 -2.2458 0.0326 -2.2909 0.0368 -2.3360 0.0415 -2.3811 0.0466 -2.4263 0.0522 -2.4714 0.0583 -2.5165 0.0649 -2.5616 0.0720 -2.6067 0.0797 -2.6518 0.0879 -2.6970 0.0966 -2.7421 0.1059 -2.7872 0.1158 -2.8323 0.1261 -2.8774 0.1370 -2.9225 0.1484 -2.9676 0.1602 -3.0128 0.1724 -3.0579 0.1850 -3.1030 0.1979 -3.1481 0.2111 -3.1932 0.2244 -3.2383 0.2379 -3.2835 0.2514 -3.3286 0.2649 -3.3737 0.2782 -3.4188 0.2914 -3.4639 0.3042 -3.5090 0.3166 -3.5542 0.3285 -3.5993 0.3398 -3.6444 0.3504 -3.6895 0.3603 -3.7346 0.3693 -3.7797 0.3774 -3.8249 0.3845 -3.8700 0.3905 -3.9151 0.3954 -3.9602 0.3992 -4.0053 0.4017 -4.0504 0.4031 -4.0956 0.4032 -4.1407 0.4021 -4.1858 0.3997 -4.2309 0.3962 -4.2760 0.3915 -4.3211 0.3857 -4.3663 0.3788 -4.4114 0.3709 -4.4565 0.3620 -4.5016 0.3523 -4.5467 0.3418 -4.5918 0.3306 -4.6370 0.3188 -4.6821 0.3065 -4.7272 0.2937 -4.7723 0.2807 -4.8174 0.2674 -4.8625 0.2539 -4.9077 0.2404 -4.9528 0.2269 -4.9979 0.2135 -5.0430 0.2003 -5.0881 0.1874 -5.1332 0.1747 -5.1784 0.1624 -5.2235 0.1505 -5.2686 0.1391 -5.3137 0.1281 -5.3588 0.1176 -5.4039 0.1077 -5.4491 0.0983 -5.4942 0.0894 -5.5393 0.0811 -5.5844 0.0734 -5.6295 0.0662 -5.6746 0.0595 -5.7198 0.0533 -5.7649 0.0476 -5.8100 0.0424 -5.8551 0.0377 -5.9002 0.0333 -5.9453 0.0294 -5.9905 0.0259 -6.0356 0.0227 -Neutrophil 1 -250 150 -2 1 2 -1 5 --10.5298 0.0245 --9.9542 0.0277 --9.3786 0.0313 --8.8030 0.0353 --8.2274 0.0396 --7.6518 0.0444 --7.0762 0.0496 --6.5006 0.0552 --5.9250 0.0613 --5.3494 0.0679 --4.7738 0.0750 --4.1982 0.0825 --3.6226 0.0906 --3.0470 0.0992 --2.4714 0.1083 --1.8958 0.1180 --1.3202 0.1281 --0.7446 0.1386 --0.1690 0.1496 -0.4066 0.1611 -0.9821 0.1729 -1.5577 0.1851 -2.1333 0.1975 -2.7089 0.2102 -3.2845 0.2231 -3.8601 0.2361 -4.4357 0.2491 -5.0113 0.2621 -5.5869 0.2750 -6.1625 0.2878 -6.7381 0.3002 -7.3137 0.3124 -7.8893 0.3240 -8.4649 0.3352 -9.0405 0.3458 -9.6161 0.3557 -10.1917 0.3648 -10.7673 0.3731 -11.3429 0.3806 -11.9185 0.3870 -12.4940 0.3925 -13.0696 0.3969 -13.6452 0.4002 -14.2208 0.4025 -14.7964 0.4035 -15.3720 0.4035 -15.9476 0.4022 -16.5232 0.3999 -17.0988 0.3964 -17.6744 0.3919 -18.2500 0.3863 -18.8256 0.3797 -19.4012 0.3722 -19.9768 0.3637 -20.5524 0.3545 -21.1280 0.3445 -21.7036 0.3339 -22.2792 0.3226 -22.8548 0.3109 -23.4304 0.2987 -24.0060 0.2862 -24.5815 0.2735 -25.1571 0.2605 -25.7327 0.2475 -26.3083 0.2345 -26.8839 0.2215 -27.4595 0.2086 -28.0351 0.1960 -28.6107 0.1835 -29.1863 0.1714 -29.7619 0.1597 -30.3375 0.1483 -30.9131 0.1373 -31.4887 0.1268 -32.0643 0.1167 -32.6399 0.1072 -33.2155 0.0981 -33.7911 0.0896 -34.3667 0.0816 -34.9423 0.0741 -35.5179 0.0670 -36.0934 0.0605 -36.6690 0.0545 -37.2446 0.0489 -37.8202 0.0438 -38.3958 0.0391 -38.9714 0.0348 -39.5470 0.0308 -40.1226 0.0273 -40.6982 0.0241 -41.2738 0.0212 -41.8494 0.0186 -42.4250 0.0163 -43.0006 0.0142 -43.5762 0.0123 -44.1518 0.0107 -44.7274 0.0093 -45.3030 0.0080 -45.8786 0.0069 -46.4542 0.0059 -47.0298 0.0050 -Weight 1 -250 150 -2 1 4 -0 -0.6306 0.0076 -0.6356 0.0089 -0.6407 0.0105 -0.6457 0.0122 -0.6507 0.0142 -0.6558 0.0164 -0.6608 0.0190 -0.6659 0.0218 -0.6709 0.0250 -0.6759 0.0286 -0.6810 0.0326 -0.6860 0.0370 -0.6910 0.0419 -0.6961 0.0473 -0.7011 0.0531 -0.7061 0.0596 -0.7112 0.0665 -0.7162 0.0741 -0.7212 0.0822 -0.7263 0.0909 -0.7313 0.1002 -0.7363 0.1101 -0.7414 0.1206 -0.7464 0.1316 -0.7514 0.1432 -0.7565 0.1553 -0.7615 0.1678 -0.7665 0.1808 -0.7716 0.1941 -0.7766 0.2076 -0.7816 0.2215 -0.7867 0.2354 -0.7917 0.2494 -0.7967 0.2633 -0.8018 0.2772 -0.8068 0.2907 -0.8119 0.3040 -0.8169 0.3168 -0.8219 0.3290 -0.8270 0.3406 -0.8320 0.3514 -0.8370 0.3614 -0.8421 0.3704 -0.8471 0.3784 -0.8521 0.3853 -0.8572 0.3910 -0.8622 0.3955 -0.8672 0.3988 -0.8723 0.4007 -0.8773 0.4013 -0.8823 0.4006 -0.8874 0.3985 -0.8924 0.3952 -0.8974 0.3906 -0.9025 0.3847 -0.9075 0.3778 -0.9125 0.3697 -0.9176 0.3605 -0.9226 0.3505 -0.9276 0.3396 -0.9327 0.3280 -0.9377 0.3157 -0.9427 0.3028 -0.9478 0.2896 -0.9528 0.2759 -0.9579 0.2621 -0.9629 0.2481 -0.9679 0.2342 -0.9730 0.2202 -0.9780 0.2064 -0.9830 0.1929 -0.9881 0.1796 -0.9931 0.1667 -0.9981 0.1542 -1.0032 0.1422 -1.0082 0.1306 -1.0132 0.1197 -1.0183 0.1092 -1.0233 0.0994 -1.0283 0.0901 -1.0334 0.0815 -1.0384 0.0734 -1.0434 0.0659 -1.0485 0.0590 -1.0535 0.0526 -1.0585 0.0468 -1.0636 0.0414 -1.0686 0.0366 -1.0736 0.0322 -1.0787 0.0283 -1.0837 0.0247 -1.0888 0.0215 -1.0938 0.0187 -1.0988 0.0162 -1.1039 0.0140 -1.1089 0.0120 -1.1139 0.0103 -1.1190 0.0088 -1.1240 0.0075 -1.1290 0.0064 -1.1341 0.0054 diff --git a/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt b/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt deleted file mode 100644 index 9b493660..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt +++ /dev/null @@ -1,433 +0,0 @@ -1 -5 -1200 1200 -Ctrq3 200 0 -MAS 320 240 -Load 0 480 -Neutrophil 400 480 -Weight 320 720 -Ctrq3 2 -250 150 -0 -4 2 3 4 5 -1.0000 1.0000 -MAS 1 -250 150 -1 1 -2 3 4 --2.2595 0.0066 --2.2129 0.0085 --2.1662 0.0109 --2.1196 0.0138 --2.0729 0.0174 --2.0263 0.0219 --1.9796 0.0272 --1.9330 0.0336 --1.8863 0.0412 --1.8397 0.0501 --1.7930 0.0606 --1.7464 0.0728 --1.6997 0.0868 --1.6531 0.1027 --1.6064 0.1208 --1.5598 0.1410 --1.5131 0.1635 --1.4665 0.1882 --1.4199 0.2151 --1.3732 0.2442 --1.3266 0.2752 --1.2799 0.3080 --1.2333 0.3423 --1.1866 0.3777 --1.1400 0.4139 --1.0933 0.4503 --1.0467 0.4866 --1.0000 0.5221 --0.9534 0.5562 --0.9067 0.5884 --0.8601 0.6182 --0.8134 0.6448 --0.7668 0.6679 --0.7201 0.6870 --0.6735 0.7017 --0.6268 0.7116 --0.5802 0.7167 --0.5335 0.7167 --0.4869 0.7117 --0.4402 0.7018 --0.3936 0.6871 --0.3470 0.6681 --0.3003 0.6450 --0.2537 0.6184 --0.2070 0.5887 --0.1604 0.5565 --0.1137 0.5223 --0.0671 0.4869 --0.0204 0.4506 -0.0262 0.4142 -0.0729 0.3780 -0.1195 0.3425 -0.1662 0.3082 -0.2128 0.2754 -0.2595 0.2444 -0.3061 0.2153 -0.3528 0.1884 -0.3994 0.1637 -0.4461 0.1412 -0.4927 0.1209 -0.5394 0.1029 -0.5860 0.0869 -0.6327 0.0729 -0.6793 0.0607 -0.7259 0.0502 -0.7726 0.0412 -0.8192 0.0336 -0.8659 0.0272 -0.9125 0.0219 -0.9592 0.0175 -1.0058 0.0139 -1.0525 0.0109 -1.0991 0.0085 -1.1458 0.0066 -1.1924 0.0051 -1.2391 0.0039 -1.2857 0.0030 -1.3324 0.0022 -1.3790 0.0017 -1.4257 0.0012 -1.4723 0.0009 -1.5190 0.0007 -1.5656 0.0005 -1.6123 0.0004 -1.6589 0.0003 -1.7056 0.0002 -1.7522 0.0001 -1.7989 0.0001 -1.8455 0.0001 -1.8921 0.0000 -1.9388 0.0000 -1.9854 0.0000 -2.0321 0.0000 -2.0787 0.0000 -2.1254 0.0000 -2.1720 0.0000 -2.2187 0.0000 -2.2653 0.0000 -2.3120 0.0000 -2.3586 0.0000 -2.4053 0.0000 -Load 1 -250 150 -2 1 2 -0 --3.0935 0.0000 --3.0388 0.0000 --2.9842 0.0000 --2.9295 0.0000 --2.8748 0.0000 --2.8202 0.0000 --2.7655 0.0000 --2.7108 0.0000 --2.6562 0.0000 --2.6015 0.0000 --2.5469 0.0000 --2.4922 0.0000 --2.4375 0.0000 --2.3829 0.0000 --2.3282 0.0000 --2.2735 0.0000 --2.2189 0.0000 --2.1642 0.0000 --2.1095 0.0000 --2.0549 0.0000 --2.0002 0.0000 --1.9456 0.0000 --1.8909 0.0000 --1.8362 0.0000 --1.7816 0.0000 --1.7269 0.0000 --1.6722 0.0000 --1.6176 0.0000 --1.5629 0.0000 --1.5083 0.0000 --1.4536 0.0000 --1.3989 0.0000 --1.3443 0.0000 --1.2896 0.0001 --1.2349 0.0001 --1.1803 0.0002 --1.1256 0.0004 --1.0709 0.0007 --1.0163 0.0011 --0.9616 0.0018 --0.9070 0.0029 --0.8523 0.0046 --0.7976 0.0070 --0.7430 0.0106 --0.6883 0.0157 --0.6336 0.0228 --0.5790 0.0326 --0.5243 0.0458 --0.4697 0.0631 --0.4150 0.0855 --0.3603 0.1138 --0.3057 0.1487 --0.2510 0.1910 --0.1963 0.2409 --0.1417 0.2985 --0.0870 0.3633 --0.0323 0.4344 -0.0223 0.5102 -0.0770 0.5887 -0.1316 0.6672 -0.1863 0.7428 -0.2410 0.8124 -0.2956 0.8728 -0.3503 0.9211 -0.4050 0.9548 -0.4596 0.9724 -0.5143 0.9727 -0.5689 0.9558 -0.6236 0.9226 -0.6783 0.8749 -0.7329 0.8149 -0.7876 0.7456 -0.8423 0.6702 -0.8969 0.5917 -0.9516 0.5132 -1.0063 0.4372 -1.0609 0.3659 -1.1156 0.3008 -1.1702 0.2430 -1.2249 0.1927 -1.2796 0.1502 -1.3342 0.1150 -1.3889 0.0865 -1.4436 0.0639 -1.4982 0.0463 -1.5529 0.0330 -1.6075 0.0231 -1.6622 0.0159 -1.7169 0.0107 -1.7715 0.0071 -1.8262 0.0047 -1.8809 0.0030 -1.9355 0.0019 -1.9902 0.0012 -2.0449 0.0007 -2.0995 0.0004 -2.1542 0.0002 -2.2088 0.0001 -2.2635 0.0001 -2.3182 0.0000 -2.3728 0.0000 -Neutrophil 1 -250 150 -2 1 2 -1 5 --2.3403 0.0002 --2.2876 0.0002 --2.2349 0.0003 --2.1823 0.0004 --2.1296 0.0005 --2.0770 0.0007 --2.0243 0.0009 --1.9716 0.0012 --1.9190 0.0015 --1.8663 0.0020 --1.8136 0.0025 --1.7610 0.0032 --1.7083 0.0040 --1.6556 0.0051 --1.6030 0.0063 --1.5503 0.0079 --1.4977 0.0097 --1.4450 0.0120 --1.3923 0.0146 --1.3397 0.0178 --1.2870 0.0215 --1.2343 0.0259 --1.1817 0.0310 --1.1290 0.0369 --1.0764 0.0437 --1.0237 0.0514 --0.9710 0.0602 --0.9184 0.0702 --0.8657 0.0813 --0.8130 0.0937 --0.7604 0.1074 --0.7077 0.1224 --0.6550 0.1388 --0.6024 0.1565 --0.5497 0.1755 --0.4971 0.1957 --0.4444 0.2171 --0.3917 0.2396 --0.3391 0.2629 --0.2864 0.2870 --0.2337 0.3116 --0.1811 0.3364 --0.1284 0.3613 --0.0758 0.3859 --0.0231 0.4099 -0.0296 0.4331 -0.0822 0.4552 -0.1349 0.4757 -0.1876 0.4946 -0.2402 0.5113 -0.2929 0.5258 -0.3456 0.5378 -0.3982 0.5471 -0.4509 0.5535 -0.5035 0.5570 -0.5562 0.5575 -0.6089 0.5549 -0.6615 0.5494 -0.7142 0.5410 -0.7669 0.5299 -0.8195 0.5162 -0.8722 0.5001 -0.9248 0.4819 -0.9775 0.4618 -1.0302 0.4402 -1.0828 0.4173 -1.1355 0.3935 -1.1882 0.3691 -1.2408 0.3443 -1.2935 0.3194 -1.3462 0.2947 -1.3988 0.2704 -1.4515 0.2469 -1.5041 0.2241 -1.5568 0.2023 -1.6095 0.1817 -1.6621 0.1623 -1.7148 0.1442 -1.7675 0.1274 -1.8201 0.1120 -1.8728 0.0979 -1.9254 0.0851 -1.9781 0.0736 -2.0308 0.0632 -2.0834 0.0541 -2.1361 0.0460 -2.1888 0.0389 -2.2414 0.0328 -2.2941 0.0274 -2.3468 0.0228 -2.3994 0.0189 -2.4521 0.0156 -2.5047 0.0127 -2.5574 0.0104 -2.6101 0.0084 -2.6627 0.0068 -2.7154 0.0054 -2.7681 0.0043 -2.8207 0.0034 -2.8734 0.0027 -2.9260 0.0021 -Weight 1 -250 150 -2 1 4 -0 --2.7996 0.0000 --2.7425 0.0000 --2.6853 0.0000 --2.6281 0.0000 --2.5709 0.0000 --2.5137 0.0000 --2.4565 0.0000 --2.3993 0.0000 --2.3421 0.0000 --2.2850 0.0001 --2.2278 0.0001 --2.1706 0.0003 --2.1134 0.0005 --2.0562 0.0008 --1.9990 0.0014 --1.9418 0.0024 --1.8846 0.0040 --1.8275 0.0064 --1.7703 0.0101 --1.7131 0.0156 --1.6559 0.0236 --1.5987 0.0350 --1.5415 0.0507 --1.4843 0.0718 --1.4271 0.0996 --1.3700 0.1353 --1.3128 0.1797 --1.2556 0.2338 --1.1984 0.2976 --1.1412 0.3707 --1.0840 0.4520 --1.0268 0.5393 --0.9696 0.6299 --0.9125 0.7200 --0.8553 0.8055 --0.7981 0.8819 --0.7409 0.9451 --0.6837 0.9913 --0.6265 1.0175 --0.5693 1.0223 --0.5121 1.0052 --0.4550 0.9673 --0.3978 0.9111 --0.3406 0.8399 --0.2834 0.7577 --0.2262 0.6691 --0.1690 0.5782 --0.1118 0.4891 --0.0546 0.4049 -0.0025 0.3280 -0.0597 0.2601 -0.1169 0.2019 -0.1741 0.1533 -0.2313 0.1140 -0.2885 0.0829 -0.3457 0.0591 -0.4029 0.0412 -0.4600 0.0281 -0.5172 0.0187 -0.5744 0.0122 -0.6316 0.0078 -0.6888 0.0049 -0.7460 0.0030 -0.8032 0.0018 -0.8603 0.0011 -0.9175 0.0006 -0.9747 0.0003 -1.0319 0.0002 -1.0891 0.0001 -1.1463 0.0001 -1.2035 0.0000 -1.2607 0.0000 -1.3178 0.0000 -1.3750 0.0000 -1.4322 0.0000 -1.4894 0.0000 -1.5466 0.0000 -1.6038 0.0000 -1.6610 0.0000 -1.7182 0.0000 -1.7753 0.0000 -1.8325 0.0000 -1.8897 0.0000 -1.9469 0.0000 -2.0041 0.0000 -2.0613 0.0000 -2.1185 0.0000 -2.1757 0.0000 -2.2328 0.0000 -2.2900 0.0000 -2.3472 0.0000 -2.4044 0.0000 -2.4616 0.0000 -2.5188 0.0000 -2.5760 0.0000 -2.6332 0.0000 -2.6903 0.0000 -2.7475 0.0000 -2.8047 0.0000 -2.8619 0.0000 -2.9191 0.0000 diff --git a/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt b/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt deleted file mode 100644 index 9f618060..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -Ctrq3 1 2 - diff --git a/sourcecodes/data/example_chl/old_gn/bWRnnode.txt b/sourcecodes/data/example_chl/old_gn/bWRnnode.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRnnode.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/example_chl/old_gn/bWRparameters.txt b/sourcecodes/data/example_chl/old_gn/bWRparameters.txt deleted file mode 100644 index 6d6eabf6..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRparameters.txt +++ /dev/null @@ -1,21 +0,0 @@ -Ctrq3 -Discrete node with 2 states -1 0.6341 -2 0.3659 - -MAS -Continuous node -0.4796 0.3499 - -Neutrophil -Continuous node -15.0488 10.8026 - -Load -Continuous node -4.0771 0.8165 - -Weight -Continuous node -0.8771 0.0875 - diff --git a/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt b/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt deleted file mode 100644 index efa98e06..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt +++ /dev/null @@ -1,7 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight -0 1 1 1 1 -0 0 1 1 0 -0 0 0 0 1 -0 0 0 0 0 -0 0 0 0 0 - diff --git a/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt b/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt deleted file mode 100644 index a6aed858..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt +++ /dev/null @@ -1,5 +0,0 @@ -Ctrq3 0.6341 0.3659 -MAS 0.0292 0.0326 0.0362 0.0401 0.0443 0.0489 0.0539 0.0592 0.0648 0.0709 0.0774 0.0842 0.0915 0.0992 0.1072 0.1157 0.1246 0.1338 0.1434 0.1534 0.1636 0.1742 0.1850 0.1961 0.2074 0.2188 0.2303 0.2419 0.2535 0.2651 0.2766 0.2879 0.2991 0.3099 0.3205 0.3307 0.3404 0.3496 0.3583 0.3663 0.3737 0.3804 0.3864 0.3916 0.3959 0.3994 0.4021 0.4038 0.4047 0.4046 0.4037 0.4018 0.3991 0.3954 0.3910 0.3857 0.3797 0.3729 0.3654 0.3572 0.3485 0.3392 0.3294 0.3192 0.3086 0.2977 0.2865 0.2752 0.2637 0.2521 0.2405 0.2289 0.2173 0.2059 0.1947 0.1837 0.1729 0.1623 0.1521 0.1422 0.1326 0.1234 0.1146 0.1062 0.0982 0.0906 0.0834 0.0765 0.0701 0.0641 0.0585 0.0532 0.0483 0.0438 0.0396 0.0357 0.0321 0.0288 0.0258 0.0231 0.0206 -Neutrophil 0.0245 0.0277 0.0313 0.0353 0.0396 0.0444 0.0496 0.0552 0.0613 0.0679 0.0750 0.0825 0.0906 0.0992 0.1083 0.1180 0.1281 0.1386 0.1496 0.1611 0.1729 0.1851 0.1975 0.2102 0.2231 0.2361 0.2491 0.2621 0.2750 0.2878 0.3002 0.3124 0.3240 0.3352 0.3458 0.3557 0.3648 0.3731 0.3806 0.3870 0.3925 0.3969 0.4002 0.4025 0.4035 0.4035 0.4022 0.3999 0.3964 0.3919 0.3863 0.3797 0.3722 0.3637 0.3545 0.3445 0.3339 0.3226 0.3109 0.2987 0.2862 0.2735 0.2605 0.2475 0.2345 0.2215 0.2086 0.1960 0.1835 0.1714 0.1597 0.1483 0.1373 0.1268 0.1167 0.1072 0.0981 0.0896 0.0816 0.0741 0.0670 0.0605 0.0545 0.0489 0.0438 0.0391 0.0348 0.0308 0.0273 0.0241 0.0212 0.0186 0.0163 0.0142 0.0123 0.0107 0.0093 0.0080 0.0069 0.0059 0.0050 -Load 0.0030 0.0036 0.0043 0.0050 0.0059 0.0069 0.0081 0.0094 0.0110 0.0127 0.0147 0.0169 0.0194 0.0222 0.0253 0.0287 0.0326 0.0368 0.0415 0.0466 0.0522 0.0583 0.0649 0.0720 0.0797 0.0879 0.0966 0.1059 0.1158 0.1261 0.1370 0.1484 0.1602 0.1724 0.1850 0.1979 0.2111 0.2244 0.2379 0.2514 0.2649 0.2782 0.2914 0.3042 0.3166 0.3285 0.3398 0.3504 0.3603 0.3693 0.3774 0.3845 0.3905 0.3954 0.3992 0.4017 0.4031 0.4032 0.4021 0.3997 0.3962 0.3915 0.3857 0.3788 0.3709 0.3620 0.3523 0.3418 0.3306 0.3188 0.3065 0.2937 0.2807 0.2674 0.2539 0.2404 0.2269 0.2135 0.2003 0.1874 0.1747 0.1624 0.1505 0.1391 0.1281 0.1176 0.1077 0.0983 0.0894 0.0811 0.0734 0.0662 0.0595 0.0533 0.0476 0.0424 0.0377 0.0333 0.0294 0.0259 0.0227 -Weight 0.0076 0.0089 0.0105 0.0122 0.0142 0.0164 0.0190 0.0218 0.0250 0.0286 0.0326 0.0370 0.0419 0.0473 0.0531 0.0596 0.0665 0.0741 0.0822 0.0909 0.1002 0.1101 0.1206 0.1316 0.1432 0.1553 0.1678 0.1808 0.1941 0.2076 0.2215 0.2354 0.2494 0.2633 0.2772 0.2907 0.3040 0.3168 0.3290 0.3406 0.3514 0.3614 0.3704 0.3784 0.3853 0.3910 0.3955 0.3988 0.4007 0.4013 0.4006 0.3985 0.3952 0.3906 0.3847 0.3778 0.3697 0.3605 0.3505 0.3396 0.3280 0.3157 0.3028 0.2896 0.2759 0.2621 0.2481 0.2342 0.2202 0.2064 0.1929 0.1796 0.1667 0.1542 0.1422 0.1306 0.1197 0.1092 0.0994 0.0901 0.0815 0.0734 0.0659 0.0590 0.0526 0.0468 0.0414 0.0366 0.0322 0.0283 0.0247 0.0215 0.0187 0.0162 0.0140 0.0120 0.0103 0.0088 0.0075 0.0064 0.0054 diff --git a/sourcecodes/data/example_chl/old_gn/bWRtype.txt b/sourcecodes/data/example_chl/old_gn/bWRtype.txt deleted file mode 100644 index 03b402ee..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight -2 1 1 1 1 diff --git a/sourcecodes/data/example_chl/old_gn/bWRvar.txt b/sourcecodes/data/example_chl/old_gn/bWRvar.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRvar.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_chl/old_gn/bWRvardata.txt b/sourcecodes/data/example_chl/old_gn/bWRvardata.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRvardata.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_chl/old_gn/bWRvarname.txt b/sourcecodes/data/example_chl/old_gn/bWRvarname.txt deleted file mode 100644 index 6ef2df09..00000000 --- a/sourcecodes/data/example_chl/old_gn/bWRvarname.txt +++ /dev/null @@ -1 +0,0 @@ -Ctrq3 \ No newline at end of file diff --git a/sourcecodes/data/example_chr2_spleen/cuLban.txt b/sourcecodes/data/example_chr2_spleen/cuLban.txt deleted file mode 100644 index fdd12dda..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLban.txt +++ /dev/null @@ -1,51 +0,0 @@ -From To -Ifih1 rs3664317 -Oas1a rs3664317 -Parp9 rs3664317 -Dhx58 rs3664317 -Cd1d1 rs3664317 -Irf7 rs3664317 -Oas3 rs3664317 -Pml rs3664317 -Mx1 rs3664317 -Ifit1 rs3664317 -Trim25 rs3664317 -Oas1g rs3664317 -Pglyrp3 rs3664317 -Ifih1 rs3664317 -Oas1a Ifih1 -Parp9 Ifih1 -Dhx58 Ifih1 -Cd1d1 Ifih1 -Irf7 Ifih1 -Oas3 Ifih1 -Pml Ifih1 -Mx1 Ifih1 -Ifit1 Ifih1 -Trim25 Ifih1 -Oas1g Ifih1 -Pglyrp3 Ifih1 -Oas1a rs3664317 -Parp9 rs3664317 -Dhx58 rs3664317 -Cd1d1 rs3664317 -Irf7 rs3664317 -Oas3 rs3664317 -Pml rs3664317 -Mx1 rs3664317 -Ifit1 rs3664317 -Trim25 rs3664317 -Oas1g rs3664317 -Pglyrp3 rs3664317 -Oas1a Ifih1 -Parp9 Ifih1 -Dhx58 Ifih1 -Cd1d1 Ifih1 -Irf7 Ifih1 -Oas3 Ifih1 -Pml Ifih1 -Mx1 Ifih1 -Ifit1 Ifih1 -Trim25 Ifih1 -Oas1g Ifih1 -Pglyrp3 Ifih1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt b/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt deleted file mode 100644 index ca8ea1e5..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt +++ /dev/null @@ -1,76 +0,0 @@ -rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 -2 1 1 1 1 1 1 1 1 1 1 1 1 1 -1 8.34 9.812 8.774 9.79 9.663 8.27 11.036 7.284 8.286 10.395 8.521 6.186 8.83 -1 8.368 9.738 8.566 9.144 9.484 8.818 11.03 6.977 8.294 10.076 8.529 5.968 8.828 -1 8.178 9.57 8.726 9.575 10.106 8.99 10.878 7.205 8.676 10.036 8.61 5.976 9.024 -1 8.116 9.901 8.904 9.959 9.793 8.336 11.105 7.598 8.316 10.292 8.401 5.814 8.836 -2 8.099 9.68 8.876 10.116 9.771 8.379 11.028 7.438 8.541 10.215 8.32 5.917 9.073 -1 8.262 9.59 8.24 10.088 8.938 7.832 10.486 6.752 7.825 9.908 8.196 6.15 8.446 -1 7.915 9.415 8.308 9.707 9.12 8.702 11.102 7.208 8.243 10.034 7.897 6.06 8.892 -2 8.565 10.002 8.96 9.779 10.322 9.24 11.278 7.644 8.893 10.42 8.773 5.914 9.407 -1 8.189 9.774 8.541 9.939 9.134 7.819 10.766 7.122 8.352 10.113 8.492 6.269 9.055 -1 8.476 9.954 8.908 9.476 9.92 8.764 11.134 7.859 8.788 10.17 8.862 6.226 9.17 -2 8.119 9.946 8.876 9.578 10.02 8.734 11.244 7.85 8.838 10.557 8.56 5.98 9.353 -2 8.305 9.713 8.972 9.789 9.839 8.804 10.948 7.682 8.896 10.181 8.854 5.979 9.567 -2 8.654 10 9.306 9.439 10.457 9.223 10.922 7.082 8.942 10.131 9.162 6.01 9.74 -1 8.105 9.748 8.725 10.119 9.782 8.575 11.113 7.63 8.674 10.355 8.59 6.279 8.908 -1 8.247 9.715 8.829 9.646 9.953 9.668 11.112 7.384 9.221 10.19 8.64 6 9.552 -1 8.511 9.994 9.014 9.89 10.266 8.444 10.599 7.331 9.153 10.012 8.837 6.148 9.023 -2 8.947 10.28 9.483 9.398 11.23 9.86 11.324 8.006 9.772 10.524 9.587 5.865 10.067 -1 8.526 9.685 8.921 9.7 10.126 9.373 11.121 7.497 9.003 10.357 8.156 6.334 9.678 -2 8.06 9.745 9.092 9.278 10.231 8.976 10.998 7.578 9.145 10.283 8.611 6.168 9.413 -2 7.93 9.728 8.694 9.512 9.826 9.016 11.276 7.604 8.767 10.378 8.577 5.963 9.264 -2 8.511 9.686 9.014 8.982 10.508 10.108 11.304 7.441 9.133 10.341 9.04 6.2 9.974 -2 8.645 9.997 8.97 9.443 10.393 9.302 11.409 7.785 8.894 10.552 9.051 5.997 9.412 -2 8.293 9.802 9.001 9.524 10.156 9.263 11.212 7.772 8.581 10.433 8.514 6.093 9.177 -1 7.781 9.712 8.97 9.375 10.12 9.484 11.317 7.347 8.972 10.393 8.352 6.193 9.587 -2 8.465 9.88 8.913 9.816 9.965 8.852 11.138 7.537 8.625 10.426 8.617 6.044 9.556 -2 8.657 10.026 9.189 9.691 10.302 9.268 11.194 7.634 9.143 10.378 9.05 6.067 9.679 -2 7.634 9.606 8.36 9.465 8.41 8.605 11.183 6.942 8.174 9.952 7.478 6.09 9.535 -1 7.669 9.494 8.779 9.552 9.362 8.52 11.024 7.131 8.378 10.391 8.114 6.07 8.851 -2 8.618 10.212 9.433 9.672 10.442 9.21 11.328 8.045 9.322 10.5 9.128 5.994 9.656 -2 8.731 10.27 9.342 9.43 10.697 10.117 11.286 7.749 9.734 10.464 9.322 6.156 9.876 -1 7.554 9.524 8.759 9.93 9.52 8.279 10.82 7.32 8.316 10.31 8.186 6.068 9.046 -1 8.262 9.677 8.75 9.444 10.052 8.634 10.888 7.32 8.562 9.893 8.644 6.212 8.918 -1 7.823 9.628 8.66 9.529 9.578 8.736 11.206 7.171 8.408 10.062 8.111 5.838 9.033 -1 8.28 9.572 8.784 9.428 9.862 9.424 11.27 7.288 8.505 10.174 8.642 6.022 9.313 -2 9.09 10.053 9.599 9.469 11.004 9.882 11.436 8.521 9.814 10.562 9.704 6.044 10.061 -1 8.446 9.989 9.297 9.688 10.577 9.129 11.102 7.718 9.484 10.231 9.072 6.17 9.21 -1 8.668 9.858 9.195 9.385 10.695 9.249 11.028 7.765 9.367 10.319 9.179 6.136 9.563 -2 8.574 10.059 9.281 9.233 10.508 9.247 11.145 8.138 9.505 10.402 9.192 5.992 9.848 -2 8.523 10.052 9.131 9.507 10.418 9.413 11.187 7.641 9.304 10.465 9.063 6.095 9.733 -1 7.987 9.748 8.766 9.578 9.781 8.482 11.279 7.52 8.364 10.141 8.207 6.192 9.133 -2 8.466 9.429 8.946 9.395 9.715 9.071 11.388 7.592 8.078 10.32 8.326 6.108 9.021 -1 7.668 9.694 8.493 10.112 9.561 8.394 10.922 7.26 8.19 10.27 7.916 5.892 8.974 -2 8.379 10.037 9.155 9.683 10.281 9.2 10.913 7.173 9.404 10.381 9.097 6.099 9.714 -2 7.805 9.654 8.454 9.198 10.065 9.468 11.217 6.917 8.43 10.459 8.11 6.068 9.068 -1 7.981 9.8 8.553 9.946 9.862 8.901 11.085 7.214 8.393 10.373 8.19 6.05 9.015 -1 7.746 9.688 8.578 9.901 9.358 7.866 10.928 7.354 7.929 10.233 8.066 5.754 8.883 -1 7.997 9.859 8.795 9.867 9.817 8.734 11.109 7.416 8.67 10.247 8.176 6.143 9.081 -1 8.674 9.689 9.06 9.81 10.544 8.995 11.189 7.781 9.219 10.07 8.98 5.992 9.143 -1 8.088 9.49 8.676 9.456 10.184 8.737 10.998 7.222 8.538 10.192 8.441 6.147 8.55 -1 8.001 9.801 8.669 9.977 9.383 8.274 11.055 7.231 7.913 10.272 8.277 5.931 9.009 -2 8.218 9.458 8.781 9.214 9.66 8.87 10.738 7.241 8.289 10.029 8.612 6.125 9.38 -1 7.684 9.56 8.75 10.077 9.686 8.27 11.102 7.206 8.13 10.212 8.07 6.018 8.984 -2 8.326 9.696 8.88 9.714 10.014 9.08 11.055 7.256 8.494 10.054 8.63 6.177 9.162 -2 8.906 10.106 9.412 9.704 11.06 9.854 11.335 7.799 10.103 10.471 9.25 6.033 9.97 -1 8.073 9.793 8.626 9.879 9.262 8.408 10.844 7.108 8.368 9.959 8.261 6.052 8.916 -2 8.527 10.026 9.143 9.244 10.597 9.566 11.108 7.778 9.748 10.351 9.153 6.055 9.698 -2 8.614 10.05 9.202 9.508 10.66 9.63 11.156 7.758 9.789 10.324 9.068 6.15 9.948 -2 8.522 10.158 8.992 9.684 9.992 8.55 11.125 7.914 8.976 10.311 8.574 5.889 9.566 -1 8.086 9.6 8.522 9.544 9.641 8.514 10.99 7.386 8.506 10.194 8.234 6.02 8.736 -1 7.873 9.596 8.452 9.422 9.278 8.509 10.958 7.057 8.081 9.981 7.969 6.136 8.958 -2 8.371 9.99 8.949 9.931 10.195 8.935 10.83 7.694 9.183 10.493 9.124 6.128 9.396 -2 8.476 9.982 9.115 9.639 10.465 9.833 11.105 8.058 9.9 10.351 9.182 6.05 9.884 -1 8.512 9.995 8.846 9.951 9.561 8.558 10.769 7.584 8.901 10.139 8.769 5.959 9.203 -1 8.358 9.858 8.99 9.981 10.123 9.368 10.989 7.463 9.327 9.93 8.54 6.02 9.543 -1 8.23 9.614 8.806 9.919 9.939 9.108 11.184 7.766 8.793 10.174 8.605 5.972 9.068 -2 8.238 9.802 8.926 9.595 10.062 8.77 11.202 7.712 9.131 10.34 8.57 6.05 9.464 -1 8.533 10.108 9.083 10.214 10.514 8.463 11.008 7.356 9.344 10.196 8.736 6.262 9.257 -1 7.866 9.444 8.223 9.865 8.95 8.539 10.935 6.754 7.748 10.177 7.826 6.29 8.716 -2 8.888 10.031 9.158 9.407 10.8 9.547 11.238 7.659 9.602 10.398 9.337 6.028 9.529 -1 8.026 9.682 8.398 9.824 9.202 8.041 10.703 7.322 8.352 10.209 8.196 6.009 9.001 -2 8.974 10.071 9.451 9.348 11.061 9.686 11.255 8.077 10.101 10.323 9.557 6.006 10.072 -1 8.181 9.432 9.045 9.544 10.651 9.18 10.832 7.419 8.742 9.818 8.546 6.33 9.201 -1 8.137 9.676 9.024 9.37 10.206 9.944 10.985 7.226 8.9 10.362 8.918 6.352 9.367 - diff --git a/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt b/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt deleted file mode 100644 index 824e26d5..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt +++ /dev/null @@ -1,32 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -rs3664317 -> Dhx58; -rs3664317 -> Cd1d1; -rs3664317 -> Ifit1; -rs3664317 -> Oas1g; -rs3664317 -> Ifih1; -Parp9 -> Oas1a; -Dhx58 -> Irf7; -Dhx58 -> Mx1; -Dhx58 -> Ifit1; -Dhx58 -> Trim25; -Dhx58 -> Oas1g; -Cd1d1 -> Oas3; -Cd1d1 -> Trim25; -Cd1d1 -> Pglyrp3; -Oas3 -> Pglyrp3; -Pml -> Oas3; -Pml -> Pglyrp3; -Ifit1 -> Irf7; -Ifit1 -> Mx1; -Trim25 -> Parp9; -Trim25 -> Pml; -Trim25 -> Pglyrp3; -Ifih1 -> Parp9; -Ifih1 -> Dhx58; -Ifih1 -> Cd1d1; -Ifih1 -> Oas3; -Ifih1 -> Ifit1; -Ifih1 -> Trim25; -} \ No newline at end of file diff --git a/sourcecodes/data/example_chr2_spleen/cuLk.txt b/sourcecodes/data/example_chr2_spleen/cuLk.txt deleted file mode 100644 index 29d6383b..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLk.txt +++ /dev/null @@ -1 +0,0 @@ -100 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmap.txt b/sourcecodes/data/example_chr2_spleen/cuLmap.txt deleted file mode 100644 index 9ca8e641..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLmap.txt +++ /dev/null @@ -1,14 +0,0 @@ -rs3664317 0.501140 1.452055 -Oas1a 0.347301 8.281466 -Parp9 0.216211 9.804164 -Dhx58 0.302026 8.891247 -Cd1d1 0.268738 9.643644 -Irf7 0.548579 10.009315 -Oas3 0.548788 8.957397 -Pml 0.190985 11.075425 -Mx1 0.336795 7.483137 -Ifit1 0.569192 8.828521 -Trim25 0.176657 10.255192 -Oas1g 0.458134 8.632151 -Pglyrp3 0.123345 6.070877 -Ifih1 0.387383 9.298137 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt b/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt deleted file mode 100644 index 64d3fc62..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -rs3664317 Ifih1 Cd1d1 Dhx58 Oas1g Trim25 Pml Oas3 Pglyrp3 Parp9 Oas1a Ifit1 Mx1 Irf7 diff --git a/sourcecodes/data/example_chr2_spleen/cuLname.txt b/sourcecodes/data/example_chr2_spleen/cuLname.txt deleted file mode 100644 index 1cc6fe19..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLname.txt +++ /dev/null @@ -1 +0,0 @@ -rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt b/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt deleted file mode 100644 index db0c7cf0..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt +++ /dev/null @@ -1,1387 +0,0 @@ -14 -1200 1400 -rs3664317 360 0 -Ifih1 480 175 -Cd1d1 160 350 -Dhx58 560 350 -Oas1g 180 525 -Trim25 480 525 -Pml 0 700 -Oas3 280 875 -Pglyrp3 360 1050 -Parp9 240 700 -Oas1a 680 875 -Ifit1 780 525 -Mx1 480 700 -Irf7 720 700 -rs3664317 2 -250 150 -0 -5 2 3 4 5 12 -1 0.5479 -2 0.4521 -Ifih1 1 -250 150 -1 1 -6 3 4 6 8 10 12 -8.0586 0.0023 -8.0826 0.0028 -8.1066 0.0034 -8.1306 0.0041 -8.1546 0.0050 -8.1787 0.0060 -8.2027 0.0071 -8.2267 0.0085 -8.2507 0.0101 -8.2747 0.0119 -8.2987 0.0140 -8.3227 0.0164 -8.3467 0.0192 -8.3707 0.0223 -8.3947 0.0259 -8.4187 0.0299 -8.4427 0.0343 -8.4667 0.0393 -8.4908 0.0449 -8.5148 0.0510 -8.5388 0.0578 -8.5628 0.0652 -8.5868 0.0733 -8.6108 0.0820 -8.6348 0.0914 -8.6588 0.1015 -8.6828 0.1124 -8.7068 0.1238 -8.7308 0.1359 -8.7548 0.1487 -8.7788 0.1620 -8.8029 0.1758 -8.8269 0.1900 -8.8509 0.2046 -8.8749 0.2195 -8.8989 0.2345 -8.9229 0.2496 -8.9469 0.2647 -8.9709 0.2795 -8.9949 0.2941 -9.0189 0.3082 -9.0429 0.3218 -9.0669 0.3347 -9.0909 0.3467 -9.1150 0.3578 -9.1390 0.3678 -9.1630 0.3766 -9.1870 0.3842 -9.2110 0.3903 -9.2350 0.3951 -9.2590 0.3984 -9.2830 0.4001 -9.3070 0.4003 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-10.1465 0.0687 -10.1642 0.0606 -10.1819 0.0532 -10.1996 0.0465 -10.2173 0.0404 -10.2350 0.0350 -10.2527 0.0302 -10.2704 0.0259 -10.2881 0.0222 -10.3058 0.0189 -10.3235 0.0160 -10.3412 0.0135 -10.3589 0.0113 -10.3766 0.0095 -10.3943 0.0079 -10.4120 0.0066 -10.4297 0.0054 -10.4473 0.0044 -10.4650 0.0036 -10.4827 0.0030 -Dhx58 1 -250 150 -2 1 2 -5 5 6 12 13 14 -7.9210 0.0024 -7.9408 0.0029 -7.9606 0.0035 -7.9804 0.0043 -8.0002 0.0053 -8.0200 0.0064 -8.0398 0.0076 -8.0596 0.0092 -8.0794 0.0110 -8.0992 0.0130 -8.1190 0.0154 -8.1388 0.0182 -8.1586 0.0213 -8.1784 0.0249 -8.1982 0.0290 -8.2180 0.0336 -8.2378 0.0388 -8.2576 0.0446 -8.2774 0.0510 -8.2972 0.0581 -8.3170 0.0659 -8.3368 0.0745 -8.3566 0.0838 -8.3764 0.0938 -8.3962 0.1046 -8.4160 0.1162 -8.4358 0.1284 -8.4556 0.1414 -8.4754 0.1550 -8.4952 0.1692 -8.5150 0.1839 -8.5348 0.1990 -8.5546 0.2145 -8.5744 0.2302 -8.5942 0.2459 -8.6140 0.2617 -8.6338 0.2772 -8.6536 0.2924 -8.6734 0.3071 -8.6932 0.3212 -8.7130 0.3346 -8.7328 0.3469 -8.7526 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0.2059 -9.5194 0.1917 -9.5543 0.1778 -9.5892 0.1643 -9.6242 0.1513 -9.6591 0.1388 -9.6940 0.1268 -9.7290 0.1155 -9.7639 0.1047 -9.7988 0.0947 -9.8338 0.0852 -9.8687 0.0765 -9.9036 0.0683 -9.9386 0.0609 -9.9735 0.0540 -10.0084 0.0477 -10.0434 0.0420 -10.0783 0.0369 -10.1133 0.0322 -10.1482 0.0281 -10.1831 0.0244 -10.2181 0.0211 -10.2530 0.0181 -10.2879 0.0156 -10.3229 0.0133 -10.3578 0.0113 -10.3927 0.0096 -10.4277 0.0081 -10.4626 0.0068 -10.4975 0.0057 -10.5325 0.0048 -10.5674 0.0040 -10.6023 0.0033 -10.6373 0.0027 -10.6722 0.0023 -Mx1 1 -250 150 -2 4 12 -0 -6.4152 0.0028 -6.4396 0.0035 -6.4641 0.0043 -6.4885 0.0053 -6.5129 0.0066 -6.5373 0.0081 -6.5618 0.0098 -6.5862 0.0119 -6.6106 0.0144 -6.6350 0.0173 -6.6595 0.0207 -6.6839 0.0246 -6.7083 0.0291 -6.7327 0.0342 -6.7572 0.0400 -6.7816 0.0465 -6.8060 0.0539 -6.8304 0.0621 -6.8549 0.0711 -6.8793 0.0811 -6.9037 0.0919 -6.9281 0.1037 -6.9526 0.1164 -6.9770 0.1300 -7.0014 0.1444 -7.0259 0.1595 -7.0503 0.1754 -7.0747 0.1918 -7.0991 0.2086 -7.1236 0.2258 -7.1480 0.2431 -7.1724 0.2604 -7.1968 0.2775 -7.2213 0.2941 -7.2457 0.3102 -7.2701 0.3254 -7.2945 0.3396 -7.3190 0.3526 -7.3434 0.3641 -7.3678 0.3742 -7.3922 0.3824 -7.4167 0.3889 -7.4411 0.3934 -7.4655 0.3959 -7.4899 0.3964 -7.5144 0.3948 -7.5388 0.3911 -7.5632 0.3855 -7.5876 0.3780 -7.6121 0.3688 -7.6365 0.3579 -7.6609 0.3455 -7.6854 0.3318 -7.7098 0.3170 -7.7342 0.3013 -7.7586 0.2849 -7.7831 0.2680 -7.8075 0.2508 -7.8319 0.2335 -7.8563 0.2162 -7.8808 0.1992 -7.9052 0.1826 -7.9296 0.1665 -7.9540 0.1510 -7.9785 0.1363 -8.0029 0.1223 -8.0273 0.1092 -8.0517 0.0970 -8.0762 0.0858 -8.1006 0.0754 -8.1250 0.0660 -8.1494 0.0574 -8.1739 0.0497 -8.1983 0.0428 -8.2227 0.0367 -8.2471 0.0312 -8.2716 0.0265 -8.2960 0.0223 -8.3204 0.0187 -8.3449 0.0156 -8.3693 0.0130 -8.3937 0.0107 -8.4181 0.0088 -8.4426 0.0072 -8.4670 0.0059 -8.4914 0.0047 -8.5158 0.0038 -8.5403 0.0031 -8.5647 0.0024 -8.5891 0.0019 -8.6135 0.0015 -8.6380 0.0012 -8.6624 0.0009 -8.6868 0.0007 -8.7112 0.0006 -8.7357 0.0004 -8.7601 0.0003 -8.7845 0.0002 -8.8089 0.0002 -8.8334 0.0001 -8.8578 0.0001 -Irf7 1 -250 150 -2 4 12 -0 -7.8614 0.0002 -7.9006 0.0003 -7.9398 0.0004 -7.9789 0.0005 -8.0181 0.0006 -8.0573 0.0008 -8.0965 0.0010 -8.1356 0.0013 -8.1748 0.0016 -8.2140 0.0021 -8.2531 0.0026 -8.2923 0.0033 -8.3315 0.0040 -8.3707 0.0050 -8.4098 0.0061 -8.4490 0.0075 -8.4882 0.0091 -8.5273 0.0111 -8.5665 0.0133 -8.6057 0.0160 -8.6449 0.0191 -8.6840 0.0226 -8.7232 0.0267 -8.7624 0.0314 -8.8015 0.0367 -8.8407 0.0428 -8.8799 0.0495 -8.9191 0.0570 -8.9582 0.0654 -8.9974 0.0746 -9.0366 0.0846 -9.0757 0.0956 -9.1149 0.1074 -9.1541 0.1201 -9.1933 0.1336 -9.2324 0.1478 -9.2716 0.1628 -9.3108 0.1784 -9.3499 0.1946 -9.3891 0.2111 -9.4283 0.2279 -9.4675 0.2448 -9.5066 0.2617 -9.5458 0.2783 -9.5850 0.2946 -9.6241 0.3102 -9.6633 0.3250 -9.7025 0.3388 -9.7417 0.3514 -9.7808 0.3627 -9.8200 0.3725 -9.8592 0.3806 -9.8983 0.3870 -9.9375 0.3916 -9.9767 0.3942 -10.0159 0.3948 -10.0550 0.3935 -10.0942 0.3903 -10.1334 0.3851 -10.1725 0.3781 -10.2117 0.3694 -10.2509 0.3591 -10.2901 0.3473 -10.3292 0.3343 -10.3684 0.3201 -10.4076 0.3050 -10.4467 0.2892 -10.4859 0.2728 -10.5251 0.2561 -10.5643 0.2392 -10.6034 0.2223 -10.6426 0.2056 -10.6818 0.1891 -10.7209 0.1732 -10.7601 0.1577 -10.7993 0.1430 -10.8385 0.1290 -10.8776 0.1157 -10.9168 0.1033 -10.9560 0.0918 -10.9951 0.0812 -11.0343 0.0714 -11.0735 0.0625 -11.1127 0.0544 -11.1518 0.0472 -11.1910 0.0407 -11.2302 0.0349 -11.2693 0.0298 -11.3085 0.0253 -11.3477 0.0214 -11.3869 0.0180 -11.4260 0.0151 -11.4652 0.0125 -11.5044 0.0104 -11.5435 0.0086 -11.5827 0.0070 -11.6219 0.0057 -11.6611 0.0047 -11.7002 0.0038 -11.7394 0.0030 -11.7786 0.0024 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnet_figure_new.txt b/sourcecodes/data/example_chr2_spleen/cuLnet_figure_new.txt deleted file mode 100644 index 7f631ad5..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLnet_figure_new.txt +++ /dev/null @@ -1,1288 +0,0 @@ -2 -14 -1200 1400 -rs3664317 360 0 -Ifih1 480 175 -Cd1d1 160 350 -Dhx58 560 350 -Oas1g 180 525 -Trim25 480 525 -Pml 0 700 -Oas3 280 875 -Pglyrp3 360 1050 -Parp9 240 700 -Oas1a 680 875 -Ifit1 780 525 -Mx1 480 700 -Irf7 720 700 -rs3664317 2 -250 150 -0 -5 2 3 4 5 12 -1 0.9980 -2 0.0020 -Ifih1 1 -250 150 -1 1 -6 3 4 6 8 10 12 --3.3510 1.0000 -Cd1d1 1 -250 150 -2 1 2 -3 6 8 9 --3.4620 0.0000 --3.3962 0.0000 --3.3304 0.0000 --3.2645 0.0000 --3.1987 0.0000 --3.1328 0.0000 --3.0670 0.0000 --3.0011 0.0000 --2.9353 0.0000 --2.8694 0.0000 --2.8036 0.0000 --2.7378 0.0001 --2.6719 0.0001 --2.6061 0.0001 --2.5402 0.0001 --2.4744 0.0002 --2.4085 0.0002 --2.3427 0.0003 --2.2768 0.0004 --2.2110 0.0006 --2.1452 0.0007 --2.0793 0.0009 --2.0135 0.0012 --1.9476 0.0016 --1.8818 0.0020 --1.8159 0.0026 --1.7501 0.0032 --1.6843 0.0041 --1.6184 0.0051 --1.5526 0.0063 --1.4867 0.0078 --1.4209 0.0097 --1.3550 0.0118 --1.2892 0.0144 --1.2233 0.0175 --1.1575 0.0210 --1.0917 0.0252 --1.0258 0.0300 --0.9600 0.0356 --0.8941 0.0419 --0.8283 0.0491 --0.7624 0.0572 --0.6966 0.0663 --0.6308 0.0765 --0.5649 0.0877 --0.4991 0.1000 --0.4332 0.1133 --0.3674 0.1278 --0.3015 0.1434 --0.2357 0.1599 --0.1698 0.1774 --0.1040 0.1957 --0.0382 0.2147 -0.0277 0.2343 -0.0935 0.2543 -0.1594 0.2744 -0.2252 0.2946 -0.2911 0.3144 -0.3569 0.3338 -0.4227 0.3524 -0.4886 0.3701 -0.5544 0.3865 -0.6203 0.4014 -0.6861 0.4146 -0.7520 0.4259 -0.8178 0.4351 -0.8837 0.4420 -0.9495 0.4466 -1.0153 0.4488 -1.0812 0.4485 -1.1470 0.4458 -1.2129 0.4407 -1.2787 0.4332 -1.3446 0.4236 -1.4104 0.4118 -1.4763 0.3983 -1.5421 0.3830 -1.6079 0.3663 -1.6738 0.3484 -1.7396 0.3296 -1.8055 0.3101 -1.8713 0.2902 -1.9372 0.2700 -2.0030 0.2499 -2.0688 0.2300 -2.1347 0.2105 -2.2005 0.1916 -2.2664 0.1735 -2.3322 0.1562 -2.3981 0.1399 -2.4639 0.1246 -2.5298 0.1103 -2.5956 0.0972 -2.6614 0.0851 -2.7273 0.0742 -2.7931 0.0643 -2.8590 0.0554 -2.9248 0.0474 -2.9907 0.0404 -3.0565 0.0343 -3.1223 0.0289 -Dhx58 1 -250 150 -2 1 2 -5 5 6 12 13 14 --3.2125 0.2772 --3.1470 0.3638 --3.0814 0.4631 --3.0159 0.5716 --2.9503 0.6843 --2.8848 0.7945 --2.8192 0.8946 --2.7536 0.9769 --2.6881 1.0347 --2.6225 1.0628 --2.5570 1.0587 --2.4914 1.0228 --2.4258 0.9583 --2.3603 0.8708 --2.2947 0.7674 --2.2292 0.6559 --2.1636 0.5437 --2.0980 0.4371 --2.0325 0.3408 --1.9669 0.2577 --1.9014 0.1890 --1.8358 0.1344 --1.7702 0.0927 --1.7047 0.0620 --1.6391 0.0402 --1.5736 0.0253 --1.5080 0.0154 --1.4425 0.0091 --1.3769 0.0052 --1.3113 0.0029 --1.2458 0.0016 --1.1802 0.0008 --1.1147 0.0004 --1.0491 0.0002 --0.9835 0.0001 --0.9180 0.0000 --0.8524 0.0000 --0.7869 0.0000 --0.7213 0.0000 --0.6557 0.0000 --0.5902 0.0000 --0.5246 0.0000 --0.4591 0.0000 --0.3935 0.0000 --0.3280 0.0000 --0.2624 0.0000 --0.1968 0.0000 --0.1313 0.0000 --0.0657 0.0000 --0.0002 0.0000 -0.0654 0.0000 -0.1310 0.0000 -0.1965 0.0000 -0.2621 0.0000 -0.3276 0.0000 -0.3932 0.0000 -0.4588 0.0000 -0.5243 0.0000 -0.5899 0.0000 -0.6554 0.0000 -0.7210 0.0000 -0.7866 0.0000 -0.8521 0.0000 -0.9177 0.0000 -0.9832 0.0000 -1.0488 0.0000 -1.1143 0.0000 -1.1799 0.0000 -1.2455 0.0000 -1.3110 0.0000 -1.3766 0.0000 -1.4421 0.0000 -1.5077 0.0000 -1.5733 0.0000 -1.6388 0.0000 -1.7044 0.0000 -1.7699 0.0000 -1.8355 0.0000 -1.9011 0.0000 -1.9666 0.0000 -2.0322 0.0000 -2.0977 0.0000 -2.1633 0.0000 -2.2288 0.0000 -2.2944 0.0000 -2.3600 0.0000 -2.4255 0.0000 -2.4911 0.0000 -2.5566 0.0000 -2.6222 0.0000 -2.6878 0.0000 -2.7533 0.0000 -2.8189 0.0000 -2.8844 0.0000 -2.9500 0.0000 -3.0156 0.0000 -3.0811 0.0000 -3.1467 0.0000 -3.2122 0.0000 -3.2778 0.0000 -3.3434 0.0000 -Oas1g 1 -250 150 -2 1 4 -0 --3.5192 0.0005 --3.4507 0.0009 --3.3821 0.0017 --3.3135 0.0030 --3.2449 0.0053 --3.1763 0.0090 --3.1077 0.0148 --3.0391 0.0238 --2.9705 0.0371 --2.9019 0.0562 --2.8334 0.0829 --2.7648 0.1187 --2.6962 0.1652 --2.6276 0.2236 --2.5590 0.2943 --2.4904 0.3764 --2.4218 0.4681 --2.3532 0.5659 --2.2847 0.6652 --2.2161 0.7600 --2.1475 0.8442 --2.0789 0.9116 --2.0103 0.9570 --1.9417 0.9767 --1.8731 0.9691 --1.8045 0.9347 --1.7359 0.8764 --1.6674 0.7989 --1.5988 0.7080 --1.5302 0.6100 --1.4616 0.5109 --1.3930 0.4159 --1.3244 0.3292 --1.2558 0.2533 --1.1872 0.1895 --1.1186 0.1378 --1.0501 0.0974 --0.9815 0.0670 --0.9129 0.0448 --0.8443 0.0291 --0.7757 0.0184 --0.7071 0.0113 --0.6385 0.0067 --0.5699 0.0039 --0.5014 0.0022 --0.4328 0.0012 --0.3642 0.0006 --0.2956 0.0003 --0.2270 0.0002 --0.1584 0.0001 --0.0898 0.0000 --0.0212 0.0000 -0.0474 0.0000 -0.1159 0.0000 -0.1845 0.0000 -0.2531 0.0000 -0.3217 0.0000 -0.3903 0.0000 -0.4589 0.0000 -0.5275 0.0000 -0.5961 0.0000 -0.6646 0.0000 -0.7332 0.0000 -0.8018 0.0000 -0.8704 0.0000 -0.9390 0.0000 -1.0076 0.0000 -1.0762 0.0000 -1.1448 0.0000 -1.2134 0.0000 -1.2819 0.0000 -1.3505 0.0000 -1.4191 0.0000 -1.4877 0.0000 -1.5563 0.0000 -1.6249 0.0000 -1.6935 0.0000 -1.7621 0.0000 -1.8307 0.0000 -1.8992 0.0000 -1.9678 0.0000 -2.0364 0.0000 -2.1050 0.0000 -2.1736 0.0000 -2.2422 0.0000 -2.3108 0.0000 -2.3794 0.0000 -2.4479 0.0000 -2.5165 0.0000 -2.5851 0.0000 -2.6537 0.0000 -2.7223 0.0000 -2.7909 0.0000 -2.8595 0.0000 -2.9281 0.0000 -2.9967 0.0000 -3.0652 0.0000 -3.1338 0.0000 -3.2024 0.0000 -3.2710 0.0000 -3.3396 0.0000 -Trim25 1 -250 150 -3 2 3 4 -3 7 9 10 --3.4748 0.0273 --3.4127 0.0331 --3.3506 0.0400 --3.2885 0.0479 --3.2263 0.0570 --3.1642 0.0675 --3.1021 0.0792 --3.0400 0.0925 --2.9779 0.1072 --2.9158 0.1235 --2.8536 0.1413 --2.7915 0.1606 --2.7294 0.1814 --2.6673 0.2034 --2.6052 0.2267 --2.5431 0.2510 --2.4810 0.2760 --2.4188 0.3015 --2.3567 0.3273 --2.2946 0.3528 --2.2325 0.3779 --2.1704 0.4021 --2.1083 0.4250 --2.0461 0.4463 --1.9840 0.4655 --1.9219 0.4824 --1.8598 0.4966 --1.7977 0.5078 --1.7356 0.5159 --1.6735 0.5207 --1.6113 0.5220 --1.5492 0.5199 --1.4871 0.5144 --1.4250 0.5056 --1.3629 0.4937 --1.3008 0.4789 --1.2386 0.4615 --1.1765 0.4417 --1.1144 0.4201 --1.0523 0.3969 --0.9902 0.3724 --0.9281 0.3472 --0.8660 0.3216 --0.8038 0.2959 --0.7417 0.2705 --0.6796 0.2456 --0.6175 0.2215 --0.5554 0.1985 --0.4933 0.1767 --0.4311 0.1562 --0.3690 0.1373 --0.3069 0.1198 --0.2448 0.1039 --0.1827 0.0894 --0.1206 0.0765 --0.0585 0.0650 -0.0037 0.0549 -0.0658 0.0461 -0.1279 0.0384 -0.1900 0.0318 -0.2521 0.0261 -0.3142 0.0213 -0.3764 0.0173 -0.4385 0.0140 -0.5006 0.0112 -0.5627 0.0089 -0.6248 0.0070 -0.6869 0.0055 -0.7490 0.0043 -0.8112 0.0033 -0.8733 0.0026 -0.9354 0.0020 -0.9975 0.0015 -1.0596 0.0011 -1.1217 0.0008 -1.1839 0.0006 -1.2460 0.0005 -1.3081 0.0003 -1.3702 0.0002 -1.4323 0.0002 -1.4944 0.0001 -1.5565 0.0001 -1.6187 0.0001 -1.6808 0.0000 -1.7429 0.0000 -1.8050 0.0000 -1.8671 0.0000 -1.9292 0.0000 -1.9914 0.0000 -2.0535 0.0000 -2.1156 0.0000 -2.1777 0.0000 -2.2398 0.0000 -2.3019 0.0000 -2.3640 0.0000 -2.4262 0.0000 -2.4883 0.0000 -2.5504 0.0000 -2.6125 0.0000 -2.6746 0.0000 -2.7367 0.0000 -Pml 1 -250 150 -1 6 -2 8 9 --4.0862 0.0013 --4.0165 0.0017 --3.9468 0.0022 --3.8770 0.0028 --3.8073 0.0036 --3.7375 0.0045 --3.6678 0.0057 --3.5980 0.0071 --3.5283 0.0088 --3.4586 0.0108 --3.3888 0.0133 --3.3191 0.0162 --3.2493 0.0196 --3.1796 0.0236 --3.1098 0.0283 --3.0401 0.0337 --2.9704 0.0399 --2.9006 0.0470 --2.8309 0.0550 --2.7611 0.0640 --2.6914 0.0741 --2.6217 0.0852 --2.5519 0.0975 --2.4822 0.1109 --2.4124 0.1254 --2.3427 0.1409 --2.2729 0.1575 --2.2032 0.1750 --2.1335 0.1934 --2.0637 0.2124 --1.9940 0.2320 --1.9242 0.2519 --1.8545 0.2720 --1.7847 0.2919 --1.7150 0.3115 --1.6453 0.3305 --1.5755 0.3487 --1.5058 0.3657 --1.4360 0.3814 --1.3663 0.3954 --1.2966 0.4075 --1.2268 0.4177 --1.1571 0.4256 --1.0873 0.4311 --1.0176 0.4343 --0.9478 0.4349 --0.8781 0.4330 --0.8084 0.4286 --0.7386 0.4218 --0.6689 0.4128 --0.5991 0.4016 --0.5294 0.3884 --0.4596 0.3736 --0.3899 0.3572 --0.3202 0.3395 --0.2504 0.3209 --0.1807 0.3016 --0.1109 0.2818 --0.0412 0.2617 -0.0286 0.2417 -0.0983 0.2220 -0.1680 0.2026 -0.2378 0.1839 -0.3075 0.1660 -0.3773 0.1489 -0.4470 0.1328 -0.5167 0.1178 -0.5865 0.1039 -0.6562 0.0911 -0.7260 0.0794 -0.7957 0.0688 -0.8655 0.0593 -0.9352 0.0508 -1.0049 0.0433 -1.0747 0.0366 -1.1444 0.0308 -1.2142 0.0258 -1.2839 0.0215 -1.3537 0.0178 -1.4234 0.0146 -1.4931 0.0120 -1.5629 0.0097 -1.6326 0.0079 -1.7024 0.0063 -1.7721 0.0051 -1.8418 0.0040 -1.9116 0.0032 -1.9813 0.0025 -2.0511 0.0019 -2.1208 0.0015 -2.1906 0.0012 -2.2603 0.0009 -2.3300 0.0007 -2.3998 0.0005 -2.4695 0.0004 -2.5393 0.0003 -2.6090 0.0002 -2.6788 0.0002 -2.7485 0.0001 -2.8182 0.0001 -2.8880 0.0001 -Oas3 1 -250 150 -3 2 3 7 -1 9 --3.0744 0.1968 --3.0125 0.2591 --2.9506 0.3326 --2.8888 0.4165 --2.8269 0.5085 --2.7650 0.6055 --2.7031 0.7031 --2.6413 0.7962 --2.5794 0.8793 --2.5175 0.9470 --2.4556 0.9947 --2.3938 1.0188 --2.3319 1.0177 --2.2700 0.9913 --2.2081 0.9417 --2.1463 0.8724 --2.0844 0.7882 --2.0225 0.6945 --1.9606 0.5967 --1.8988 0.5000 --1.8369 0.4086 --1.7750 0.3256 --1.7132 0.2531 --1.6513 0.1918 --1.5894 0.1418 --1.5275 0.1022 --1.4657 0.0718 --1.4038 0.0492 --1.3419 0.0329 --1.2800 0.0215 --1.2182 0.0136 --1.1563 0.0085 --1.0944 0.0051 --1.0325 0.0030 --0.9707 0.0017 --0.9088 0.0010 --0.8469 0.0005 --0.7850 0.0003 --0.7232 0.0001 --0.6613 0.0001 --0.5994 0.0000 --0.5375 0.0000 --0.4757 0.0000 --0.4138 0.0000 --0.3519 0.0000 --0.2901 0.0000 --0.2282 0.0000 --0.1663 0.0000 --0.1044 0.0000 --0.0426 0.0000 -0.0193 0.0000 -0.0812 0.0000 -0.1431 0.0000 -0.2049 0.0000 -0.2668 0.0000 -0.3287 0.0000 -0.3906 0.0000 -0.4524 0.0000 -0.5143 0.0000 -0.5762 0.0000 -0.6381 0.0000 -0.6999 0.0000 -0.7618 0.0000 -0.8237 0.0000 -0.8856 0.0000 -0.9474 0.0000 -1.0093 0.0000 -1.0712 0.0000 -1.1331 0.0000 -1.1949 0.0000 -1.2568 0.0000 -1.3187 0.0000 -1.3805 0.0000 -1.4424 0.0000 -1.5043 0.0000 -1.5662 0.0000 -1.6280 0.0000 -1.6899 0.0000 -1.7518 0.0000 -1.8137 0.0000 -1.8755 0.0000 -1.9374 0.0000 -1.9993 0.0000 -2.0612 0.0000 -2.1230 0.0000 -2.1849 0.0000 -2.2468 0.0000 -2.3087 0.0000 -2.3705 0.0000 -2.4324 0.0000 -2.4943 0.0000 -2.5562 0.0000 -2.6180 0.0000 -2.6799 0.0000 -2.7418 0.0000 -2.8037 0.0000 -2.8655 0.0000 -2.9274 0.0000 -2.9893 0.0000 -3.0511 0.0000 -3.1130 0.0000 -Pglyrp3 1 -250 150 -4 3 6 7 8 -0 --3.5690 0.0027 --3.5005 0.0034 --3.4321 0.0041 --3.3636 0.0050 --3.2951 0.0061 --3.2266 0.0074 --3.1581 0.0089 --3.0897 0.0106 --3.0212 0.0127 --2.9527 0.0150 --2.8842 0.0178 --2.8157 0.0209 --2.7472 0.0245 --2.6788 0.0285 --2.6103 0.0331 --2.5418 0.0383 --2.4733 0.0441 --2.4048 0.0505 --2.3364 0.0576 --2.2679 0.0655 --2.1994 0.0740 --2.1309 0.0833 --2.0624 0.0934 --1.9939 0.1042 --1.9255 0.1158 --1.8570 0.1281 --1.7885 0.1411 --1.7200 0.1547 --1.6515 0.1689 --1.5831 0.1835 --1.5146 0.1986 --1.4461 0.2140 --1.3776 0.2295 --1.3091 0.2450 --1.2406 0.2605 --1.1722 0.2757 --1.1037 0.2906 --1.0352 0.3049 --0.9667 0.3185 --0.8982 0.3312 --0.8298 0.3429 --0.7613 0.3535 --0.6928 0.3628 --0.6243 0.3707 --0.5558 0.3771 --0.4873 0.3819 --0.4189 0.3851 --0.3504 0.3866 --0.2819 0.3865 --0.2134 0.3846 --0.1449 0.3810 --0.0765 0.3758 --0.0080 0.3691 -0.0605 0.3609 -0.1290 0.3513 -0.1975 0.3404 -0.2660 0.3285 -0.3344 0.3155 -0.4029 0.3018 -0.4714 0.2874 -0.5399 0.2724 -0.6084 0.2571 -0.6769 0.2416 -0.7453 0.2261 -0.8138 0.2106 -0.8823 0.1953 -0.9508 0.1803 -1.0193 0.1657 -1.0877 0.1517 -1.1562 0.1382 -1.2247 0.1254 -1.2932 0.1132 -1.3617 0.1018 -1.4302 0.0911 -1.4986 0.0812 -1.5671 0.0721 -1.6356 0.0637 -1.7041 0.0560 -1.7726 0.0490 -1.8410 0.0428 -1.9095 0.0371 -1.9780 0.0321 -2.0465 0.0276 -2.1150 0.0236 -2.1835 0.0202 -2.2519 0.0171 -2.3204 0.0145 -2.3889 0.0122 -2.4574 0.0102 -2.5259 0.0085 -2.5943 0.0071 -2.6628 0.0058 -2.7313 0.0048 -2.7998 0.0039 -2.8683 0.0032 -2.9368 0.0026 -3.0052 0.0021 -3.0737 0.0017 -3.1422 0.0014 -3.2107 0.0011 -3.2792 0.0009 -Parp9 1 -250 150 -2 2 6 -1 11 --2.7999 0.3911 --2.7399 0.4346 --2.6799 0.4778 --2.6199 0.5196 --2.5599 0.5590 --2.4999 0.5949 --2.4399 0.6263 --2.3799 0.6523 --2.3199 0.6721 --2.2599 0.6850 --2.1999 0.6907 --2.1398 0.6890 --2.0798 0.6798 --2.0198 0.6636 --1.9598 0.6408 --1.8998 0.6122 --1.8398 0.5785 --1.7798 0.5408 --1.7198 0.5002 --1.6598 0.4576 --1.5998 0.4141 --1.5398 0.3708 --1.4798 0.3284 --1.4198 0.2878 --1.3598 0.2494 --1.2997 0.2139 --1.2397 0.1814 --1.1797 0.1522 --1.1197 0.1264 --1.0597 0.1038 --0.9997 0.0843 --0.9397 0.0678 --0.8797 0.0539 --0.8197 0.0424 --0.7597 0.0330 --0.6997 0.0254 --0.6397 0.0193 --0.5797 0.0145 --0.5197 0.0108 --0.4596 0.0080 --0.3996 0.0058 --0.3396 0.0042 --0.2796 0.0030 --0.2196 0.0021 --0.1596 0.0015 --0.0996 0.0010 --0.0396 0.0007 -0.0204 0.0005 -0.0804 0.0003 -0.1404 0.0002 -0.2004 0.0001 -0.2604 0.0001 -0.3204 0.0001 -0.3805 0.0000 -0.4405 0.0000 -0.5005 0.0000 -0.5605 0.0000 -0.6205 0.0000 -0.6805 0.0000 -0.7405 0.0000 -0.8005 0.0000 -0.8605 0.0000 -0.9205 0.0000 -0.9805 0.0000 -1.0405 0.0000 -1.1005 0.0000 -1.1605 0.0000 -1.2206 0.0000 -1.2806 0.0000 -1.3406 0.0000 -1.4006 0.0000 -1.4606 0.0000 -1.5206 0.0000 -1.5806 0.0000 -1.6406 0.0000 -1.7006 0.0000 -1.7606 0.0000 -1.8206 0.0000 -1.8806 0.0000 -1.9406 0.0000 -2.0006 0.0000 -2.0607 0.0000 -2.1207 0.0000 -2.1807 0.0000 -2.2407 0.0000 -2.3007 0.0000 -2.3607 0.0000 -2.4207 0.0000 -2.4807 0.0000 -2.5407 0.0000 -2.6007 0.0000 -2.6607 0.0000 -2.7207 0.0000 -2.7807 0.0000 -2.8407 0.0000 -2.9008 0.0000 -2.9608 0.0000 -3.0208 0.0000 -3.0808 0.0000 -3.1408 0.0000 -3.2008 0.0000 -Oas1a 1 -250 150 -1 10 -0 --3.0946 0.0747 --3.0304 0.0873 --2.9662 0.1013 --2.9019 0.1168 --2.8377 0.1338 --2.7735 0.1522 --2.7093 0.1720 --2.6450 0.1932 --2.5808 0.2155 --2.5166 0.2388 --2.4524 0.2629 --2.3881 0.2875 --2.3239 0.3124 --2.2597 0.3371 --2.1955 0.3615 --2.1312 0.3850 --2.0670 0.4074 --2.0028 0.4282 --1.9385 0.4472 --1.8743 0.4639 --1.8101 0.4780 --1.7459 0.4894 --1.6816 0.4977 --1.6174 0.5029 --1.5532 0.5047 --1.4890 0.5032 --1.4247 0.4985 --1.3605 0.4905 --1.2963 0.4795 --1.2320 0.4656 --1.1678 0.4492 --1.1036 0.4304 --1.0394 0.4098 --0.9751 0.3876 --0.9109 0.3642 --0.8467 0.3399 --0.7825 0.3152 --0.7182 0.2903 --0.6540 0.2656 --0.5898 0.2415 --0.5256 0.2181 --0.4613 0.1956 --0.3971 0.1744 --0.3329 0.1544 --0.2686 0.1358 --0.2044 0.1186 --0.1402 0.1030 --0.0760 0.0888 --0.0117 0.0761 -0.0525 0.0647 -0.1167 0.0547 -0.1809 0.0459 -0.2452 0.0383 -0.3094 0.0318 -0.3736 0.0262 -0.4378 0.0214 -0.5021 0.0174 -0.5663 0.0140 -0.6305 0.0113 -0.6948 0.0090 -0.7590 0.0071 -0.8232 0.0056 -0.8874 0.0044 -0.9517 0.0034 -1.0159 0.0026 -1.0801 0.0020 -1.1443 0.0015 -1.2086 0.0011 -1.2728 0.0009 -1.3370 0.0006 -1.4012 0.0005 -1.4655 0.0003 -1.5297 0.0003 -1.5939 0.0002 -1.6582 0.0001 -1.7224 0.0001 -1.7866 0.0001 -1.8508 0.0000 -1.9151 0.0000 -1.9793 0.0000 -2.0435 0.0000 -2.1077 0.0000 -2.1720 0.0000 -2.2362 0.0000 -2.3004 0.0000 -2.3646 0.0000 -2.4289 0.0000 -2.4931 0.0000 -2.5573 0.0000 -2.6216 0.0000 -2.6858 0.0000 -2.7500 0.0000 -2.8142 0.0000 -2.8785 0.0000 -2.9427 0.0000 -3.0069 0.0000 -3.0711 0.0000 -3.1354 0.0000 -3.1996 0.0000 -3.2638 0.0000 -3.3280 0.0000 -Ifit1 1 -250 150 -3 1 2 4 -2 13 14 --2.8983 0.9160 --2.8370 1.0549 --2.7756 1.1688 --2.7142 1.2459 --2.6528 1.2777 --2.5915 1.2606 --2.5301 1.1965 --2.4687 1.0926 --2.4073 0.9599 --2.3460 0.8113 --2.2846 0.6598 --2.2232 0.5161 --2.1618 0.3885 --2.1005 0.2813 --2.0391 0.1960 --1.9777 0.1313 --1.9164 0.0847 --1.8550 0.0525 --1.7936 0.0313 --1.7322 0.0180 --1.6709 0.0099 --1.6095 0.0053 --1.5481 0.0027 --1.4867 0.0013 --1.4254 0.0006 --1.3640 0.0003 --1.3026 0.0001 --1.2412 0.0001 --1.1799 0.0000 --1.1185 0.0000 --1.0571 0.0000 --0.9957 0.0000 --0.9344 0.0000 --0.8730 0.0000 --0.8116 0.0000 --0.7502 0.0000 --0.6889 0.0000 --0.6275 0.0000 --0.5661 0.0000 --0.5047 0.0000 --0.4434 0.0000 --0.3820 0.0000 --0.3206 0.0000 --0.2592 0.0000 --0.1979 0.0000 --0.1365 0.0000 --0.0751 0.0000 --0.0137 0.0000 -0.0476 0.0000 -0.1090 0.0000 -0.1704 0.0000 -0.2318 0.0000 -0.2931 0.0000 -0.3545 0.0000 -0.4159 0.0000 -0.4773 0.0000 -0.5386 0.0000 -0.6000 0.0000 -0.6614 0.0000 -0.7228 0.0000 -0.7841 0.0000 -0.8455 0.0000 -0.9069 0.0000 -0.9682 0.0000 -1.0296 0.0000 -1.0910 0.0000 -1.1524 0.0000 -1.2137 0.0000 -1.2751 0.0000 -1.3365 0.0000 -1.3979 0.0000 -1.4592 0.0000 -1.5206 0.0000 -1.5820 0.0000 -1.6434 0.0000 -1.7047 0.0000 -1.7661 0.0000 -1.8275 0.0000 -1.8889 0.0000 -1.9502 0.0000 -2.0116 0.0000 -2.0730 0.0000 -2.1344 0.0000 -2.1957 0.0000 -2.2571 0.0000 -2.3185 0.0000 -2.3799 0.0000 -2.4412 0.0000 -2.5026 0.0000 -2.5640 0.0000 -2.6254 0.0000 -2.6867 0.0000 -2.7481 0.0000 -2.8095 0.0000 -2.8709 0.0000 -2.9322 0.0000 -2.9936 0.0000 -3.0550 0.0000 -3.1164 0.0000 -3.1777 0.0000 -3.2391 0.0000 -Mx1 1 -250 150 -2 4 12 -0 --3.1709 0.1330 --3.0983 0.1643 --3.0258 0.2000 --2.9533 0.2398 --2.8808 0.2834 --2.8082 0.3299 --2.7357 0.3785 --2.6632 0.4278 --2.5907 0.4764 --2.5181 0.5228 --2.4456 0.5653 --2.3731 0.6022 --2.3006 0.6321 --2.2280 0.6538 --2.1555 0.6662 --2.0830 0.6690 --2.0105 0.6619 --1.9379 0.6452 --1.8654 0.6197 --1.7929 0.5865 --1.7204 0.5469 --1.6479 0.5024 --1.5753 0.4548 --1.5028 0.4057 --1.4303 0.3566 --1.3578 0.3088 --1.2852 0.2635 --1.2127 0.2215 --1.1402 0.1835 --1.0677 0.1497 --0.9951 0.1204 --0.9226 0.0954 --0.8501 0.0745 --0.7776 0.0573 --0.7050 0.0434 --0.6325 0.0324 --0.5600 0.0239 --0.4875 0.0173 --0.4149 0.0124 --0.3424 0.0087 --0.2699 0.0060 --0.1974 0.0041 --0.1248 0.0028 --0.0523 0.0018 -0.0202 0.0012 -0.0927 0.0008 -0.1653 0.0005 -0.2378 0.0003 -0.3103 0.0002 -0.3828 0.0001 -0.4554 0.0001 -0.5279 0.0000 -0.6004 0.0000 -0.6729 0.0000 -0.7455 0.0000 -0.8180 0.0000 -0.8905 0.0000 -0.9630 0.0000 -1.0356 0.0000 -1.1081 0.0000 -1.1806 0.0000 -1.2531 0.0000 -1.3257 0.0000 -1.3982 0.0000 -1.4707 0.0000 -1.5432 0.0000 -1.6158 0.0000 -1.6883 0.0000 -1.7608 0.0000 -1.8333 0.0000 -1.9059 0.0000 -1.9784 0.0000 -2.0509 0.0000 -2.1234 0.0000 -2.1959 0.0000 -2.2685 0.0000 -2.3410 0.0000 -2.4135 0.0000 -2.4860 0.0000 -2.5586 0.0000 -2.6311 0.0000 -2.7036 0.0000 -2.7761 0.0000 -2.8487 0.0000 -2.9212 0.0000 -2.9937 0.0000 -3.0662 0.0000 -3.1388 0.0000 -3.2113 0.0000 -3.2838 0.0000 -3.3563 0.0000 -3.4289 0.0000 -3.5014 0.0000 -3.5739 0.0000 -3.6464 0.0000 -3.7190 0.0000 -3.7915 0.0000 -3.8640 0.0000 -3.9365 0.0000 -4.0091 0.0000 -4.0816 0.0000 -Irf7 1 -250 150 -2 4 12 -0 --3.9154 0.0040 --3.8440 0.0068 --3.7726 0.0113 --3.7012 0.0181 --3.6298 0.0282 --3.5583 0.0429 --3.4869 0.0635 --3.4155 0.0916 --3.3441 0.1284 --3.2727 0.1753 --3.2013 0.2330 --3.1299 0.3015 --3.0585 0.3798 --2.9871 0.4657 --2.9157 0.5560 --2.8443 0.6461 --2.7729 0.7310 --2.7015 0.8051 --2.6301 0.8632 --2.5587 0.9010 --2.4873 0.9155 --2.4159 0.9056 --2.3445 0.8721 --2.2730 0.8175 --2.2016 0.7461 --2.1302 0.6628 --2.0588 0.5732 --1.9874 0.4827 --1.9160 0.3956 --1.8446 0.3157 --1.7732 0.2452 --1.7018 0.1854 --1.6304 0.1365 --1.5590 0.0978 --1.4876 0.0682 --1.4162 0.0463 --1.3448 0.0306 --1.2734 0.0197 --1.2020 0.0124 --1.1306 0.0075 --1.0592 0.0045 --0.9878 0.0026 --0.9163 0.0015 --0.8449 0.0008 --0.7735 0.0004 --0.7021 0.0002 --0.6307 0.0001 --0.5593 0.0001 --0.4879 0.0000 --0.4165 0.0000 --0.3451 0.0000 --0.2737 0.0000 --0.2023 0.0000 --0.1309 0.0000 --0.0595 0.0000 -0.0119 0.0000 -0.0833 0.0000 -0.1547 0.0000 -0.2261 0.0000 -0.2975 0.0000 -0.3690 0.0000 -0.4404 0.0000 -0.5118 0.0000 -0.5832 0.0000 -0.6546 0.0000 -0.7260 0.0000 -0.7974 0.0000 -0.8688 0.0000 -0.9402 0.0000 -1.0116 0.0000 -1.0830 0.0000 -1.1544 0.0000 -1.2258 0.0000 -1.2972 0.0000 -1.3686 0.0000 -1.4400 0.0000 -1.5114 0.0000 -1.5828 0.0000 -1.6543 0.0000 -1.7257 0.0000 -1.7971 0.0000 -1.8685 0.0000 -1.9399 0.0000 -2.0113 0.0000 -2.0827 0.0000 -2.1541 0.0000 -2.2255 0.0000 -2.2969 0.0000 -2.3683 0.0000 -2.4397 0.0000 -2.5111 0.0000 -2.5825 0.0000 -2.6539 0.0000 -2.7253 0.0000 -2.7967 0.0000 -2.8681 0.0000 -2.9396 0.0000 -3.0110 0.0000 -3.0824 0.0000 -3.1538 0.0000 -3.2252 0.0000 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt b/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt deleted file mode 100644 index 605579c3..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -rs3664317 1 2 - diff --git a/sourcecodes/data/example_chr2_spleen/cuLnnode.txt b/sourcecodes/data/example_chr2_spleen/cuLnnode.txt deleted file mode 100644 index 8351c193..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLnnode.txt +++ /dev/null @@ -1 +0,0 @@ -14 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnrows.txt b/sourcecodes/data/example_chr2_spleen/cuLnrows.txt deleted file mode 100644 index fff0a247..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLnrows.txt +++ /dev/null @@ -1 +0,0 @@ -74 diff --git a/sourcecodes/data/example_chr2_spleen/cuLparameters.txt b/sourcecodes/data/example_chr2_spleen/cuLparameters.txt deleted file mode 100644 index 545d6e91..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLparameters.txt +++ /dev/null @@ -1,57 +0,0 @@ -rs3664317 -Discrete node with 2 states -1 0.5479 -2 0.4521 - -Oas1a -Continuous node -8.2815 0.3487 - -Parp9 -Continuous node -9.8042 0.2165 - -Dhx58 -Continuous node -8.8912 0.3029 - -Cd1d1 -Continuous node -9.6436 0.2679 - -Irf7 -Continuous node -10.0093 0.5542 - -Oas3 -Continuous node -8.9574 0.5062 - -Pml -Continuous node -11.0754 0.1911 - -Mx1 -Continuous node -7.4831 0.3389 - -Ifit1 -Continuous node -8.8285 0.5736 - -Trim25 -Continuous node -10.2552 0.1765 - -Oas1g -Continuous node -8.6322 0.4619 - -Pglyrp3 -Continuous node -6.0709 0.1286 - -Ifih1 -Continuous node -9.2981 0.3860 - diff --git a/sourcecodes/data/example_chr2_spleen/cuLparent.txt b/sourcecodes/data/example_chr2_spleen/cuLparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt deleted file mode 100644 index f0815c7a..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt +++ /dev/null @@ -1,14 +0,0 @@ -rs3664317 0.5479 0.4521 -Dhx58 0.0024 0.0029 0.0035 0.0043 0.0053 0.0064 0.0076 0.0092 0.0110 0.0130 0.0154 0.0182 0.0213 0.0249 0.0290 0.0336 0.0388 0.0446 0.0510 0.0581 0.0659 0.0745 0.0838 0.0938 0.1046 0.1162 0.1284 0.1414 0.1550 0.1692 0.1839 0.1990 0.2145 0.2302 0.2459 0.2617 0.2772 0.2924 0.3071 0.3212 0.3346 0.3469 0.3582 0.3683 0.3771 0.3844 0.3902 0.3944 0.3970 0.3978 0.3970 0.3944 0.3902 0.3845 0.3771 0.3684 0.3583 0.3470 0.3346 0.3213 0.3072 0.2925 0.2773 0.2617 0.2460 0.2302 0.2146 0.1991 0.1840 0.1693 0.1551 0.1415 0.1285 0.1162 0.1047 0.0939 0.0838 0.0745 0.0660 0.0582 0.0510 0.0446 0.0388 0.0337 0.0290 0.0250 0.0213 0.0182 0.0154 0.0130 0.0110 0.0092 0.0077 0.0064 0.0053 0.0043 0.0035 0.0029 0.0024 0.0019 0.0015 -Cd1d1 0.0010 0.0012 0.0015 0.0019 0.0023 0.0029 0.0035 0.0043 0.0052 0.0064 0.0077 0.0092 0.0110 0.0131 0.0156 0.0184 0.0216 0.0253 0.0295 0.0342 0.0395 0.0455 0.0521 0.0594 0.0674 0.0762 0.0857 0.0960 0.1072 0.1190 0.1316 0.1449 0.1589 0.1734 0.1885 0.2039 0.2197 0.2357 0.2517 0.2677 0.2834 0.2987 0.3135 0.3276 0.3408 0.3530 0.3641 0.3739 0.3823 0.3891 0.3944 0.3980 0.3999 0.4000 0.3984 0.3951 0.3901 0.3835 0.3753 0.3658 0.3549 0.3428 0.3297 0.3158 0.3011 0.2858 0.2702 0.2543 0.2382 0.2223 0.2064 0.1909 0.1758 0.1612 0.1471 0.1337 0.1210 0.1090 0.0978 0.0873 0.0776 0.0687 0.0606 0.0532 0.0465 0.0404 0.0350 0.0302 0.0259 0.0222 0.0189 0.0160 0.0135 0.0113 0.0095 0.0079 0.0066 0.0054 0.0044 0.0036 0.0030 -Ifit1 0.0063 0.0075 0.0089 0.0105 0.0124 0.0145 0.0169 0.0197 0.0228 0.0264 0.0303 0.0347 0.0397 0.0451 0.0511 0.0577 0.0649 0.0728 0.0812 0.0904 0.1002 0.1106 0.1217 0.1333 0.1456 0.1584 0.1717 0.1854 0.1995 0.2138 0.2284 0.2430 0.2576 0.2720 0.2862 0.3001 0.3134 0.3261 0.3381 0.3492 0.3593 0.3684 0.3763 0.3830 0.3883 0.3922 0.3948 0.3958 0.3954 0.3936 0.3902 0.3855 0.3795 0.3721 0.3635 0.3539 0.3432 0.3316 0.3192 0.3061 0.2925 0.2784 0.2641 0.2495 0.2349 0.2203 0.2059 0.1917 0.1778 0.1643 0.1513 0.1388 0.1268 0.1155 0.1047 0.0947 0.0852 0.0765 0.0683 0.0609 0.0540 0.0477 0.0420 0.0369 0.0322 0.0281 0.0244 0.0211 0.0181 0.0156 0.0133 0.0113 0.0096 0.0081 0.0068 0.0057 0.0048 0.0040 0.0033 0.0027 0.0023 -Oas1g 0.0009 0.0011 0.0014 0.0018 0.0022 0.0028 0.0034 0.0042 0.0052 0.0063 0.0076 0.0092 0.0111 0.0133 0.0158 0.0187 0.0221 0.0260 0.0304 0.0353 0.0409 0.0472 0.0542 0.0619 0.0704 0.0797 0.0899 0.1008 0.1125 0.1251 0.1383 0.1523 0.1670 0.1822 0.1978 0.2138 0.2300 0.2464 0.2626 0.2787 0.2943 0.3094 0.3238 0.3373 0.3497 0.3609 0.3707 0.3791 0.3858 0.3909 0.3942 0.3956 0.3953 0.3931 0.3891 0.3834 0.3761 0.3672 0.3568 0.3451 0.3323 0.3184 0.3038 0.2884 0.2726 0.2565 0.2401 0.2238 0.2077 0.1918 0.1763 0.1613 0.1469 0.1332 0.1202 0.1080 0.0965 0.0859 0.0761 0.0671 0.0589 0.0514 0.0447 0.0387 0.0334 0.0286 0.0244 0.0208 0.0176 0.0148 0.0124 0.0103 0.0086 0.0071 0.0058 0.0048 0.0039 0.0032 0.0025 0.0020 0.0016 -Ifih1 0.0023 0.0028 0.0034 0.0041 0.0050 0.0060 0.0071 0.0085 0.0101 0.0119 0.0140 0.0164 0.0192 0.0223 0.0259 0.0299 0.0343 0.0393 0.0449 0.0510 0.0578 0.0652 0.0733 0.0820 0.0914 0.1015 0.1124 0.1238 0.1359 0.1487 0.1620 0.1758 0.1900 0.2046 0.2195 0.2345 0.2496 0.2647 0.2795 0.2941 0.3082 0.3218 0.3347 0.3467 0.3578 0.3678 0.3766 0.3842 0.3903 0.3951 0.3984 0.4001 0.4003 0.3990 0.3961 0.3917 0.3859 0.3787 0.3702 0.3605 0.3497 0.3379 0.3252 0.3118 0.2978 0.2834 0.2685 0.2535 0.2384 0.2234 0.2084 0.1938 0.1794 0.1655 0.1521 0.1392 0.1269 0.1153 0.1043 0.0940 0.0844 0.0755 0.0672 0.0597 0.0527 0.0464 0.0407 0.0356 0.0310 0.0269 0.0232 0.0200 0.0171 0.0146 0.0124 0.0105 0.0089 0.0075 0.0063 0.0052 0.0043 -Parp9 0.0080 0.0094 0.0111 0.0130 0.0152 0.0177 0.0205 0.0237 0.0272 0.0312 0.0357 0.0406 0.0461 0.0521 0.0587 0.0659 0.0737 0.0821 0.0912 0.1009 0.1112 0.1222 0.1337 0.1458 0.1585 0.1716 0.1851 0.1990 0.2132 0.2276 0.2420 0.2565 0.2709 0.2850 0.2988 0.3121 0.3249 0.3369 0.3482 0.3586 0.3679 0.3761 0.3832 0.3889 0.3934 0.3964 0.3981 0.3983 0.3971 0.3945 0.3905 0.3851 0.3785 0.3706 0.3617 0.3516 0.3406 0.3288 0.3163 0.3031 0.2894 0.2754 0.2611 0.2467 0.2322 0.2178 0.2035 0.1895 0.1759 0.1626 0.1498 0.1375 0.1258 0.1146 0.1041 0.0942 0.0849 0.0763 0.0683 0.0609 0.0541 0.0480 0.0423 0.0372 0.0326 0.0285 0.0247 0.0214 0.0185 0.0159 0.0137 0.0117 0.0099 0.0084 0.0071 0.0060 0.0050 0.0042 0.0035 0.0029 0.0024 -Oas1a 0.0034 0.0042 0.0051 0.0061 0.0073 0.0087 0.0104 0.0124 0.0146 0.0172 0.0201 0.0235 0.0273 0.0316 0.0364 0.0417 0.0477 0.0543 0.0616 0.0695 0.0782 0.0876 0.0977 0.1085 0.1201 0.1323 0.1452 0.1586 0.1727 0.1871 0.2020 0.2172 0.2325 0.2479 0.2633 0.2785 0.2933 0.3077 0.3214 0.3344 0.3465 0.3576 0.3675 0.3761 0.3834 0.3892 0.3935 0.3963 0.3974 0.3969 0.3947 0.3910 0.3857 0.3790 0.3708 0.3613 0.3507 0.3389 0.3263 0.3128 0.2986 0.2839 0.2689 0.2536 0.2382 0.2228 0.2075 0.1925 0.1779 0.1637 0.1500 0.1369 0.1245 0.1127 0.1016 0.0912 0.0816 0.0726 0.0644 0.0569 0.0501 0.0439 0.0383 0.0332 0.0288 0.0248 0.0213 0.0182 0.0155 0.0131 0.0111 0.0093 0.0078 0.0065 0.0054 0.0045 0.0037 0.0030 0.0025 0.0020 0.0016 -Irf7 0.0002 0.0003 0.0004 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0040 0.0050 0.0061 0.0075 0.0091 0.0111 0.0133 0.0160 0.0191 0.0226 0.0267 0.0314 0.0367 0.0428 0.0495 0.0570 0.0654 0.0746 0.0846 0.0956 0.1074 0.1201 0.1336 0.1478 0.1628 0.1784 0.1946 0.2111 0.2279 0.2448 0.2617 0.2783 0.2946 0.3102 0.3250 0.3388 0.3514 0.3627 0.3725 0.3806 0.3870 0.3916 0.3942 0.3948 0.3935 0.3903 0.3851 0.3781 0.3694 0.3591 0.3473 0.3343 0.3201 0.3050 0.2892 0.2728 0.2561 0.2392 0.2223 0.2056 0.1891 0.1732 0.1577 0.1430 0.1290 0.1157 0.1033 0.0918 0.0812 0.0714 0.0625 0.0544 0.0472 0.0407 0.0349 0.0298 0.0253 0.0214 0.0180 0.0151 0.0125 0.0104 0.0086 0.0070 0.0057 0.0047 0.0038 0.0030 0.0024 -Mx1 0.0028 0.0035 0.0043 0.0053 0.0066 0.0081 0.0098 0.0119 0.0144 0.0173 0.0207 0.0246 0.0291 0.0342 0.0400 0.0465 0.0539 0.0621 0.0711 0.0811 0.0919 0.1037 0.1164 0.1300 0.1444 0.1595 0.1754 0.1918 0.2086 0.2258 0.2431 0.2604 0.2775 0.2941 0.3102 0.3254 0.3396 0.3526 0.3641 0.3742 0.3824 0.3889 0.3934 0.3959 0.3964 0.3948 0.3911 0.3855 0.3780 0.3688 0.3579 0.3455 0.3318 0.3170 0.3013 0.2849 0.2680 0.2508 0.2335 0.2162 0.1992 0.1826 0.1665 0.1510 0.1363 0.1223 0.1092 0.0970 0.0858 0.0754 0.0660 0.0574 0.0497 0.0428 0.0367 0.0312 0.0265 0.0223 0.0187 0.0156 0.0130 0.0107 0.0088 0.0072 0.0059 0.0047 0.0038 0.0031 0.0024 0.0019 0.0015 0.0012 0.0009 0.0007 0.0006 0.0004 0.0003 0.0002 0.0002 0.0001 0.0001 -Trim25 0.0009 0.0012 0.0014 0.0018 0.0022 0.0026 0.0032 0.0039 0.0047 0.0056 0.0068 0.0081 0.0096 0.0113 0.0133 0.0156 0.0183 0.0213 0.0247 0.0286 0.0329 0.0377 0.0431 0.0490 0.0556 0.0628 0.0706 0.0791 0.0883 0.0982 0.1087 0.1200 0.1319 0.1444 0.1575 0.1711 0.1851 0.1996 0.2144 0.2293 0.2444 0.2594 0.2743 0.2889 0.3031 0.3168 0.3299 0.3422 0.3535 0.3638 0.3730 0.3809 0.3875 0.3927 0.3964 0.3987 0.3993 0.3985 0.3961 0.3922 0.3868 0.3801 0.3720 0.3627 0.3522 0.3408 0.3284 0.3153 0.3015 0.2872 0.2725 0.2576 0.2426 0.2275 0.2126 0.1979 0.1835 0.1695 0.1559 0.1429 0.1304 0.1186 0.1075 0.0970 0.0872 0.0781 0.0696 0.0619 0.0548 0.0483 0.0424 0.0371 0.0323 0.0281 0.0243 0.0209 0.0180 0.0153 0.0131 0.0111 0.0094 -Oas3 0.0017 0.0021 0.0026 0.0032 0.0039 0.0048 0.0059 0.0072 0.0087 0.0104 0.0125 0.0149 0.0177 0.0209 0.0246 0.0289 0.0337 0.0391 0.0452 0.0520 0.0595 0.0679 0.0771 0.0871 0.0980 0.1098 0.1224 0.1358 0.1501 0.1651 0.1808 0.1971 0.2139 0.2311 0.2486 0.2662 0.2837 0.3011 0.3181 0.3345 0.3502 0.3650 0.3787 0.3911 0.4021 0.4116 0.4195 0.4255 0.4297 0.4320 0.4324 0.4308 0.4273 0.4220 0.4148 0.4059 0.3954 0.3835 0.3702 0.3558 0.3405 0.3243 0.3075 0.2903 0.2728 0.2552 0.2377 0.2204 0.2034 0.1869 0.1709 0.1557 0.1411 0.1273 0.1144 0.1023 0.0911 0.0807 0.0712 0.0626 0.0547 0.0476 0.0413 0.0356 0.0306 0.0262 0.0223 0.0189 0.0159 0.0134 0.0112 0.0093 0.0077 0.0064 0.0052 0.0043 0.0035 0.0028 0.0023 0.0018 0.0015 -Pglyrp3 0.0011 0.0014 0.0017 0.0021 0.0026 0.0032 0.0039 0.0047 0.0057 0.0069 0.0083 0.0100 0.0119 0.0141 0.0166 0.0196 0.0229 0.0267 0.0310 0.0359 0.0413 0.0474 0.0541 0.0614 0.0695 0.0783 0.0878 0.0981 0.1091 0.1208 0.1332 0.1462 0.1598 0.1739 0.1885 0.2034 0.2185 0.2337 0.2490 0.2640 0.2788 0.2931 0.3069 0.3199 0.3320 0.3431 0.3530 0.3617 0.3690 0.3748 0.3790 0.3817 0.3827 0.3821 0.3798 0.3759 0.3705 0.3635 0.3552 0.3455 0.3347 0.3228 0.3100 0.2964 0.2822 0.2675 0.2525 0.2373 0.2220 0.2069 0.1919 0.1773 0.1631 0.1493 0.1362 0.1236 0.1118 0.1006 0.0902 0.0804 0.0715 0.0632 0.0557 0.0489 0.0427 0.0371 0.0321 0.0277 0.0238 0.0203 0.0173 0.0147 0.0124 0.0104 0.0087 0.0072 0.0060 0.0050 0.0041 0.0033 0.0027 -Pml 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0040 0.0049 0.0060 0.0073 0.0089 0.0107 0.0129 0.0154 0.0184 0.0218 0.0257 0.0302 0.0353 0.0411 0.0476 0.0548 0.0628 0.0716 0.0813 0.0918 0.1032 0.1155 0.1285 0.1424 0.1570 0.1722 0.1880 0.2043 0.2209 0.2377 0.2546 0.2713 0.2877 0.3036 0.3188 0.3332 0.3466 0.3587 0.3695 0.3787 0.3863 0.3922 0.3962 0.3983 0.3985 0.3967 0.3930 0.3875 0.3802 0.3713 0.3608 0.3489 0.3357 0.3215 0.3064 0.2906 0.2743 0.2576 0.2408 0.2240 0.2073 0.1910 0.1751 0.1597 0.1450 0.1310 0.1178 0.1054 0.0938 0.0831 0.0733 0.0643 0.0562 0.0488 0.0422 0.0363 0.0311 0.0265 0.0225 0.0190 0.0159 0.0133 0.0111 0.0092 0.0076 0.0062 diff --git a/sourcecodes/data/example_chr2_spleen/cuLthr.txt b/sourcecodes/data/example_chr2_spleen/cuLthr.txt deleted file mode 100644 index b63ba696..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.9 diff --git a/sourcecodes/data/example_chr2_spleen/cuLtier.txt b/sourcecodes/data/example_chr2_spleen/cuLtier.txt deleted file mode 100644 index e71cfdda..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLtier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,1,rs3664317,Tier2,1,Ifih1,Tier3,12,Oas1a,Parp9,Dhx58,Cd1d1,Irf7,Oas3,Pml,Mx1,Ifit1,Trim25,Oas1g,Pglyrp3, \ No newline at end of file diff --git a/sourcecodes/data/example_chr2_spleen/cuLtype.txt b/sourcecodes/data/example_chr2_spleen/cuLtype.txt deleted file mode 100644 index 1b707710..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 -2 1 1 1 1 1 1 1 1 1 1 1 1 1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLwhite.txt b/sourcecodes/data/example_chr2_spleen/cuLwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example_chr2_spleen/old/cuLrun_evidencemodified.sh b/sourcecodes/data/example_chr2_spleen/old/cuLrun_evidencemodified.sh deleted file mode 100644 index 5a228612..00000000 --- a/sourcecodes/data/example_chr2_spleen/old/cuLrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified cuL -fi -exit diff --git a/sourcecodes/data/example_chr2_spleen/old/cuLrun_initialstructure.sh b/sourcecodes/data/example_chr2_spleen/old/cuLrun_initialstructure.sh deleted file mode 100644 index 1d0835a4..00000000 --- a/sourcecodes/data/example_chr2_spleen/old/cuLrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure cuL -fi -exit diff --git a/sourcecodes/data/example_sample/sample_input.txt~ b/sourcecodes/data/example_sample/sample_input.txt~ deleted file mode 100644 index 62705bb9..00000000 --- a/sourcecodes/data/example_sample/sample_input.txt~ +++ /dev/null @@ -1,42 +0,0 @@ -Ctrq3 MAS Neutrophil Load Weight -2 0.969230769 3 3.252367514 1 -2 0.925170068 1.6 2.46322088 1.033472803 -1 0.427272727 33.8 4.206610024 0.831372549 -2 0.877835951 8.3 3.764250875 0.967153285 -2 0.914862915 4.4 3.691700208 1.046025105 -2 0.560334528 4.9 2.604550033 0.98046875 -1 0.383073497 13.1 4.273556814 0.812316716 -1 0.101010101 18.6 5.089640217 0.771929825 -1 0.106719368 18.9 4.915125346 0.80994152 -2 0.894736842 2.5 2.691700208 0.995515695 -1 0.067226891 19.8 4.878194228 0.846153846 -2 0.921022067 2.9 4.127428778 1.03875969 -2 0.938701923 0.7 4.366310867 0.984732824 -1 0.658008658 15.7 4.531121115 0.884210526 -2 0.9 4.8 2.604550033 0.913194444 -2 0.790923825 10.4 2.390670213 0.892857143 -1 0.295539033 8.6 4.24137213 0.85840708 -2 0.317757009 12.2 4.449648073 0.889830508 -1 0.032418953 20.2 5.053428044 0.811320755 -1 0.603960396 23.4 4.283775979 0.805460751 -2 0.939351199 3.6 2.349277527 0.952380952 -1 0.978448276 0.4 3.495405563 0.8875 -1 0.1 23.2 4.675613388 0.766101695 -1 0.036363636 32.6 4.938109253 0.828125 -1 0.660247593 9.2 3.826398782 0.921052632 -1 0.078651685 35.8 4.513630383 0.852112676 -1 0.186915888 20.7 5.048247532 0.779761905 -1 0.071578947 35.6 4.574586809 0.797356828 -1 0.239520958 15.4 4.331548761 0.941176471 -1 0.205741627 24.5 5.058547488 0.774193548 -1 0.062300319 13.4 4.594790195 0.832236842 -2 0.599675851 5 4.18178644 0.969348659 -1 0.324246772 13.5 4.252367514 0.858585859 -1 0.87628866 14.2 2.929061124 0.869863014 -1 0.146103896 15.6 4.579726449 0.9 -1 0.257383966 22.5 5.210214148 0.75 -1 0.033333333 31.1 4.632578756 0.718644068 -1 0.29739777 36.1 3.880756445 0.798353909 -2 0.872979215 4.2 4.097465554 0.856756757 -2 0.909221902 4.3 3.650307523 0.976 -1 0.10041841 28.3 4.46322088 0.757462687 diff --git a/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt b/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt deleted file mode 100644 index b31e4c3c..00000000 --- a/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt +++ /dev/null @@ -1,6 +0,0 @@ -Genotype -Gene3 -Gene2 -Phenotype -Gene1 - diff --git a/sourcecodes/data/example_sci/Lluban.txt b/sourcecodes/data/example_sci/Lluban.txt deleted file mode 100644 index 38108f00..00000000 --- a/sourcecodes/data/example_sci/Lluban.txt +++ /dev/null @@ -1,15 +0,0 @@ -From To -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Genotype -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 -Phenotype Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 diff --git a/sourcecodes/data/example_sci/Llucontinuous_input.txt b/sourcecodes/data/example_sci/Llucontinuous_input.txt deleted file mode 100644 index 79295d7e..00000000 --- a/sourcecodes/data/example_sci/Llucontinuous_input.txt +++ /dev/null @@ -1,503 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 -2 -1.0008 -0.44837 0.21808 -1.196 -1 -0.29368 -0.53043 -1.0893 -0.10136 -2 0.70835 0.72886 -0.18098 -0.42907 -1 0.63703 0.86428 1.7013 0.1425 -1 -1.2402 -0.69712 -1.7002 -0.71634 -1 -1.1952 0.27155 -0.79413 -1.0965 -2 0.62914 0.94265 1.8385 0.6135 -1 -1.91 -2.379 -3.1094 -1.0924 -2 -0.83436 -0.90968 -1.3598 1.335 -1 0.15685 0.4766 1.2891 -1.3309 -2 0.7047 1.0623 1.9811 1.2821 -1 0.59747 -0.023123 0.88555 -0.8844 -1 -1.0557 -1.5548 -1.3016 -0.77687 -2 1.5206 2.0289 0.90366 1.8089 -1 0.65525 -0.47226 -1.1824 0.41863 -2 -0.39262 0.382 -0.64829 0.40947 -2 0.14966 0.22972 0.33797 0.69647 -1 -1.8836 -0.68534 -0.99941 -0.78961 -1 0.48181 0.01241 1.2145 0.16835 -2 1.4673 2.0438 2.4674 2.5234 -1 -1.3242 -0.80218 -1.6446 -0.31044 -1 -1.2471 -2.0351 -1.0296 -1.937 -1 0.23695 -0.01724 -0.32851 -0.16484 -1 -0.13986 -0.6065 -0.8491 -0.95538 -2 0.90888 1.0365 2.7222 1.3507 -1 -0.30556 -1.1546 -0.86033 -2.2006 -2 0.5391 0.99532 0.96947 1.1575 -2 1.1235 0.37982 0.64439 0.94362 -2 1.7073 1.9303 2.8018 1.9158 -1 -0.20553 -0.074104 -0.50073 -1.0697 -1 -0.27415 0.23076 -0.27564 -0.11286 -1 -1.304 -1.1213 -0.71793 -1.3462 -2 0.54315 0.55846 0.87411 1.2432 -1 -1.0659 -0.38067 -1.4372 -2.0927 -1 0.21278 -1.0115 -1.0984 -0.72751 -1 -2.9061 -1.3118 -3.8372 -2.0448 -2 -0.69608 -0.61145 -1.0037 0.12181 -1 0.66835 0.018886 -1.0081 -1.4165 -1 0.32575 -0.51767 1.0187 -0.40914 -2 0.65837 1.2791 1.8388 2.2906 -2 0.37574 0.21618 -0.89435 1.2643 -1 0.13513 -0.31405 -0.16057 0.77712 -2 0.16054 0.40635 0.036165 1.6374 -1 1.9393 1.5717 2.6922 1.1933 -1 -0.59118 -0.47154 -0.20293 -1.5576 -1 -0.35938 -0.49565 -0.20837 0.61043 -2 -0.57133 0.15921 -0.44158 0.43312 -1 0.31835 0.49002 2.2029 0.17685 -1 -0.0093708 -0.85889 -1.0934 -1.6905 -1 -0.90501 -1.4637 -1.5526 -1.828 -2 0.11531 -0.022781 0.88843 0.8607 -1 0.34978 -0.34306 0.95301 -0.056177 -2 -0.22236 -0.13023 0.37608 0.18027 -1 -0.90103 -0.38393 -1.1513 -0.78153 -2 0.66848 0.81005 1.3945 3.3654 -2 0.10539 0.59781 0.77864 0.63865 -1 -1.15 -1.4531 -2.929 -1.6867 -1 0.20842 -0.0039076 -0.12879 -0.31459 -2 0.52155 1.248 1.0411 1.9656 -2 0.041926 0.86223 1.2222 1.0289 -1 -0.70875 -0.15791 -1.1581 -0.77456 -1 -1.1701 -0.57889 -0.8843 -0.11873 -2 0.98106 1.0805 0.95484 2.1834 -2 0.26676 0.7527 0.61491 1.9024 -1 -0.64765 0.19831 -1.4399 1.3127 -2 0.92209 2.2111 1.208 2.7402 -2 -0.93755 -0.26009 0.54448 0.20265 -2 1.2403 1.8468 1.6169 1.8359 -1 -0.1313 0.14288 -0.48278 -0.96105 -1 -0.7222 -0.25191 -1.2122 -0.59027 -2 -0.57013 -0.061267 -0.5438 0.18234 -1 -1.5355 -1.1998 -2.6613 -0.2634 -2 0.86507 0.60361 1.2411 -0.29711 -1 -0.60117 -0.7424 -0.79575 -0.5736 -1 -0.91776 -1.5669 -2.1735 -0.56602 -2 0.9917 2.3088 1.7993 2.645 -1 0.17017 0.53321 0.84278 -1.4458 -2 -0.22306 0.262 -0.86259 0.87407 -1 -0.42107 -0.69813 -0.48166 -1.009 -1 0.46913 -0.76457 0.11077 -0.21258 -1 0.066036 -0.48665 -0.74847 0.38785 -1 0.16465 -0.57268 0.19043 0.23 -1 -1.2044 -2.2027 -2.9688 -2.5546 -1 -0.3031 -2.0277 -1.3027 -2.6541 -2 -0.20063 0.3886 1.2227 0.84669 -2 -0.23897 0.0036995 -1.4547 0.37173 -1 2.197 0.41411 0.68339 -1.2721 -2 1.9922 2.748 3.0416 3.1268 -1 -1.7922 -1.2233 -3.1352 -0.98514 -2 0.66968 0.81377 1.9112 1.7507 -2 1.048 1.3718 1.5938 1.4847 -1 0.56532 -0.97153 -0.91123 -2.4761 -2 -0.53609 -0.30043 -0.65398 -0.38562 -2 1.0012 1.3344 2.0595 2.8441 -1 -3.4639 -2.4231 -3.9055 -2.3575 -1 0.79272 -0.78962 -0.40706 -1.1306 -1 0.78178 0.32152 0.79399 0.14086 -2 -0.28587 0.20138 0.78238 2.1602 -2 1.4137 1.6184 2.2458 2.1799 -2 1.409 1.6079 2.4053 2.0587 -2 -0.049571 1.1163 2.0792 0.99457 -1 -1.394 -0.67782 -2.2302 -0.33872 -2 0.5374 1.8476 2.205 2.0025 -1 -1.4988 -0.90782 -1.4206 -1.2048 -1 -2.2683 -1.7667 -3.7613 -2.0306 -1 0.5275 -0.34657 0.11355 -0.6761 -1 -1.89 -2.1862 -2.3535 -2.2032 -2 1.4183 2.5108 2.4607 1.7296 -1 -0.19829 0.031868 0.014954 -1.7813 -2 1.9842 2.0081 3.2753 3.6534 -1 0.60225 0.089417 0.37343 -1.396 -2 0.15127 0.55563 -0.099824 1.684 -1 -0.30521 -0.0050244 -0.68635 -0.42167 -2 0.65124 0.2796 -0.22261 1.4011 -1 -0.71925 -1.8908 -2.0898 -1.2222 -2 -0.56741 0.091717 -0.37763 0.40742 -1 -2.8956 -2.2286 -3.4496 -3.429 -2 -0.89598 1.0267 -0.4909 1.1085 -1 -0.94952 -0.7555 -1.795 -0.13335 -2 1.2407 2.0614 2.5452 1.9642 -1 -0.11717 -0.54282 -1.9921 -0.72275 -1 -0.45987 -0.58174 -1.1552 -0.76589 -2 1.4219 1.7052 1.3243 2.0381 -1 0.17284 -1.1866 0.12735 -0.89424 -1 -1.5493 -1.5627 -2.191 -1.4248 -2 -0.52149 0.50488 0.88087 1.9829 -2 -0.073205 0.87222 -0.68612 1.5622 -1 -0.20595 -0.60619 -1.2632 -0.31189 -1 -1.6215 -2.0613 -2.6335 -2.0367 -2 0.91305 1.4897 2.1731 2.2545 -1 1.142 1.8275 1.8053 1.0419 -1 -0.45335 -1.322 -1.3973 -0.48254 -2 0.74114 1.8757 1.4174 2.1017 -1 -0.38344 -0.17813 -0.23266 -0.41796 -2 0.92714 1.7223 2.7582 1.4736 -1 -0.96407 -1.004 -1.3232 -0.72647 -1 -0.17388 -0.55234 -0.16535 -1.1821 -1 -1.4482 -1.0906 -1.9966 -0.2562 -1 -1.5948 -1.656 -2.1184 -1.9089 -1 0.30118 -0.24953 0.3965 -1.2012 -1 0.040955 -1.5321 -0.0067596 -1.8302 -2 -0.47573 0.19062 -0.38082 1.4748 -1 -0.57924 -0.90781 -1.0718 -0.87675 -2 1.2355 1.6025 0.66291 1.3094 -1 -0.85148 -1.0376 -0.35579 -0.84493 -1 0.62128 -0.097245 1.1169 1.1175 -1 -1.0166 -0.95689 -0.54272 -1.0278 -2 2.2273 2.234 3.0504 2.9534 -2 0.39445 0.74964 0.49728 0.40693 -1 -1.0992 -1.0596 -0.34052 -1.6927 -2 -0.87373 -0.044581 -0.87888 -0.87457 -1 -0.17361 -1.0992 -0.61197 -0.52145 -2 -0.81143 -0.23214 0.019331 -0.021054 -2 0.4003 0.84559 1.3177 0.22445 -2 2.4797 2.3692 3.1041 1.2821 -2 -1.2217 0.28611 -0.91875 0.53117 -1 -0.37718 -1.1674 1.1769 -0.7679 -2 0.69641 1.3615 1.2907 1.7631 -1 0.058157 -1.4908 -1.6127 -2.051 -2 -0.10351 -0.26543 -1.1031 1.4271 -2 1.5874 1.159 2.1284 1.6052 -2 0.7304 1.8986 1.8219 2.6148 -2 1.2822 1.2151 1.6436 0.45098 -1 -0.67686 -0.50447 -0.81689 -0.47995 -2 0.099845 0.22575 -0.38467 1.3463 -1 -0.60473 -0.56624 -1.0822 -0.9277 -2 -0.09599 -0.052173 0.60328 0.36281 -1 1.3654 0.15181 1.0298 -1.196 -2 -1.4158 -1.1006 -1.9009 0.73982 -1 -0.035902 -0.11554 0.031789 0.15859 -2 -0.41972 -0.75665 -0.12297 -1.1222 -2 0.5198 1.1791 1.4405 0.74397 -2 0.48739 -0.18437 0.062889 1.33 -1 -0.40637 -0.97335 -1.7407 -1.7785 -2 1.2506 2.1236 2.544 2.21 -1 0.2246 0.14729 0.19402 -0.0184 -1 -2.9787 -2.8634 -3.6482 -3.2628 -2 -0.34778 -0.88344 -0.53681 -0.1392 -2 -1.8429 -1.7447 -1.2394 0.076896 -2 0.19618 1.4064 0.26418 1.4885 -1 1.1131 -0.28387 -0.062115 -0.38574 -2 0.49115 0.78076 1.4226 0.55504 -1 -1.8202 -1.2481 -2.3751 -1.7518 -2 1.2174 2.2183 1.4501 3.6806 -1 -1.9377 -1.6646 -3.3068 -2.1189 -2 0.54181 0.5947 0.58072 0.40033 -1 -0.66287 -0.68746 -0.096024 -1.7397 -1 0.40851 0.30851 -0.17237 -0.50364 -2 0.75742 0.4505 -0.78196 0.44425 -1 -1.4505 0.020384 -0.43303 -0.95328 -2 -0.028847 0.15037 0.5137 0.46568 -2 -0.63541 0.3954 -0.8684 1.5549 -1 0.33942 -0.38445 -0.041492 -1.4867 -2 0.47366 1.145 0.23226 1.7193 -1 0.023382 -0.041247 -0.82666 0.080651 -1 -1.1404 -1.0549 -2.3807 -2.1069 -2 0.33731 1.2985 0.71006 3.2157 -1 1.14 -0.87596 0.068296 -0.74487 -2 -0.049493 0.63 0.61696 0.5656 -1 -0.4566 0.65674 0.031943 0.92164 -2 0.017518 0.38805 0.53672 0.36798 -2 0.48676 0.83957 0.81814 1.0935 -2 2.7892 2.4059 4.9329 2.8726 -1 0.43253 0.11799 1.095 -0.30789 -1 -1.1828 -0.8044 -0.85393 -0.88528 -1 -1.5592 -2.1209 -2.309 -3.1197 -2 -1.2601 -1.2767 -1.6618 -0.50383 -2 2.1516 2.1742 2.8387 1.8793 -2 0.24623 0.69241 -0.010176 0.53935 -1 -0.22259 -0.40572 0.11176 -1.348 -1 -0.50134 -1.5699 0.070888 -1.576 -1 -0.59262 -0.25483 -0.97248 -0.80873 -2 0.59278 2.3224 1.2169 3.7789 -2 1.8088 2.2184 2.3414 2.2607 -1 -1.4547 -0.92385 -2.0514 -1.4636 -1 -1.0861 -0.97609 -1.4805 0.049658 -2 -1.3983 -1.4913 -1.5386 -0.37917 -1 0.39015 -0.60643 0.29969 -1.038 -2 -0.56574 0.93819 0.41397 3.0029 -1 0.33141 0.18418 -0.58313 -0.55312 -1 -1.0672 -1.2348 -1.7643 -1.8829 -1 -2.6167 -2.6369 -2.7652 -3.2899 -2 0.86111 1.9481 1.9289 2.6912 -2 -0.17146 0.59905 -0.32254 0.90592 -1 0.56296 0.22567 0.50046 -0.015986 -1 0.27356 0.014082 0.53515 -1.2915 -2 0.028483 0.74312 0.032785 0.86451 -2 0.45844 1.8271 1.9607 1.5293 -1 -1.0948 -0.81939 -1.3227 -1.7485 -2 -1.9435 -1.416 -2.3622 -0.083073 -2 1.9356 2.3905 3.3874 3.3754 -2 -0.51503 -0.61825 -1.0265 1.0355 -1 -0.069375 -0.38404 0.76998 -1.0565 -1 -0.99145 -1.4551 -0.3469 -1.1237 -2 0.22687 0.42981 -0.57465 1.7352 -1 -0.6192 -0.85621 -1.5754 -2.1116 -2 0.044283 0.22217 -0.46803 0.077448 -2 0.25206 0.75089 2.0777 1.6582 -1 -1.4421 0.36925 -1.3094 1.5023 -2 -0.37483 0.92607 0.66991 1.5735 -2 0.96079 1.4626 2.6634 1.8589 -1 -1.3318 -0.19963 -1.0137 -0.69936 -1 1.7601 1.2466 2.176 0.32938 -1 0.30315 -0.016251 0.51713 -0.89472 -2 -1.4913 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b/sourcecodes/data/example_sci/Llugraphviz.txt deleted file mode 100644 index 88bbd3ba..00000000 --- a/sourcecodes/data/example_sci/Llugraphviz.txt +++ /dev/null @@ -1,10 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Genotype -> Gene3; -Genotype -> Gene1; -Gene3 -> Phenotype; -Gene2 -> Gene3; -Gene2 -> Phenotype; -Gene1 -> Gene2; -} \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluk.txt b/sourcecodes/data/example_sci/Lluk.txt deleted file mode 100644 index 83b33d23..00000000 --- a/sourcecodes/data/example_sci/Lluk.txt +++ /dev/null @@ -1 +0,0 @@ -1000 diff --git a/sourcecodes/data/example_sci/Llumap.txt b/sourcecodes/data/example_sci/Llumap.txt deleted file mode 100644 index dfe8ca75..00000000 --- a/sourcecodes/data/example_sci/Llumap.txt +++ /dev/null @@ -1,5 +0,0 @@ -Genotype 0.500305 1.514000 -Gene3 1.027261 -0.015284 -Gene2 1.160583 0.138097 -Phenotype 1.554104 0.069005 -Gene1 1.515414 0.174451 diff --git a/sourcecodes/data/example_sci/Llumapdata.txt b/sourcecodes/data/example_sci/Llumapdata.txt deleted file mode 100644 index d684ea06..00000000 --- a/sourcecodes/data/example_sci/Llumapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene1 Gene2 Gene3 Phenotype diff --git a/sourcecodes/data/example_sci/Lluname.txt b/sourcecodes/data/example_sci/Lluname.txt deleted file mode 100644 index f3a1f5bf..00000000 --- a/sourcecodes/data/example_sci/Lluname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 diff --git a/sourcecodes/data/example_sci/Llunet_figure.txt b/sourcecodes/data/example_sci/Llunet_figure.txt deleted file mode 100644 index 2f383b1a..00000000 --- a/sourcecodes/data/example_sci/Llunet_figure.txt +++ /dev/null @@ -1,433 +0,0 @@ -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1 0.4860 -2 0.5140 -Gene1 1 -250 150 -1 1 -1 3 --5.1315 0.0009 --5.0254 0.0012 --4.9193 0.0015 --4.8131 0.0019 --4.7070 0.0024 --4.6009 0.0030 --4.4947 0.0037 --4.3886 0.0046 --4.2825 0.0056 --4.1764 0.0069 --4.0702 0.0083 --3.9641 0.0101 --3.8580 0.0121 --3.7518 0.0145 --3.6457 0.0174 --3.5396 0.0206 --3.4334 0.0243 --3.3273 0.0286 --3.2212 0.0335 --3.1151 0.0389 --3.0089 0.0451 --2.9028 0.0520 --2.7967 0.0597 --2.6905 0.0682 --2.5844 0.0775 --2.4783 0.0876 --2.3722 0.0986 --2.2660 0.1105 --2.1599 0.1231 --2.0538 0.1366 --1.9476 0.1508 --1.8415 0.1657 --1.7354 0.1811 --1.6292 0.1971 --1.5231 0.2134 --1.4170 0.2300 --1.3109 0.2467 --1.2047 0.2633 --1.0986 0.2797 --0.9925 0.2956 --0.8863 0.3110 --0.7802 0.3256 --0.6741 0.3392 --0.5680 0.3517 --0.4618 0.3629 --0.3557 0.3726 --0.2496 0.3808 --0.1434 0.3873 --0.0373 0.3920 -0.0688 0.3948 -0.1749 0.3958 -0.2811 0.3948 -0.3872 0.3920 -0.4933 0.3872 -0.5995 0.3807 -0.7056 0.3726 -0.8117 0.3628 -0.9179 0.3516 -1.0240 0.3391 -1.1301 0.3254 -1.2362 0.3108 -1.3424 0.2955 -1.4485 0.2795 -1.5546 0.2631 -1.6608 0.2465 -1.7669 0.2299 -1.8730 0.2133 -1.9791 0.1969 -2.0853 0.1810 -2.1914 0.1655 -2.2975 0.1507 -2.4037 0.1365 -2.5098 0.1230 -2.6159 0.1103 -2.7221 0.0985 -2.8282 0.0875 -2.9343 0.0774 -3.0404 0.0681 -3.1466 0.0596 -3.2527 0.0520 -3.3588 0.0451 -3.4650 0.0389 -3.5711 0.0334 -3.6772 0.0286 -3.7833 0.0243 -3.8895 0.0206 -3.9956 0.0173 -4.1017 0.0145 -4.2079 0.0121 -4.3140 0.0101 -4.4201 0.0083 -4.5263 0.0068 -4.6324 0.0056 -4.7385 0.0046 -4.8446 0.0037 -4.9508 0.0030 -5.0569 0.0024 -5.1630 0.0019 -5.2692 0.0015 -5.3753 0.0012 -5.4814 0.0009 -Gene2 1 -250 150 -1 2 -2 4 5 --4.0240 0.0008 --3.9383 0.0010 --3.8526 0.0013 --3.7669 0.0016 --3.6813 0.0020 --3.5956 0.0026 --3.5099 0.0032 --3.4242 0.0041 --3.3385 0.0050 --3.2528 0.0062 --3.1672 0.0077 --3.0815 0.0094 --2.9958 0.0114 --2.9101 0.0138 --2.8244 0.0166 --2.7387 0.0199 --2.6531 0.0237 --2.5674 0.0281 --2.4817 0.0331 --2.3960 0.0388 --2.3103 0.0453 --2.2246 0.0526 --2.1390 0.0607 --2.0533 0.0696 --1.9676 0.0795 --1.8819 0.0903 --1.7962 0.1021 --1.7106 0.1147 --1.6249 0.1282 --1.5392 0.1426 --1.4535 0.1578 --1.3678 0.1736 --1.2821 0.1900 --1.1965 0.2069 --1.1108 0.2241 --1.0251 0.2414 --0.9394 0.2587 --0.8537 0.2758 --0.7680 0.2924 --0.6824 0.3084 --0.5967 0.3236 --0.5110 0.3377 --0.4253 0.3506 --0.3396 0.3621 --0.2539 0.3719 --0.1683 0.3800 --0.0826 0.3863 -0.0031 0.3905 -0.0888 0.3927 -0.1745 0.3929 -0.2601 0.3910 -0.3458 0.3870 -0.4315 0.3811 -0.5172 0.3732 -0.6029 0.3636 -0.6886 0.3524 -0.7742 0.3397 -0.8599 0.3258 -0.9456 0.3108 -1.0313 0.2949 -1.1170 0.2783 -1.2027 0.2613 -1.2883 0.2440 -1.3740 0.2267 -1.4597 0.2095 -1.5454 0.1925 -1.6311 0.1760 -1.7168 0.1601 -1.8024 0.1449 -1.8881 0.1304 -1.9738 0.1167 -2.0595 0.1039 -2.1452 0.0920 -2.2309 0.0811 -2.3165 0.0711 -2.4022 0.0620 -2.4879 0.0537 -2.5736 0.0464 -2.6593 0.0398 -2.7449 0.0340 -2.8306 0.0288 -2.9163 0.0243 -3.0020 0.0205 -3.0877 0.0171 -3.1734 0.0142 -3.2590 0.0117 -3.3447 0.0097 -3.4304 0.0079 -3.5161 0.0064 -3.6018 0.0052 -3.6875 0.0042 -3.7731 0.0034 -3.8588 0.0027 -3.9445 0.0021 -4.0302 0.0017 -4.1159 0.0013 -4.2016 0.0010 -4.2872 0.0008 -4.3729 0.0006 -4.4586 0.0005 -4.5443 0.0004 -Gene3 1 -250 150 -2 1 3 -1 5 --4.4912 0.0001 --4.4081 0.0001 --4.3250 0.0001 --4.2419 0.0001 --4.1589 0.0002 --4.0758 0.0002 --3.9927 0.0003 --3.9096 0.0004 --3.8266 0.0006 --3.7435 0.0008 --3.6604 0.0010 --3.5773 0.0013 --3.4942 0.0018 --3.4112 0.0023 --3.3281 0.0029 --3.2450 0.0037 --3.1619 0.0047 --3.0789 0.0059 --2.9958 0.0074 --2.9127 0.0092 --2.8296 0.0113 --2.7466 0.0139 --2.6635 0.0170 --2.5804 0.0206 --2.4973 0.0248 --2.4143 0.0297 --2.3312 0.0354 --2.2481 0.0419 --2.1650 0.0493 --2.0820 0.0576 --1.9989 0.0669 --1.9158 0.0773 --1.8327 0.0887 --1.7496 0.1012 --1.6666 0.1147 --1.5835 0.1292 --1.5004 0.1447 --1.4173 0.1610 --1.3343 0.1781 --1.2512 0.1958 --1.1681 0.2139 --1.0850 0.2323 --1.0020 0.2507 --0.9189 0.2688 --0.8358 0.2866 --0.7527 0.3036 --0.6697 0.3197 --0.5866 0.3345 --0.5035 0.3479 --0.4204 0.3597 --0.3373 0.3695 --0.2543 0.3773 --0.1712 0.3828 --0.0881 0.3861 --0.0050 0.3870 -0.0780 0.3855 -0.1611 0.3817 -0.2442 0.3756 -0.3273 0.3673 -0.4103 0.3570 -0.4934 0.3449 -0.5765 0.3311 -0.6596 0.3160 -0.7426 0.2996 -0.8257 0.2824 -0.9088 0.2645 -0.9919 0.2463 -1.0749 0.2279 -1.1580 0.2095 -1.2411 0.1915 -1.3242 0.1740 -1.4073 0.1570 -1.4903 0.1409 -1.5734 0.1256 -1.6565 0.1114 -1.7396 0.0981 -1.8226 0.0859 -1.9057 0.0747 -1.9888 0.0646 -2.0719 0.0555 -2.1549 0.0474 -2.2380 0.0402 -2.3211 0.0340 -2.4042 0.0285 -2.4872 0.0237 -2.5703 0.0197 -2.6534 0.0162 -2.7365 0.0132 -2.8195 0.0108 -2.9026 0.0087 -2.9857 0.0070 -3.0688 0.0056 -3.1519 0.0044 -3.2349 0.0035 -3.3180 0.0027 -3.4011 0.0021 -3.4842 0.0016 -3.5672 0.0013 -3.6503 0.0010 -3.7334 0.0007 -3.8165 0.0006 -Phenotype 1 -250 150 -2 3 4 -0 --5.4596 0.0010 --5.3401 0.0013 --5.2207 0.0016 --5.1012 0.0021 --4.9817 0.0026 --4.8623 0.0033 --4.7428 0.0042 --4.6233 0.0052 --4.5039 0.0065 --4.3844 0.0080 --4.2649 0.0098 --4.1455 0.0120 --4.0260 0.0146 --3.9065 0.0176 --3.7871 0.0212 --3.6676 0.0253 --3.5481 0.0300 --3.4287 0.0354 --3.3092 0.0416 --3.1897 0.0486 --3.0703 0.0564 --2.9508 0.0651 --2.8314 0.0748 --2.7119 0.0854 --2.5924 0.0970 --2.4730 0.1096 --2.3535 0.1230 --2.2340 0.1374 --2.1146 0.1526 --1.9951 0.1685 --1.8756 0.1850 --1.7562 0.2021 --1.6367 0.2195 --1.5172 0.2370 --1.3978 0.2545 --1.2783 0.2718 --1.1588 0.2887 --1.0394 0.3049 --0.9199 0.3202 --0.8004 0.3344 --0.6810 0.3473 --0.5615 0.3587 --0.4420 0.3684 --0.3226 0.3763 --0.2031 0.3822 --0.0836 0.3860 -0.0358 0.3877 -0.1553 0.3872 -0.2748 0.3846 -0.3942 0.3798 -0.5137 0.3731 -0.6332 0.3644 -0.7526 0.3539 -0.8721 0.3418 -0.9916 0.3283 -1.1110 0.3136 -1.2305 0.2979 -1.3500 0.2813 -1.4694 0.2643 -1.5889 0.2468 -1.7084 0.2293 -1.8278 0.2118 -1.9473 0.1945 -2.0668 0.1777 -2.1862 0.1614 -2.3057 0.1458 -2.4252 0.1310 -2.5446 0.1170 -2.6641 0.1039 -2.7836 0.0918 -2.9030 0.0806 -3.0225 0.0704 -3.1420 0.0612 -3.2614 0.0529 -3.3809 0.0454 -3.5004 0.0388 -3.6198 0.0329 -3.7393 0.0278 -3.8588 0.0234 -3.9782 0.0195 -4.0977 0.0162 -4.2171 0.0134 -4.3366 0.0110 -4.4561 0.0090 -4.5755 0.0073 -4.6950 0.0059 -4.8145 0.0047 -4.9339 0.0038 -5.0534 0.0030 -5.1729 0.0024 -5.2923 0.0019 -5.4118 0.0015 -5.5313 0.0011 -5.6507 0.0009 -5.7702 0.0007 -5.8897 0.0005 -6.0091 0.0004 -6.1286 0.0003 -6.2481 0.0002 -6.3675 0.0002 -6.4870 0.0001 diff --git a/sourcecodes/data/example_sci/Llunet_figure_new.txt b/sourcecodes/data/example_sci/Llunet_figure_new.txt deleted file mode 100644 index 7e6f0d97..00000000 --- a/sourcecodes/data/example_sci/Llunet_figure_new.txt +++ /dev/null @@ -1,433 +0,0 @@ -1 -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1.0000 1.0000 -Gene1 1 -250 150 -1 1 -1 3 --3.5013 0.0000 --3.4313 0.0000 --3.3613 0.0000 --3.2912 0.0000 --3.2212 0.0000 --3.1512 0.0000 --3.0811 0.0000 --3.0111 0.0000 --2.9411 0.0000 --2.8710 0.0000 --2.8010 0.0000 --2.7310 0.0000 --2.6609 0.0000 --2.5909 0.0000 --2.5209 0.0001 --2.4508 0.0002 --2.3808 0.0004 --2.3108 0.0007 --2.2407 0.0014 --2.1707 0.0026 --2.1007 0.0046 --2.0306 0.0079 --1.9606 0.0133 --1.8906 0.0217 --1.8205 0.0344 --1.7505 0.0529 --1.6805 0.0791 --1.6104 0.1147 --1.5404 0.1615 --1.4704 0.2207 --1.4003 0.2928 --1.3303 0.3771 --1.2603 0.4715 --1.1902 0.5723 --1.1202 0.6743 --1.0502 0.7713 --0.9801 0.8564 --0.9101 0.9232 --0.8401 0.9660 --0.7700 0.9813 --0.7000 0.9676 --0.6300 0.9263 --0.5599 0.8608 --0.4899 0.7765 --0.4199 0.6800 --0.3498 0.5781 --0.2798 0.4771 --0.2098 0.3822 --0.1397 0.2973 --0.0697 0.2244 -0.0003 0.1645 -0.0704 0.1170 -0.1404 0.0808 -0.2104 0.0542 -0.2805 0.0353 -0.3505 0.0223 -0.4205 0.0137 -0.4906 0.0081 -0.5606 0.0047 -0.6306 0.0026 -0.7007 0.0014 -0.7707 0.0008 -0.8407 0.0004 -0.9108 0.0002 -0.9808 0.0001 -1.0508 0.0000 -1.1209 0.0000 -1.1909 0.0000 -1.2609 0.0000 -1.3310 0.0000 -1.4010 0.0000 -1.4710 0.0000 -1.5411 0.0000 -1.6111 0.0000 -1.6811 0.0000 -1.7512 0.0000 -1.8212 0.0000 -1.8912 0.0000 -1.9613 0.0000 -2.0313 0.0000 -2.1013 0.0000 -2.1714 0.0000 -2.2414 0.0000 -2.3114 0.0000 -2.3815 0.0000 -2.4515 0.0000 -2.5215 0.0000 -2.5916 0.0000 -2.6616 0.0000 -2.7316 0.0000 -2.8017 0.0000 -2.8717 0.0000 -2.9417 0.0000 -3.0118 0.0000 -3.0818 0.0000 -3.1518 0.0000 -3.2219 0.0000 -3.2919 0.0000 -3.3619 0.0000 -3.4320 0.0000 -3.5020 0.0000 -Gene2 1 -250 150 -1 2 -2 4 5 --3.5862 0.0000 --3.5124 0.0000 --3.4385 0.0000 --3.3647 0.0000 --3.2909 0.0000 --3.2171 0.0001 --3.1432 0.0001 --3.0694 0.0002 --2.9956 0.0003 --2.9218 0.0005 --2.8479 0.0008 --2.7741 0.0012 --2.7003 0.0018 --2.6264 0.0028 --2.5526 0.0041 --2.4788 0.0060 --2.4050 0.0087 --2.3311 0.0124 --2.2573 0.0175 --2.1835 0.0242 --2.1097 0.0329 --2.0358 0.0441 --1.9620 0.0583 --1.8882 0.0759 --1.8143 0.0974 --1.7405 0.1230 --1.6667 0.1530 --1.5929 0.1874 --1.5190 0.2262 --1.4452 0.2689 --1.3714 0.3148 --1.2976 0.3631 --1.2237 0.4126 --1.1499 0.4617 --1.0761 0.5089 --1.0022 0.5525 --0.9284 0.5908 --0.8546 0.6224 --0.7808 0.6458 --0.7069 0.6600 --0.6331 0.6644 --0.5593 0.6588 --0.4855 0.6434 --0.4116 0.6190 --0.3378 0.5866 --0.2640 0.5475 --0.1901 0.5034 --0.1163 0.4558 --0.0425 0.4066 -0.0313 0.3573 -0.1052 0.3092 -0.1790 0.2636 -0.2528 0.2213 -0.3266 0.1830 -0.4005 0.1491 -0.4743 0.1197 -0.5481 0.0946 -0.6220 0.0736 -0.6958 0.0565 -0.7696 0.0426 -0.8434 0.0317 -0.9173 0.0233 -0.9911 0.0168 -1.0649 0.0119 -1.1387 0.0084 -1.2126 0.0058 -1.2864 0.0039 -1.3602 0.0026 -1.4341 0.0017 -1.5079 0.0011 -1.5817 0.0007 -1.6555 0.0005 -1.7294 0.0003 -1.8032 0.0002 -1.8770 0.0001 -1.9508 0.0001 -2.0247 0.0000 -2.0985 0.0000 -2.1723 0.0000 -2.2462 0.0000 -2.3200 0.0000 -2.3938 0.0000 -2.4676 0.0000 -2.5415 0.0000 -2.6153 0.0000 -2.6891 0.0000 -2.7629 0.0000 -2.8368 0.0000 -2.9106 0.0000 -2.9844 0.0000 -3.0583 0.0000 -3.1321 0.0000 -3.2059 0.0000 -3.2797 0.0000 -3.3536 0.0000 -3.4274 0.0000 -3.5012 0.0000 -3.5750 0.0000 -3.6489 0.0000 -3.7227 0.0000 -3.7965 0.0000 -Gene3 1 -250 150 -2 1 3 -1 5 --4.3571 0.0002 --4.2762 0.0002 --4.1954 0.0003 --4.1145 0.0004 --4.0336 0.0005 --3.9527 0.0007 --3.8719 0.0010 --3.7910 0.0013 --3.7101 0.0017 --3.6293 0.0022 --3.5484 0.0028 --3.4675 0.0036 --3.3866 0.0046 --3.3058 0.0059 --3.2249 0.0074 --3.1440 0.0093 --3.0632 0.0115 --2.9823 0.0143 --2.9014 0.0175 --2.8205 0.0214 --2.7397 0.0260 --2.6588 0.0313 --2.5779 0.0374 --2.4971 0.0445 --2.4162 0.0526 --2.3353 0.0617 --2.2544 0.0719 --2.1736 0.0833 --2.0927 0.0958 --2.0118 0.1095 --1.9310 0.1243 --1.8501 0.1403 --1.7692 0.1572 --1.6883 0.1750 --1.6075 0.1936 --1.5266 0.2127 --1.4457 0.2322 --1.3648 0.2518 --1.2840 0.2713 --1.2031 0.2904 --1.1222 0.3088 --1.0414 0.3263 --0.9605 0.3424 --0.8796 0.3570 --0.7987 0.3698 --0.7179 0.3806 --0.6370 0.3890 --0.5561 0.3951 --0.4753 0.3987 --0.3944 0.3996 --0.3135 0.3980 --0.2326 0.3937 --0.1518 0.3869 --0.0709 0.3778 -0.0100 0.3665 -0.0908 0.3532 -0.1717 0.3381 -0.2526 0.3216 -0.3335 0.3039 -0.4143 0.2852 -0.4952 0.2660 -0.5761 0.2464 -0.6569 0.2268 -0.7378 0.2074 -0.8187 0.1884 -0.8996 0.1700 -0.9804 0.1524 -1.0613 0.1358 -1.1422 0.1201 -1.2230 0.1056 -1.3039 0.0922 -1.3848 0.0800 -1.4657 0.0690 -1.5465 0.0591 -1.6274 0.0502 -1.7083 0.0425 -1.7891 0.0357 -1.8700 0.0297 -1.9509 0.0246 -2.0318 0.0203 -2.1126 0.0166 -2.1935 0.0135 -2.2744 0.0109 -2.3552 0.0087 -2.4361 0.0070 -2.5170 0.0055 -2.5979 0.0043 -2.6787 0.0034 -2.7596 0.0026 -2.8405 0.0020 -2.9213 0.0015 -3.0022 0.0012 -3.0831 0.0009 -3.1640 0.0007 -3.2448 0.0005 -3.3257 0.0004 -3.4066 0.0003 -3.4874 0.0002 -3.5683 0.0001 -3.6492 0.0001 -3.7301 0.0001 -Phenotype 1 -250 150 -2 3 4 -0 --3.5574 0.0004 --3.4806 0.0006 --3.4037 0.0008 --3.3268 0.0012 --3.2499 0.0016 --3.1731 0.0022 --3.0962 0.0030 --3.0193 0.0040 --2.9425 0.0054 --2.8656 0.0071 --2.7887 0.0093 --2.7118 0.0121 --2.6350 0.0155 --2.5581 0.0198 --2.4812 0.0250 --2.4044 0.0313 --2.3275 0.0389 --2.2506 0.0479 --2.1737 0.0584 --2.0969 0.0706 --2.0200 0.0846 --1.9431 0.1005 --1.8663 0.1184 --1.7894 0.1381 --1.7125 0.1597 --1.6356 0.1831 --1.5588 0.2081 --1.4819 0.2343 --1.4050 0.2615 --1.3282 0.2893 --1.2513 0.3173 --1.1744 0.3448 --1.0975 0.3714 --1.0207 0.3966 --0.9438 0.4197 --0.8669 0.4402 --0.7901 0.4576 --0.7132 0.4716 --0.6363 0.4816 --0.5594 0.4875 --0.4826 0.4891 --0.4057 0.4864 --0.3288 0.4794 --0.2520 0.4684 --0.1751 0.4535 --0.0982 0.4353 --0.0213 0.4140 -0.0555 0.3904 -0.1324 0.3648 -0.2093 0.3379 -0.2861 0.3102 -0.3630 0.2822 -0.4399 0.2545 -0.5168 0.2275 -0.5936 0.2016 -0.6705 0.1770 -0.7474 0.1541 -0.8242 0.1329 -0.9011 0.1136 -0.9780 0.0963 -1.0549 0.0809 -1.1317 0.0673 -1.2086 0.0556 -1.2855 0.0455 -1.3623 0.0368 -1.4392 0.0296 -1.5161 0.0236 -1.5930 0.0186 -1.6698 0.0146 -1.7467 0.0113 -1.8236 0.0087 -1.9004 0.0066 -1.9773 0.0050 -2.0542 0.0037 -2.1311 0.0028 -2.2079 0.0020 -2.2848 0.0015 -2.3617 0.0011 -2.4385 0.0008 -2.5154 0.0005 -2.5923 0.0004 -2.6692 0.0003 -2.7460 0.0002 -2.8229 0.0001 -2.8998 0.0001 -2.9766 0.0001 -3.0535 0.0000 -3.1304 0.0000 -3.2073 0.0000 -3.2841 0.0000 -3.3610 0.0000 -3.4379 0.0000 -3.5147 0.0000 -3.5916 0.0000 -3.6685 0.0000 -3.7454 0.0000 -3.8222 0.0000 -3.8991 0.0000 -3.9760 0.0000 -4.0528 0.0000 -4.1297 0.0000 diff --git a/sourcecodes/data/example_sci/Llunlevels.txt b/sourcecodes/data/example_sci/Llunlevels.txt deleted file mode 100644 index 714e56bd..00000000 --- a/sourcecodes/data/example_sci/Llunlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype 1 2 - diff --git a/sourcecodes/data/example_sci/Llunnode.txt b/sourcecodes/data/example_sci/Llunnode.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/example_sci/Llunnode.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/example_sci/Llunrows.txt b/sourcecodes/data/example_sci/Llunrows.txt deleted file mode 100644 index c15fb720..00000000 --- a/sourcecodes/data/example_sci/Llunrows.txt +++ /dev/null @@ -1 +0,0 @@ -501 diff --git a/sourcecodes/data/example_sci/Lluparameters.txt b/sourcecodes/data/example_sci/Lluparameters.txt deleted file mode 100644 index 11583baa..00000000 --- a/sourcecodes/data/example_sci/Lluparameters.txt +++ /dev/null @@ -1,21 +0,0 @@ -Genotype -Discrete node with 2 states -1 0.4860 -2 0.5140 - -Gene3 -Continuous node --0.0150 1.0589 - -Gene2 -Continuous node -0.1381 1.1779 - -Phenotype -Continuous node -0.0693 1.5989 - -Gene1 -Continuous node -0.1745 1.5275 - diff --git a/sourcecodes/data/example_sci/Lluparent.txt b/sourcecodes/data/example_sci/Lluparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example_sci/Lluparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example_sci/Llustructure_old.txt b/sourcecodes/data/example_sci/Llustructure_old.txt deleted file mode 100644 index 5b464577..00000000 --- a/sourcecodes/data/example_sci/Llustructure_old.txt +++ /dev/null @@ -1,5 +0,0 @@ -Genotype 0.4860 0.5140 -Gene3 0.0001 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0006 0.0008 0.0010 0.0013 0.0018 0.0023 0.0029 0.0037 0.0047 0.0059 0.0074 0.0092 0.0113 0.0139 0.0170 0.0206 0.0248 0.0297 0.0354 0.0419 0.0493 0.0576 0.0669 0.0773 0.0887 0.1012 0.1147 0.1292 0.1447 0.1610 0.1781 0.1958 0.2139 0.2323 0.2507 0.2688 0.2866 0.3036 0.3197 0.3345 0.3479 0.3597 0.3695 0.3773 0.3828 0.3861 0.3870 0.3855 0.3817 0.3756 0.3673 0.3570 0.3449 0.3311 0.3160 0.2996 0.2824 0.2645 0.2463 0.2279 0.2095 0.1915 0.1740 0.1570 0.1409 0.1256 0.1114 0.0981 0.0859 0.0747 0.0646 0.0555 0.0474 0.0402 0.0340 0.0285 0.0237 0.0197 0.0162 0.0132 0.0108 0.0087 0.0070 0.0056 0.0044 0.0035 0.0027 0.0021 0.0016 0.0013 0.0010 0.0007 0.0006 -Gene1 0.0009 0.0012 0.0015 0.0019 0.0024 0.0030 0.0037 0.0046 0.0056 0.0069 0.0083 0.0101 0.0121 0.0145 0.0174 0.0206 0.0243 0.0286 0.0335 0.0389 0.0451 0.0520 0.0597 0.0682 0.0775 0.0876 0.0986 0.1105 0.1231 0.1366 0.1508 0.1657 0.1811 0.1971 0.2134 0.2300 0.2467 0.2633 0.2797 0.2956 0.3110 0.3256 0.3392 0.3517 0.3629 0.3726 0.3808 0.3873 0.3920 0.3948 0.3958 0.3948 0.3920 0.3872 0.3807 0.3726 0.3628 0.3516 0.3391 0.3254 0.3108 0.2955 0.2795 0.2631 0.2465 0.2299 0.2133 0.1969 0.1810 0.1655 0.1507 0.1365 0.1230 0.1103 0.0985 0.0875 0.0774 0.0681 0.0596 0.0520 0.0451 0.0389 0.0334 0.0286 0.0243 0.0206 0.0173 0.0145 0.0121 0.0101 0.0083 0.0068 0.0056 0.0046 0.0037 0.0030 0.0024 0.0019 0.0015 0.0012 0.0009 -Phenotype 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0042 0.0052 0.0065 0.0080 0.0098 0.0120 0.0146 0.0176 0.0212 0.0253 0.0300 0.0354 0.0416 0.0486 0.0564 0.0651 0.0748 0.0854 0.0970 0.1096 0.1230 0.1374 0.1526 0.1685 0.1850 0.2021 0.2195 0.2370 0.2545 0.2718 0.2887 0.3049 0.3202 0.3344 0.3473 0.3587 0.3684 0.3763 0.3822 0.3860 0.3877 0.3872 0.3846 0.3798 0.3731 0.3644 0.3539 0.3418 0.3283 0.3136 0.2979 0.2813 0.2643 0.2468 0.2293 0.2118 0.1945 0.1777 0.1614 0.1458 0.1310 0.1170 0.1039 0.0918 0.0806 0.0704 0.0612 0.0529 0.0454 0.0388 0.0329 0.0278 0.0234 0.0195 0.0162 0.0134 0.0110 0.0090 0.0073 0.0059 0.0047 0.0038 0.0030 0.0024 0.0019 0.0015 0.0011 0.0009 0.0007 0.0005 0.0004 0.0003 0.0002 0.0002 0.0001 -Gene2 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0041 0.0050 0.0062 0.0077 0.0094 0.0114 0.0138 0.0166 0.0199 0.0237 0.0281 0.0331 0.0388 0.0453 0.0526 0.0607 0.0696 0.0795 0.0903 0.1021 0.1147 0.1282 0.1426 0.1578 0.1736 0.1900 0.2069 0.2241 0.2414 0.2587 0.2758 0.2924 0.3084 0.3236 0.3377 0.3506 0.3621 0.3719 0.3800 0.3863 0.3905 0.3927 0.3929 0.3910 0.3870 0.3811 0.3732 0.3636 0.3524 0.3397 0.3258 0.3108 0.2949 0.2783 0.2613 0.2440 0.2267 0.2095 0.1925 0.1760 0.1601 0.1449 0.1304 0.1167 0.1039 0.0920 0.0811 0.0711 0.0620 0.0537 0.0464 0.0398 0.0340 0.0288 0.0243 0.0205 0.0171 0.0142 0.0117 0.0097 0.0079 0.0064 0.0052 0.0042 0.0034 0.0027 0.0021 0.0017 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004 diff --git a/sourcecodes/data/example_sci/Lluthr.txt b/sourcecodes/data/example_sci/Lluthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example_sci/Lluthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example_sci/Llutier.txt b/sourcecodes/data/example_sci/Llutier.txt deleted file mode 100644 index da7084fb..00000000 --- a/sourcecodes/data/example_sci/Llutier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,1,Genotype,Tier2,3,Gene1,Gene2,Gene3,Tier3,1,Phenotype, \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Llutype.txt b/sourcecodes/data/example_sci/Llutype.txt deleted file mode 100644 index 9ea66ce4..00000000 --- a/sourcecodes/data/example_sci/Llutype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 diff --git a/sourcecodes/data/example_sci/Lluvar.txt b/sourcecodes/data/example_sci/Lluvar.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_sci/Lluvar.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluvardata.txt b/sourcecodes/data/example_sci/Lluvardata.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_sci/Lluvardata.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluvarname.txt b/sourcecodes/data/example_sci/Lluvarname.txt deleted file mode 100644 index 3fe283bd..00000000 --- a/sourcecodes/data/example_sci/Lluvarname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluwhite.txt b/sourcecodes/data/example_sci/Lluwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example_sci/Lluwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example_sci/old/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci/old/Llurun_evidencemodified.sh deleted file mode 100644 index ee0dde13..00000000 --- a/sourcecodes/data/example_sci/old/Llurun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified Llu -fi -exit diff --git a/sourcecodes/data/example_sci/old/Llurun_initialstructure.sh b/sourcecodes/data/example_sci/old/Llurun_initialstructure.sh deleted file mode 100644 index adde14dd..00000000 --- a/sourcecodes/data/example_sci/old/Llurun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Llu -fi -exit diff --git a/sourcecodes/data/example_time_series/TEbban.txt b/sourcecodes/data/example_time_series/TEbban.txt deleted file mode 100644 index 7b0aa551..00000000 --- a/sourcecodes/data/example_time_series/TEbban.txt +++ /dev/null @@ -1,73 +0,0 @@ -From To -TraitA_T1 Genotype -TraitB_T1 Genotype -TraitC_T1 Genotype -TraitA_T2 Genotype -TraitB_T2 Genotype -TraitC_T2 Genotype -TraitA_T3 Genotype -TraitB_T3 Genotype -TraitC_T3 Genotype -TraitA_T1 Genotype -TraitB_T1 Genotype -TraitC_T1 Genotype -TraitA_T2 TraitA_T1 -TraitA_T2 TraitB_T1 -TraitA_T2 TraitC_T1 -TraitB_T2 TraitA_T1 -TraitB_T2 TraitB_T1 -TraitB_T2 TraitC_T1 -TraitC_T2 TraitA_T1 -TraitC_T2 TraitB_T1 -TraitC_T2 TraitC_T1 -TraitA_T3 TraitA_T1 -TraitA_T3 TraitB_T1 -TraitA_T3 TraitC_T1 -TraitB_T3 TraitA_T1 -TraitB_T3 TraitB_T1 -TraitB_T3 TraitC_T1 -TraitC_T3 TraitA_T1 -TraitC_T3 TraitB_T1 -TraitC_T3 TraitC_T1 -TraitA_T2 Genotype -TraitB_T2 Genotype -TraitC_T2 Genotype -TraitA_T2 TraitA_T1 -TraitA_T2 TraitB_T1 -TraitA_T2 TraitC_T1 -TraitB_T2 TraitA_T1 -TraitB_T2 TraitB_T1 -TraitB_T2 TraitC_T1 -TraitC_T2 TraitA_T1 -TraitC_T2 TraitB_T1 -TraitC_T2 TraitC_T1 -TraitA_T3 TraitA_T2 -TraitA_T3 TraitB_T2 -TraitA_T3 TraitC_T2 -TraitB_T3 TraitA_T2 -TraitB_T3 TraitB_T2 -TraitB_T3 TraitC_T2 -TraitC_T3 TraitA_T2 -TraitC_T3 TraitB_T2 -TraitC_T3 TraitC_T2 -TraitA_T3 Genotype -TraitB_T3 Genotype -TraitC_T3 Genotype -TraitA_T3 TraitA_T1 -TraitA_T3 TraitB_T1 -TraitA_T3 TraitC_T1 -TraitB_T3 TraitA_T1 -TraitB_T3 TraitB_T1 -TraitB_T3 TraitC_T1 -TraitC_T3 TraitA_T1 -TraitC_T3 TraitB_T1 -TraitC_T3 TraitC_T1 -TraitA_T3 TraitA_T2 -TraitA_T3 TraitB_T2 -TraitA_T3 TraitC_T2 -TraitB_T3 TraitA_T2 -TraitB_T3 TraitB_T2 -TraitB_T3 TraitC_T2 -TraitC_T3 TraitA_T2 -TraitC_T3 TraitB_T2 -TraitC_T3 TraitC_T2 diff --git a/sourcecodes/data/example_time_series/TEbcontinuous_input.txt b/sourcecodes/data/example_time_series/TEbcontinuous_input.txt deleted file mode 100644 index 34b3b957..00000000 --- a/sourcecodes/data/example_time_series/TEbcontinuous_input.txt +++ /dev/null @@ -1,503 +0,0 @@ -Genotype TraitA_T1 TraitA_T2 TraitA_T3 TraitB_T1 TraitB_T2 TraitB_T3 TraitC_T1 TraitC_T2 TraitC_T3 -2 1 1 1 1 1 1 1 1 1 -1 1.4297 -0.13715 -0.33041 1.3972 -0.17802 1.0272 -1.322 0.0027715 0.85527 -1 2.0687 -2.5819 -0.71386 -0.25338 0.64604 -0.25402 -1.1947 0.60348 1.5977 -2 0.52771 0.19656 0.40967 0.039336 1.57 -0.036341 -1.6301 -0.15434 0.93397 -1 1.7929 -0.85399 -0.21102 0.36528 0.14997 -0.072283 0.25214 1.8044 1.4149 -1 -0.090929 -0.17288 -2.808 0.79192 -1.5175 -0.90041 0.39689 -0.18146 -0.55432 -1 0.86086 -0.049472 -0.82074 0.18954 0.51157 0.30995 -0.50952 -0.047852 0.25632 -1 0.37794 -0.49737 -1.5634 -0.61123 -1.6172 -0.025387 -0.50463 1.0061 -0.55909 -1 0.061886 -1.3173 -0.38674 0.66584 0.023432 -1.0821 0.14268 -0.21189 -0.60498 -1 0.96427 -1.6652 -0.61177 -0.295 0.12641 -1.6644 -1.0372 0.033566 1.3366 -2 0.16295 0.59047 0.7747 -0.32623 1.6996 -0.042892 -0.0034198 -0.30944 0.67765 -1 1.7419 -0.94567 -1.8121 0.80385 0.23144 -1.4004 2.0605 -0.83835 1.3823 -2 -0.92772 0.34934 0.87438 -0.62792 0.7641 -0.5865 0.24522 0.6353 -0.0017539 -2 -2.9367 1.609 2.0928 0.61651 -2.0775 -0.24164 -0.3587 -0.95545 -3.0393 -1 0.52613 0.43773 0.75866 0.73066 0.46388 -1.4681 -1.5908 1.6872 0.89314 -2 -0.10721 1.7759 1.6821 -0.56868 1.6447 -0.92002 -0.27447 -0.62549 0.91373 -1 -1.073 -1.8228 -0.34751 -0.54007 -1.7593 -0.7431 0.61821 -0.054988 -1.7414 -2 -1.0532 1.0319 1.0531 -0.09473 -0.82174 0.45084 -0.38299 -0.6361 -0.90619 -1 1.7064 -1.8984 -2.6061 0.99661 -0.67065 0.17936 0.97103 0.38751 -0.11531 -2 -3.2527 -1.1361 0.56795 -0.39584 -1.5189 -1.7637 1.2149 -1.3971 -1.8622 -1 2.3471 -2.1036 -2.092 1.544 -0.21178 0.3446 1.0474 -0.64427 0.73628 -2 -0.63792 1.3156 0.92169 -0.67815 1.4089 1.1938 0.82905 0.16566 0.09164 -2 -2.0379 0.74861 0.16368 0.58693 -0.67589 0.81824 0.33633 -0.19727 -1.243 -2 -1.7441 2.4915 0.89809 -1.0265 0.35767 -1.159 0.63023 0.97341 0.29971 -2 -1.9637 0.94259 1.169 1.9451 -0.96485 0.49152 -1.1393 -1.2415 -0.58885 -2 -1.0536 2.4253 0.94996 -2.3874 0.23825 0.224 -0.073329 -1.2231 -0.24801 -1 -0.032849 -1.1426 -1.1507 -0.10711 -1.6383 -0.80394 1.5126 0.28303 0.083105 -2 -2.2192 0.84322 0.73021 0.71513 -0.79164 0.61126 -1.2986 0.89057 -1.4685 -1 0.42429 -0.65294 -1.9493 -0.77983 -1.2761 0.99263 0.051924 0.83436 -0.0079187 -2 -0.85155 0.9691 1.1731 1.0504 0.39302 0.030178 -0.70262 -0.014959 -0.31945 -1 -1.4662 -0.5934 -2.0914 -0.76279 -1.7903 0.94245 0.96374 -1.6733 -1.8091 -1 2.0716 -0.52844 -0.183 -0.032514 1.4843 0.28402 0.37221 -1.4476 2.8712 -2 -1.0437 1.5094 -0.23396 -0.84804 0.43785 0.19966 0.3728 0.15043 0.10549 -1 1.0647 -0.35638 -1.0854 0.78756 -0.99107 0.098816 -0.32975 -0.68451 0.71344 -1 0.58146 -0.46614 -2.9113 -0.032848 0.052376 -0.36411 0.87461 0.28033 -0.61848 -2 -0.6251 1.3257 0.36072 -0.042944 0.66071 -0.33981 2.0873 1.2161 0.089706 -1 1.57 -1.26 -2.0278 1.5331 -1.5343 0.019093 -0.73556 1.0316 0.41452 -2 -1.6998 1.0471 -0.0095397 -0.72037 0.30428 0.18062 0.86143 -0.31801 -0.86127 -2 -1.0544 1.9761 1.1994 1.7876 -0.24561 0.01978 1.4123 0.19675 -0.022687 -2 0.38235 2.3798 0.42045 0.97856 1.7099 0.20914 1.0505 1.9808 1.482 -1 1.8991 -2.1024 -0.53897 0.20839 1.3568 -1.4725 0.16263 0.069291 1.5719 -2 -2.2901 1.333 1.1433 -0.53918 -0.41394 -1.0484 -1.2332 0.068735 -2.0475 -1 1.9123 0.027091 -0.067604 -0.86429 -0.73426 0.65875 -0.59697 1.1903 -0.068242 -2 -1.8834 1.7232 1.3404 -0.096031 -0.1779 1.2453 0.23601 -0.81722 -0.8237 -1 -0.33029 -1.4141 -0.24236 0.3117 -0.28893 -1.536 0.63391 0.97915 -0.30591 -2 -1.0004 -0.17153 0.80903 -1.3152 -0.28004 -2.5356 0.25062 -1.6221 -0.2114 -2 0.92525 0.78374 0.44585 0.87215 0.67229 1.6991 -0.45347 0.21751 0.95898 -1 0.47842 -0.79727 0.0099566 0.8919 0.31135 -0.62503 -0.99073 1.5268 0.43918 -1 -0.52618 -0.57407 -1.5704 -1.9977 -1.8715 0.99632 1.124 2.1038 -1.3776 -2 -0.8334 1.5897 0.82506 -0.045645 0.23407 -1.1836 -0.86756 0.52102 0.23901 -1 1.0179 -0.6531 -0.53277 0.32403 1.226 -0.27361 -1.5967 -0.20229 1.5482 -2 -0.82762 0.26361 2.4807 -0.49628 -0.44792 1.295 -1.0416 0.29424 -1.0789 -1 1.569 0.14532 -1.3216 -1.1622 -0.46791 0.10723 -0.74658 1.7246 0.087136 -1 0.93783 -1.0786 -1.6758 -2.3367 -1.4745 -0.78743 0.85399 0.0085691 0.79439 -2 -2.9555 1.122 1.8506 0.65602 -0.66402 0.25697 0.75048 0.21667 -2.1374 -2 -1.5843 0.24076 0.71071 -0.16959 -1.0254 0.44363 1.1218 1.0872 -1.2214 -2 0.82202 1.2273 -0.2641 1.1674 0.72576 -0.6655 -0.33565 -0.57264 1.0462 -1 0.83408 -0.90235 -0.3935 0.086621 1.5353 -0.37978 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@@ -1,11 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Genotype -> TraitA_T1; -Genotype -> TraitA_T2; -Genotype -> TraitA_T3; -Genotype -> TraitB_T2; -TraitA_T1 -> TraitB_T2; -TraitA_T1 -> TraitC_T3; -TraitB_T2 -> TraitC_T3; -} \ No newline at end of file diff --git a/sourcecodes/data/example_time_series/TEbk.txt b/sourcecodes/data/example_time_series/TEbk.txt deleted file mode 100644 index 29d6383b..00000000 --- a/sourcecodes/data/example_time_series/TEbk.txt +++ /dev/null @@ -1 +0,0 @@ -100 diff --git a/sourcecodes/data/example_time_series/TEbmap.txt b/sourcecodes/data/example_time_series/TEbmap.txt deleted file mode 100644 index 20f9b470..00000000 --- a/sourcecodes/data/example_time_series/TEbmap.txt +++ /dev/null @@ -1,10 +0,0 @@ -Genotype 0.499053 1.462000 -TraitA_T1 1.306059 0.037189 -TraitA_T2 1.304164 -0.061147 -TraitA_T3 1.174305 -0.083449 -TraitB_T1 0.929161 -0.056347 -TraitB_T2 1.021691 -0.045299 -TraitB_T3 0.940946 0.012204 -TraitC_T1 0.907725 -0.001607 -TraitC_T2 0.923711 0.091657 -TraitC_T3 1.015189 0.017718 diff --git a/sourcecodes/data/example_time_series/TEbmapdata.txt b/sourcecodes/data/example_time_series/TEbmapdata.txt deleted file mode 100644 index 7e9af6ce..00000000 --- a/sourcecodes/data/example_time_series/TEbmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -TraitC_T2 TraitC_T1 TraitB_T3 TraitB_T1 Genotype TraitA_T3 TraitA_T2 TraitA_T1 TraitB_T2 TraitC_T3 diff --git a/sourcecodes/data/example_time_series/TEbname.txt b/sourcecodes/data/example_time_series/TEbname.txt deleted file mode 100644 index 69919d0f..00000000 --- a/sourcecodes/data/example_time_series/TEbname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype TraitA_T1 TraitA_T2 TraitA_T3 TraitB_T1 TraitB_T2 TraitB_T3 TraitC_T1 TraitC_T2 TraitC_T3 diff --git a/sourcecodes/data/example_time_series/TEbnet_figure.txt b/sourcecodes/data/example_time_series/TEbnet_figure.txt deleted file mode 100644 index 1cceadd2..00000000 --- a/sourcecodes/data/example_time_series/TEbnet_figure.txt +++ /dev/null @@ -1,963 +0,0 @@ -10 -1500 1200 -TraitC_T2 0 0 -TraitC_T1 250 0 -TraitB_T3 500 0 -TraitB_T1 750 0 -Genotype 1000 0 -TraitA_T3 275 240 -TraitA_T2 650 240 -TraitA_T1 1025 240 -TraitB_T2 500 480 -TraitC_T3 650 720 -TraitC_T2 1 -250 150 -0 -0 --3.6677 0.0001 --3.5949 0.0002 --3.5222 0.0002 --3.4494 0.0003 --3.3767 0.0004 --3.3039 0.0005 --3.2311 0.0007 --3.1584 0.0009 --3.0856 0.0012 --3.0129 0.0015 --2.9401 0.0020 --2.8673 0.0025 --2.7946 0.0032 --2.7218 0.0041 --2.6490 0.0052 --2.5763 0.0065 --2.5035 0.0081 --2.4308 0.0101 --2.3580 0.0124 --2.2852 0.0152 --2.2125 0.0185 --2.1397 0.0224 --2.0669 0.0269 --1.9942 0.0322 --1.9214 0.0382 --1.8487 0.0451 --1.7759 0.0529 --1.7031 0.0617 --1.6304 0.0716 --1.5576 0.0824 --1.4848 0.0944 --1.4121 0.1074 --1.3393 0.1215 --1.2666 0.1366 --1.1938 0.1526 --1.1210 0.1695 --1.0483 0.1871 --0.9755 0.2052 --0.9027 0.2238 --0.8300 0.2425 --0.7572 0.2612 --0.6845 0.2796 --0.6117 0.2975 --0.5389 0.3147 --0.4662 0.3308 --0.3934 0.3456 --0.3206 0.3588 --0.2479 0.3703 --0.1751 0.3799 --0.1024 0.3873 --0.0296 0.3924 -0.0432 0.3952 -0.1159 0.3956 -0.1887 0.3936 -0.2614 0.3892 -0.3342 0.3826 -0.4070 0.3737 -0.4797 0.3629 -0.5525 0.3502 -0.6253 0.3358 -0.6980 0.3202 -0.7708 0.3033 -0.8435 0.2857 -0.9163 0.2674 -0.9891 0.2487 -1.0618 0.2300 -1.1346 0.2114 -1.2074 0.1930 -1.2801 0.1753 -1.3529 0.1581 -1.4256 0.1418 -1.4984 0.1264 -1.5712 0.1120 -1.6439 0.0986 -1.7167 0.0863 -1.7895 0.0751 -1.8622 0.0649 -1.9350 0.0558 -2.0077 0.0476 -2.0805 0.0404 -2.1533 0.0341 -2.2260 0.0286 -2.2988 0.0238 -2.3716 0.0197 -2.4443 0.0163 -2.5171 0.0133 -2.5898 0.0108 -2.6626 0.0087 -2.7354 0.0070 -2.8081 0.0056 -2.8809 0.0045 -2.9537 0.0035 -3.0264 0.0028 -3.0992 0.0021 -3.1719 0.0017 -3.2447 0.0013 -3.3175 0.0010 -3.3902 0.0007 -3.4630 0.0006 -3.5357 0.0004 -3.6085 0.0003 -TraitC_T1 1 -250 150 -0 -0 --3.4884 0.0003 --3.4129 0.0004 --3.3374 0.0005 --3.2619 0.0007 --3.1864 0.0009 --3.1109 0.0012 --3.0354 0.0016 --2.9599 0.0021 --2.8844 0.0028 --2.8089 0.0036 --2.7334 0.0046 --2.6579 0.0059 --2.5824 0.0074 --2.5069 0.0093 --2.4314 0.0116 --2.3559 0.0144 --2.2804 0.0178 --2.2049 0.0218 --2.1294 0.0265 --2.0539 0.0320 --1.9784 0.0384 --1.9029 0.0457 --1.8274 0.0540 --1.7519 0.0635 --1.6764 0.0741 --1.6009 0.0859 --1.5254 0.0989 --1.4499 0.1131 --1.3744 0.1284 --1.2989 0.1448 --1.2234 0.1623 --1.1479 0.1806 --1.0724 0.1995 --0.9969 0.2190 --0.9214 0.2388 --0.8459 0.2585 --0.7704 0.2781 --0.6949 0.2970 --0.6194 0.3151 --0.5439 0.3320 --0.4684 0.3475 --0.3929 0.3612 --0.3174 0.3729 --0.2419 0.3824 --0.1664 0.3894 --0.0909 0.3939 --0.0154 0.3957 -0.0601 0.3949 -0.1356 0.3914 -0.2111 0.3852 -0.2866 0.3766 -0.3620 0.3657 -0.4375 0.3527 -0.5130 0.3379 -0.5885 0.3215 -0.6640 0.3038 -0.7395 0.2851 -0.8150 0.2657 -0.8905 0.2460 -0.9660 0.2262 -1.0415 0.2066 -1.1170 0.1874 -1.1925 0.1689 -1.2680 0.1511 -1.3435 0.1343 -1.4190 0.1186 -1.4945 0.1040 -1.5700 0.0905 -1.6455 0.0783 -1.7210 0.0673 -1.7965 0.0574 -1.8720 0.0486 -1.9475 0.0409 -2.0230 0.0342 -2.0985 0.0284 -2.1740 0.0234 -2.2495 0.0192 -2.3250 0.0156 -2.4005 0.0126 -2.4760 0.0101 -2.5515 0.0081 -2.6270 0.0064 -2.7025 0.0050 -2.7780 0.0039 -2.8535 0.0030 -2.9290 0.0023 -3.0045 0.0018 -3.0800 0.0014 -3.1555 0.0010 -3.2310 0.0008 -3.3065 0.0006 -3.3820 0.0004 -3.4575 0.0003 -3.5330 0.0002 -3.6085 0.0002 -3.6840 0.0001 -3.7595 0.0001 -3.8350 0.0001 -3.9105 0.0000 -3.9860 0.0000 -4.0615 0.0000 -TraitB_T3 1 -250 150 -0 -0 --3.6093 0.0003 --3.5383 0.0004 --3.4673 0.0005 --3.3963 0.0006 --3.3252 0.0008 --3.2542 0.0011 --3.1832 0.0014 --3.1122 0.0017 --3.0411 0.0022 --2.9701 0.0028 --2.8991 0.0036 --2.8281 0.0045 --2.7570 0.0056 --2.6860 0.0069 --2.6150 0.0085 --2.5440 0.0105 --2.4729 0.0128 --2.4019 0.0155 --2.3309 0.0187 --2.2599 0.0225 --2.1888 0.0268 --2.1178 0.0318 --2.0468 0.0375 --1.9758 0.0440 --1.9047 0.0513 --1.8337 0.0596 --1.7627 0.0687 --1.6917 0.0788 --1.6206 0.0899 --1.5496 0.1020 --1.4786 0.1151 --1.4076 0.1291 --1.3365 0.1440 --1.2655 0.1597 --1.1945 0.1762 --1.1235 0.1933 --1.0524 0.2108 --0.9814 0.2286 --0.9104 0.2466 --0.8394 0.2645 --0.7683 0.2821 --0.6973 0.2992 --0.6263 0.3155 --0.5553 0.3309 --0.4842 0.3451 --0.4132 0.3579 --0.3422 0.3691 --0.2712 0.3785 --0.2001 0.3860 --0.1291 0.3914 --0.0581 0.3947 -0.0129 0.3958 -0.0839 0.3946 -0.1550 0.3913 -0.2260 0.3858 -0.2970 0.3783 -0.3680 0.3689 -0.4391 0.3577 -0.5101 0.3448 -0.5811 0.3306 -0.6521 0.3152 -0.7232 0.2988 -0.7942 0.2817 -0.8652 0.2641 -0.9362 0.2462 -1.0073 0.2283 -1.0783 0.2104 -1.1493 0.1929 -1.2203 0.1758 -1.2914 0.1594 -1.3624 0.1437 -1.4334 0.1288 -1.5044 0.1148 -1.5755 0.1018 -1.6465 0.0897 -1.7175 0.0786 -1.7885 0.0685 -1.8596 0.0594 -1.9306 0.0512 -2.0016 0.0439 -2.0726 0.0374 -2.1437 0.0317 -2.2147 0.0267 -2.2857 0.0224 -2.3567 0.0186 -2.4278 0.0155 -2.4988 0.0127 -2.5698 0.0104 -2.6408 0.0085 -2.7119 0.0069 -2.7829 0.0056 -2.8539 0.0044 -2.9249 0.0035 -2.9960 0.0028 -3.0670 0.0022 -3.1380 0.0017 -3.2090 0.0014 -3.2801 0.0010 -3.3511 0.0008 -3.4221 0.0006 -3.4931 0.0005 -TraitB_T1 1 -250 150 -0 -0 --3.5085 0.0004 --3.4347 0.0006 --3.3609 0.0008 --3.2872 0.0010 --3.2134 0.0013 --3.1397 0.0018 --3.0659 0.0023 --2.9921 0.0029 --2.9184 0.0037 --2.8446 0.0047 --2.7709 0.0059 --2.6971 0.0074 --2.6234 0.0093 --2.5496 0.0114 --2.4758 0.0141 --2.4021 0.0172 --2.3283 0.0209 --2.2546 0.0252 --2.1808 0.0302 --2.1070 0.0360 --2.0333 0.0427 --1.9595 0.0502 --1.8858 0.0587 --1.8120 0.0683 --1.7382 0.0789 --1.6645 0.0906 --1.5907 0.1034 --1.5170 0.1173 --1.4432 0.1322 --1.3694 0.1481 --1.2957 0.1649 --1.2219 0.1824 --1.1482 0.2006 --1.0744 0.2192 --1.0006 0.2381 --0.9269 0.2570 --0.8531 0.2756 --0.7794 0.2938 --0.7056 0.3112 --0.6319 0.3277 --0.5581 0.3429 --0.4843 0.3565 --0.4106 0.3685 --0.3368 0.3784 --0.2631 0.3863 --0.1893 0.3918 --0.1155 0.3950 --0.0418 0.3957 -0.0320 0.3940 -0.1057 0.3899 -0.1795 0.3834 -0.2533 0.3747 -0.3270 0.3640 -0.4008 0.3513 -0.4745 0.3370 -0.5483 0.3213 -0.6221 0.3045 -0.6958 0.2867 -0.7696 0.2683 -0.8433 0.2495 -0.9171 0.2306 -0.9909 0.2118 -1.0646 0.1934 -1.1384 0.1754 -1.2121 0.1582 -1.2859 0.1417 -1.3596 0.1262 -1.4334 0.1117 -1.5072 0.0982 -1.5809 0.0859 -1.6547 0.0746 -1.7284 0.0644 -1.8022 0.0553 -1.8760 0.0471 -1.9497 0.0399 -2.0235 0.0336 -2.0972 0.0281 -2.1710 0.0234 -2.2448 0.0194 -2.3185 0.0159 -2.3923 0.0130 -2.4660 0.0105 -2.5398 0.0085 -2.6136 0.0068 -2.6873 0.0054 -2.7611 0.0043 -2.8348 0.0034 -2.9086 0.0026 -2.9824 0.0020 -3.0561 0.0016 -3.1299 0.0012 -3.2036 0.0009 -3.2774 0.0007 -3.3511 0.0005 -3.4249 0.0004 -3.4987 0.0003 -3.5724 0.0002 -3.6462 0.0002 -3.7199 0.0001 -3.7937 0.0001 -3.8675 0.0001 -Genotype 2 -250 150 -0 -4 6 7 8 9 -1 0.5380 -2 0.4620 -TraitA_T3 1 -250 150 -1 5 -0 --4.3220 0.0007 --4.2395 0.0008 --4.1570 0.0011 --4.0746 0.0013 --3.9921 0.0017 --3.9096 0.0021 --3.8271 0.0027 --3.7446 0.0033 --3.6621 0.0041 --3.5797 0.0050 --3.4972 0.0062 --3.4147 0.0075 --3.3322 0.0092 --3.2497 0.0111 --3.1673 0.0133 --3.0848 0.0159 --3.0023 0.0189 --2.9198 0.0224 --2.8373 0.0264 --2.7548 0.0310 --2.6724 0.0362 --2.5899 0.0421 --2.5074 0.0486 --2.4249 0.0559 --2.3424 0.0641 --2.2600 0.0730 --2.1775 0.0828 --2.0950 0.0934 --2.0125 0.1049 --1.9300 0.1172 --1.8475 0.1304 --1.7651 0.1443 --1.6826 0.1589 --1.6001 0.1742 --1.5176 0.1900 --1.4351 0.2062 --1.3526 0.2227 --1.2702 0.2394 --1.1877 0.2561 --1.1052 0.2727 --1.0227 0.2889 --0.9402 0.3046 --0.8578 0.3195 --0.7753 0.3336 --0.6928 0.3467 --0.6103 0.3585 --0.5278 0.3688 --0.4453 0.3777 --0.3629 0.3849 --0.2804 0.3903 --0.1979 0.3939 --0.1154 0.3956 --0.0329 0.3954 -0.0495 0.3933 -0.1320 0.3893 -0.2145 0.3834 -0.2970 0.3759 -0.3795 0.3666 -0.4620 0.3559 -0.5444 0.3438 -0.6269 0.3306 -0.7094 0.3162 -0.7919 0.3011 -0.8744 0.2853 -0.9568 0.2690 -1.0393 0.2524 -1.1218 0.2357 -1.2043 0.2190 -1.2868 0.2025 -1.3693 0.1864 -1.4517 0.1707 -1.5342 0.1556 -1.6167 0.1411 -1.6992 0.1273 -1.7817 0.1144 -1.8642 0.1022 -1.9466 0.0909 -2.0291 0.0805 -2.1116 0.0709 -2.1941 0.0622 -2.2766 0.0542 -2.3590 0.0471 -2.4415 0.0407 -2.5240 0.0350 -2.6065 0.0299 -2.6890 0.0255 -2.7715 0.0216 -2.8539 0.0182 -2.9364 0.0153 -3.0189 0.0128 -3.1014 0.0106 -3.1839 0.0088 -3.2663 0.0072 -3.3488 0.0059 -3.4313 0.0048 -3.5138 0.0039 -3.5963 0.0032 -3.6788 0.0025 -3.7612 0.0020 -3.8437 0.0016 -3.9262 0.0013 -TraitA_T2 1 -250 150 -1 5 -0 --4.7209 0.0007 --4.6314 0.0009 --4.5418 0.0012 --4.4523 0.0015 --4.3628 0.0019 --4.2733 0.0023 --4.1838 0.0029 --4.0943 0.0036 --4.0048 0.0044 --3.9153 0.0054 --3.8258 0.0066 --3.7362 0.0079 --3.6467 0.0096 --3.5572 0.0115 --3.4677 0.0138 --3.3782 0.0164 --3.2887 0.0194 --3.1992 0.0229 --3.1097 0.0269 --3.0201 0.0314 --2.9306 0.0365 --2.8411 0.0423 --2.7516 0.0487 --2.6621 0.0559 --2.5726 0.0638 --2.4831 0.0725 --2.3936 0.0820 --2.3041 0.0923 --2.2145 0.1035 --2.1250 0.1154 --2.0355 0.1281 --1.9460 0.1416 --1.8565 0.1558 --1.7670 0.1705 --1.6775 0.1859 --1.5880 0.2016 --1.4985 0.2177 --1.4089 0.2340 --1.3194 0.2503 --1.2299 0.2666 --1.1404 0.2825 --1.0509 0.2981 --0.9614 0.3131 --0.8719 0.3272 --0.7824 0.3405 --0.6929 0.3526 --0.6033 0.3635 --0.5138 0.3730 --0.4243 0.3810 --0.3348 0.3873 --0.2453 0.3919 --0.1558 0.3948 --0.0663 0.3958 -0.0232 0.3950 -0.1127 0.3923 -0.2023 0.3879 -0.2918 0.3818 -0.3813 0.3740 -0.4708 0.3647 -0.5603 0.3539 -0.6498 0.3419 -0.7393 0.3288 -0.8288 0.3147 -0.9183 0.2998 -1.0079 0.2844 -1.0974 0.2684 -1.1869 0.2522 -1.2764 0.2359 -1.3659 0.2196 -1.4554 0.2034 -1.5449 0.1876 -1.6344 0.1723 -1.7239 0.1574 -1.8135 0.1432 -1.9030 0.1296 -1.9925 0.1168 -2.0820 0.1048 -2.1715 0.0936 -2.2610 0.0832 -2.3505 0.0736 -2.4400 0.0648 -2.5295 0.0568 -2.6191 0.0495 -2.7086 0.0430 -2.7981 0.0372 -2.8876 0.0320 -2.9771 0.0274 -3.0666 0.0233 -3.1561 0.0198 -3.2456 0.0167 -3.3352 0.0141 -3.4247 0.0118 -3.5142 0.0098 -3.6037 0.0081 -3.6932 0.0067 -3.7827 0.0055 -3.8722 0.0045 -3.9617 0.0037 -4.0512 0.0030 -4.1408 0.0024 -4.2303 0.0019 -TraitA_T1 1 -250 150 -1 5 -2 9 10 --5.7657 0.0000 --5.6659 0.0000 --5.5661 0.0000 --5.4664 0.0001 --5.3666 0.0001 --5.2669 0.0001 --5.1671 0.0002 --5.0673 0.0002 --4.9676 0.0003 --4.8678 0.0004 --4.7681 0.0005 --4.6683 0.0007 --4.5685 0.0009 --4.4688 0.0011 --4.3690 0.0015 --4.2693 0.0019 --4.1695 0.0024 --4.0697 0.0030 --3.9700 0.0039 --3.8702 0.0048 --3.7705 0.0060 --3.6707 0.0075 --3.5709 0.0093 --3.4712 0.0114 --3.3714 0.0139 --3.2717 0.0168 --3.1719 0.0203 --3.0721 0.0243 --2.9724 0.0290 --2.8726 0.0344 --2.7729 0.0406 --2.6731 0.0475 --2.5733 0.0554 --2.4736 0.0642 --2.3738 0.0740 --2.2741 0.0848 --2.1743 0.0965 --2.0745 0.1093 --1.9748 0.1231 --1.8750 0.1378 --1.7753 0.1534 --1.6755 0.1698 --1.5757 0.1869 --1.4760 0.2044 --1.3762 0.2224 --1.2765 0.2406 --1.1767 0.2587 --1.0769 0.2767 --0.9772 0.2941 --0.8774 0.3109 --0.7776 0.3268 --0.6779 0.3415 --0.5781 0.3548 --0.4784 0.3666 --0.3786 0.3765 --0.2788 0.3845 --0.1791 0.3905 --0.0793 0.3942 -0.0204 0.3957 -0.1202 0.3950 -0.2200 0.3920 -0.3197 0.3868 -0.4195 0.3794 -0.5192 0.3701 -0.6190 0.3590 -0.7188 0.3461 -0.8185 0.3319 -0.9183 0.3164 -1.0180 0.2999 -1.1178 0.2826 -1.2176 0.2648 -1.3173 0.2467 -1.4171 0.2285 -1.5168 0.2105 -1.6166 0.1927 -1.7164 0.1755 -1.8161 0.1588 -1.9159 0.1430 -2.0156 0.1280 -2.1154 0.1139 -2.2152 0.1007 -2.3149 0.0886 -2.4147 0.0775 -2.5144 0.0674 -2.6142 0.0583 -2.7140 0.0501 -2.8137 0.0428 -2.9135 0.0364 -3.0132 0.0307 -3.1130 0.0258 -3.2128 0.0216 -3.3125 0.0179 -3.4123 0.0148 -3.5120 0.0122 -3.6118 0.0099 -3.7116 0.0081 -3.8113 0.0065 -3.9111 0.0052 -4.0108 0.0042 -4.1106 0.0033 -4.2104 0.0026 -TraitB_T2 1 -250 150 -2 5 8 -1 10 --3.7882 0.0006 --3.7109 0.0008 --3.6337 0.0010 --3.5564 0.0013 --3.4791 0.0017 --3.4019 0.0021 --3.3246 0.0027 --3.2473 0.0034 --3.1700 0.0043 --3.0928 0.0053 --3.0155 0.0066 --2.9382 0.0081 --2.8610 0.0100 --2.7837 0.0122 --2.7064 0.0148 --2.6292 0.0178 --2.5519 0.0214 --2.4746 0.0255 --2.3974 0.0302 --2.3201 0.0357 --2.2428 0.0419 --2.1656 0.0489 --2.0883 0.0568 --2.0110 0.0655 --1.9338 0.0752 --1.8565 0.0858 --1.7792 0.0975 --1.7020 0.1100 --1.6247 0.1235 --1.5474 0.1379 --1.4702 0.1532 --1.3929 0.1692 --1.3156 0.1858 --1.2384 0.2029 --1.1611 0.2204 --1.0838 0.2381 --1.0065 0.2557 --0.9293 0.2732 --0.8520 0.2902 --0.7747 0.3066 --0.6975 0.3222 --0.6202 0.3366 --0.5429 0.3498 --0.4657 0.3615 --0.3884 0.3715 --0.3111 0.3797 --0.2339 0.3859 --0.1566 0.3901 --0.0793 0.3921 --0.0021 0.3920 -0.0752 0.3897 -0.1525 0.3853 -0.2297 0.3788 -0.3070 0.3704 -0.3843 0.3602 -0.4615 0.3483 -0.5388 0.3350 -0.6161 0.3204 -0.6933 0.3047 -0.7706 0.2882 -0.8479 0.2711 -0.9251 0.2536 -1.0024 0.2359 -1.0797 0.2183 -1.1569 0.2008 -1.2342 0.1838 -1.3115 0.1672 -1.3888 0.1513 -1.4660 0.1362 -1.5433 0.1219 -1.6206 0.1085 -1.6978 0.0960 -1.7751 0.0845 -1.8524 0.0740 -1.9296 0.0644 -2.0069 0.0558 -2.0842 0.0480 -2.1614 0.0411 -2.2387 0.0350 -2.3160 0.0296 -2.3932 0.0250 -2.4705 0.0209 -2.5478 0.0174 -2.6250 0.0144 -2.7023 0.0119 -2.7796 0.0097 -2.8568 0.0079 -2.9341 0.0064 -3.0114 0.0052 -3.0886 0.0041 -3.1659 0.0033 -3.2432 0.0026 -3.3204 0.0021 -3.3977 0.0016 -3.4750 0.0013 -3.5523 0.0010 -3.6295 0.0008 -3.7068 0.0006 -3.7841 0.0004 -3.8613 0.0003 -3.9386 0.0003 -TraitC_T3 1 -250 150 -2 8 9 -0 --4.7490 0.0000 --4.6626 0.0000 --4.5763 0.0000 --4.4899 0.0000 --4.4036 0.0000 --4.3172 0.0001 --4.2309 0.0001 --4.1445 0.0001 --4.0582 0.0002 --3.9718 0.0002 --3.8855 0.0003 --3.7991 0.0005 --3.7127 0.0006 --3.6264 0.0008 --3.5400 0.0011 --3.4537 0.0015 --3.3673 0.0019 --3.2810 0.0025 --3.1946 0.0033 --3.1083 0.0042 --3.0219 0.0054 --2.9356 0.0069 --2.8492 0.0087 --2.7629 0.0109 --2.6765 0.0135 --2.5901 0.0167 --2.5038 0.0205 --2.4174 0.0250 --2.3311 0.0303 --2.2447 0.0364 --2.1584 0.0435 --2.0720 0.0516 --1.9857 0.0608 --1.8993 0.0711 --1.8130 0.0826 --1.7266 0.0953 --1.6403 0.1091 --1.5539 0.1242 --1.4675 0.1403 --1.3812 0.1575 --1.2948 0.1755 --1.2085 0.1943 --1.1221 0.2136 --1.0358 0.2331 --0.9494 0.2527 --0.8631 0.2721 --0.7767 0.2910 --0.6904 0.3090 --0.6040 0.3259 --0.5177 0.3413 --0.4313 0.3550 --0.3449 0.3667 --0.2586 0.3762 --0.1722 0.3833 --0.0859 0.3878 -0.0005 0.3897 -0.0868 0.3889 -0.1732 0.3854 -0.2595 0.3793 -0.3459 0.3708 -0.4322 0.3599 -0.5186 0.3470 -0.6049 0.3322 -0.6913 0.3159 -0.7777 0.2983 -0.8640 0.2797 -0.9504 0.2605 -1.0367 0.2410 -1.1231 0.2214 -1.2094 0.2019 -1.2958 0.1829 -1.3821 0.1646 -1.4685 0.1471 -1.5548 0.1305 -1.6412 0.1150 -1.7275 0.1007 -1.8139 0.0875 -1.9003 0.0755 -1.9866 0.0648 -2.0730 0.0551 -2.1593 0.0466 -2.2457 0.0391 -2.3320 0.0326 -2.4184 0.0270 -2.5047 0.0222 -2.5911 0.0182 -2.6774 0.0147 -2.7638 0.0119 -2.8501 0.0095 -2.9365 0.0075 -3.0229 0.0060 -3.1092 0.0047 -3.1956 0.0036 -3.2819 0.0028 -3.3683 0.0022 -3.4546 0.0016 -3.5410 0.0012 -3.6273 0.0009 -3.7137 0.0007 -3.8000 0.0005 -3.8864 0.0004 diff --git a/sourcecodes/data/example_time_series/TEbnet_figure_new.txt b/sourcecodes/data/example_time_series/TEbnet_figure_new.txt deleted file mode 100644 index 4dd4fcc9..00000000 --- a/sourcecodes/data/example_time_series/TEbnet_figure_new.txt +++ /dev/null @@ -1,864 +0,0 @@ -8 -10 -1500 1200 -TraitC_T2 0 0 -TraitC_T1 250 0 -TraitB_T3 500 0 -TraitB_T1 750 0 -Genotype 1000 0 -TraitA_T3 275 240 -TraitA_T2 650 240 -TraitA_T1 1025 240 -TraitB_T2 500 480 -TraitC_T3 650 720 -TraitC_T2 1 -250 150 -0 -0 --4.0699 0.0001 --3.9911 0.0002 --3.9123 0.0002 --3.8335 0.0003 --3.7548 0.0004 --3.6760 0.0005 --3.5972 0.0007 --3.5185 0.0009 --3.4397 0.0012 --3.3609 0.0015 --3.2821 0.0020 --3.2034 0.0025 --3.1246 0.0032 --3.0458 0.0041 --2.9670 0.0052 --2.8883 0.0065 --2.8095 0.0081 --2.7307 0.0101 --2.6520 0.0124 --2.5732 0.0152 --2.4944 0.0185 --2.4156 0.0224 --2.3369 0.0269 --2.2581 0.0322 --2.1793 0.0382 --2.1006 0.0451 --2.0218 0.0529 --1.9430 0.0617 --1.8642 0.0716 --1.7855 0.0824 --1.7067 0.0944 --1.6279 0.1074 --1.5492 0.1215 --1.4704 0.1366 --1.3916 0.1526 --1.3128 0.1695 --1.2341 0.1871 --1.1553 0.2052 --1.0765 0.2238 --0.9978 0.2425 --0.9190 0.2612 --0.8402 0.2796 --0.7614 0.2975 --0.6827 0.3147 --0.6039 0.3308 --0.5251 0.3456 --0.4464 0.3588 --0.3676 0.3703 --0.2888 0.3799 --0.2100 0.3873 --0.1313 0.3924 --0.0525 0.3952 -0.0263 0.3956 -0.1050 0.3936 -0.1838 0.3892 -0.2626 0.3826 -0.3414 0.3737 -0.4201 0.3629 -0.4989 0.3502 -0.5777 0.3358 -0.6564 0.3202 -0.7352 0.3033 -0.8140 0.2857 -0.8928 0.2674 -0.9715 0.2487 -1.0503 0.2300 -1.1291 0.2114 -1.2078 0.1930 -1.2866 0.1753 -1.3654 0.1581 -1.4442 0.1418 -1.5229 0.1264 -1.6017 0.1120 -1.6805 0.0986 -1.7592 0.0863 -1.8380 0.0751 -1.9168 0.0649 -1.9956 0.0558 -2.0743 0.0476 -2.1531 0.0404 -2.2319 0.0341 -2.3106 0.0286 -2.3894 0.0238 -2.4682 0.0197 -2.5470 0.0163 -2.6257 0.0133 -2.7045 0.0108 -2.7833 0.0087 -2.8620 0.0070 -2.9408 0.0056 -3.0196 0.0045 -3.0984 0.0035 -3.1771 0.0028 -3.2559 0.0021 -3.3347 0.0017 -3.4134 0.0013 -3.4922 0.0010 -3.5710 0.0007 -3.6498 0.0006 -3.7285 0.0004 -3.8073 0.0003 -TraitC_T1 1 -250 150 -0 -0 --3.8413 0.0003 --3.7581 0.0004 --3.6749 0.0005 --3.5917 0.0007 --3.5086 0.0009 --3.4254 0.0012 --3.3422 0.0016 --3.2591 0.0021 --3.1759 0.0028 --3.0927 0.0036 --3.0095 0.0046 --2.9264 0.0059 --2.8432 0.0074 --2.7600 0.0093 --2.6768 0.0116 --2.5937 0.0144 --2.5105 0.0178 --2.4273 0.0218 --2.3441 0.0265 --2.2610 0.0320 --2.1778 0.0384 --2.0946 0.0457 --2.0114 0.0540 --1.9283 0.0635 --1.8451 0.0741 --1.7619 0.0859 --1.6787 0.0989 --1.5956 0.1131 --1.5124 0.1284 --1.4292 0.1448 --1.3460 0.1623 --1.2629 0.1806 --1.1797 0.1995 --1.0965 0.2190 --1.0133 0.2388 --0.9302 0.2585 --0.8470 0.2781 --0.7638 0.2970 --0.6806 0.3151 --0.5975 0.3320 --0.5143 0.3475 --0.4311 0.3612 --0.3479 0.3729 --0.2648 0.3824 --0.1816 0.3894 --0.0984 0.3939 --0.0152 0.3957 -0.0679 0.3949 -0.1511 0.3914 -0.2343 0.3852 -0.3174 0.3766 -0.4006 0.3657 -0.4838 0.3527 -0.5670 0.3379 -0.6501 0.3215 -0.7333 0.3038 -0.8165 0.2851 -0.8997 0.2657 -0.9828 0.2460 -1.0660 0.2262 -1.1492 0.2066 -1.2324 0.1874 -1.3155 0.1689 -1.3987 0.1511 -1.4819 0.1343 -1.5651 0.1186 -1.6482 0.1040 -1.7314 0.0905 -1.8146 0.0783 -1.8978 0.0673 -1.9809 0.0574 -2.0641 0.0486 -2.1473 0.0409 -2.2305 0.0342 -2.3136 0.0284 -2.3968 0.0234 -2.4800 0.0192 -2.5632 0.0156 -2.6463 0.0126 -2.7295 0.0101 -2.8127 0.0081 -2.8959 0.0064 -2.9790 0.0050 -3.0622 0.0039 -3.1454 0.0030 -3.2286 0.0023 -3.3117 0.0018 -3.3949 0.0014 -3.4781 0.0010 -3.5613 0.0008 -3.6444 0.0006 -3.7276 0.0004 -3.8108 0.0003 -3.8940 0.0002 -3.9771 0.0002 -4.0603 0.0001 -4.1435 0.0001 -4.2266 0.0001 -4.3098 0.0000 -4.3930 0.0000 -4.4762 0.0000 -TraitB_T3 1 -250 150 -0 -0 --3.8488 0.0003 --3.7734 0.0004 --3.6979 0.0005 --3.6224 0.0006 --3.5469 0.0008 --3.4714 0.0011 --3.3959 0.0014 --3.3205 0.0017 --3.2450 0.0022 --3.1695 0.0028 --3.0940 0.0036 --3.0185 0.0045 --2.9430 0.0056 --2.8676 0.0069 --2.7921 0.0085 --2.7166 0.0105 --2.6411 0.0128 --2.5656 0.0155 --2.4902 0.0187 --2.4147 0.0225 --2.3392 0.0268 --2.2637 0.0318 --2.1882 0.0375 --2.1127 0.0440 --2.0373 0.0513 --1.9618 0.0596 --1.8863 0.0687 --1.8108 0.0788 --1.7353 0.0899 --1.6598 0.1020 --1.5844 0.1151 --1.5089 0.1291 --1.4334 0.1440 --1.3579 0.1597 --1.2824 0.1762 --1.2070 0.1933 --1.1315 0.2108 --1.0560 0.2286 --0.9805 0.2466 --0.9050 0.2645 --0.8295 0.2821 --0.7541 0.2992 --0.6786 0.3155 --0.6031 0.3309 --0.5276 0.3451 --0.4521 0.3579 --0.3766 0.3691 --0.3012 0.3785 --0.2257 0.3860 --0.1502 0.3914 --0.0747 0.3947 -0.0008 0.3958 -0.0762 0.3946 -0.1517 0.3913 -0.2272 0.3858 -0.3027 0.3783 -0.3782 0.3689 -0.4537 0.3577 -0.5291 0.3448 -0.6046 0.3306 -0.6801 0.3152 -0.7556 0.2988 -0.8311 0.2817 -0.9066 0.2641 -0.9820 0.2462 -1.0575 0.2283 -1.1330 0.2104 -1.2085 0.1929 -1.2840 0.1758 -1.3595 0.1594 -1.4349 0.1437 -1.5104 0.1288 -1.5859 0.1148 -1.6614 0.1018 -1.7369 0.0897 -1.8123 0.0786 -1.8878 0.0685 -1.9633 0.0594 -2.0388 0.0512 -2.1143 0.0439 -2.1898 0.0374 -2.2652 0.0317 -2.3407 0.0267 -2.4162 0.0224 -2.4917 0.0186 -2.5672 0.0155 -2.6427 0.0127 -2.7181 0.0104 -2.7936 0.0085 -2.8691 0.0069 -2.9446 0.0056 -3.0201 0.0044 -3.0955 0.0035 -3.1710 0.0028 -3.2465 0.0022 -3.3220 0.0017 -3.3975 0.0014 -3.4730 0.0010 -3.5484 0.0008 -3.6239 0.0006 -3.6994 0.0005 -TraitB_T1 1 -250 150 -0 -0 --3.7153 0.0004 --3.6359 0.0006 --3.5565 0.0008 --3.4772 0.0010 --3.3978 0.0013 --3.3184 0.0018 --3.2390 0.0023 --3.1596 0.0029 --3.0802 0.0037 --3.0009 0.0047 --2.9215 0.0059 --2.8421 0.0074 --2.7627 0.0093 --2.6833 0.0114 --2.6039 0.0141 --2.5246 0.0172 --2.4452 0.0209 --2.3658 0.0252 --2.2864 0.0302 --2.2070 0.0360 --2.1277 0.0427 --2.0483 0.0502 --1.9689 0.0587 --1.8895 0.0683 --1.8101 0.0789 --1.7307 0.0906 --1.6514 0.1034 --1.5720 0.1173 --1.4926 0.1322 --1.4132 0.1481 --1.3338 0.1649 --1.2544 0.1824 --1.1751 0.2006 --1.0957 0.2192 --1.0163 0.2381 --0.9369 0.2570 --0.8575 0.2756 --0.7781 0.2938 --0.6988 0.3112 --0.6194 0.3277 --0.5400 0.3429 --0.4606 0.3565 --0.3812 0.3685 --0.3019 0.3784 --0.2225 0.3863 --0.1431 0.3918 --0.0637 0.3950 -0.0157 0.3957 -0.0951 0.3940 -0.1744 0.3899 -0.2538 0.3834 -0.3332 0.3747 -0.4126 0.3640 -0.4920 0.3513 -0.5714 0.3370 -0.6507 0.3213 -0.7301 0.3045 -0.8095 0.2867 -0.8889 0.2683 -0.9683 0.2495 -1.0477 0.2306 -1.1270 0.2118 -1.2064 0.1934 -1.2858 0.1754 -1.3652 0.1582 -1.4446 0.1417 -1.5239 0.1262 -1.6033 0.1117 -1.6827 0.0982 -1.7621 0.0859 -1.8415 0.0746 -1.9209 0.0644 -2.0002 0.0553 -2.0796 0.0471 -2.1590 0.0399 -2.2384 0.0336 -2.3178 0.0281 -2.3972 0.0234 -2.4765 0.0194 -2.5559 0.0159 -2.6353 0.0130 -2.7147 0.0105 -2.7941 0.0085 -2.8735 0.0068 -2.9528 0.0054 -3.0322 0.0043 -3.1116 0.0034 -3.1910 0.0026 -3.2704 0.0020 -3.3497 0.0016 -3.4291 0.0012 -3.5085 0.0009 -3.5879 0.0007 -3.6673 0.0005 -3.7467 0.0004 -3.8260 0.0003 -3.9054 0.0002 -3.9848 0.0002 -4.0642 0.0001 -4.1436 0.0001 -4.2230 0.0001 -Genotype 2 -250 150 -0 -4 6 7 8 9 -1 0.9800 -2 0.0200 -TraitA_T3 1 -250 150 -1 5 -0 --3.6094 0.0000 --3.5392 0.0000 --3.4689 0.0000 --3.3987 0.0000 --3.3285 0.0000 --3.2582 0.0000 --3.1880 0.0000 --3.1177 0.0000 --3.0475 0.0001 --2.9773 0.0001 --2.9070 0.0002 --2.8368 0.0003 --2.7665 0.0004 --2.6963 0.0007 --2.6261 0.0012 --2.5558 0.0019 --2.4856 0.0029 --2.4154 0.0044 --2.3451 0.0067 --2.2749 0.0100 --2.2046 0.0145 --2.1344 0.0208 --2.0642 0.0293 --1.9939 0.0405 --1.9237 0.0552 --1.8534 0.0738 --1.7832 0.0970 --1.7130 0.1254 --1.6427 0.1592 --1.5725 0.1988 --1.5022 0.2440 --1.4320 0.2943 --1.3618 0.3489 --1.2915 0.4067 --1.2213 0.4658 --1.1510 0.5245 --1.0808 0.5805 --1.0106 0.6315 --0.9403 0.6752 --0.8701 0.7097 --0.7999 0.7331 --0.7296 0.7444 --0.6594 0.7430 --0.5891 0.7289 --0.5189 0.7029 --0.4487 0.6662 --0.3784 0.6206 --0.3082 0.5683 --0.2379 0.5116 --0.1677 0.4526 --0.0975 0.3936 --0.0272 0.3364 -0.0430 0.2827 -0.1133 0.2334 -0.1835 0.1895 -0.2537 0.1512 -0.3240 0.1186 -0.3942 0.0914 -0.4645 0.0692 -0.5347 0.0516 -0.6049 0.0378 -0.6752 0.0272 -0.7454 0.0192 -0.8156 0.0134 -0.8859 0.0091 -0.9561 0.0061 -1.0264 0.0040 -1.0966 0.0026 -1.1668 0.0017 -1.2371 0.0010 -1.3073 0.0006 -1.3776 0.0004 -1.4478 0.0002 -1.5180 0.0001 -1.5883 0.0001 -1.6585 0.0000 -1.7288 0.0000 -1.7990 0.0000 -1.8692 0.0000 -1.9395 0.0000 -2.0097 0.0000 -2.0799 0.0000 -2.1502 0.0000 -2.2204 0.0000 -2.2907 0.0000 -2.3609 0.0000 -2.4311 0.0000 -2.5014 0.0000 -2.5716 0.0000 -2.6419 0.0000 -2.7121 0.0000 -2.7823 0.0000 -2.8526 0.0000 -2.9228 0.0000 -2.9931 0.0000 -3.0633 0.0000 -3.1335 0.0000 -3.2038 0.0000 -3.2740 0.0000 -3.3443 0.0000 -3.4145 0.0000 -TraitA_T2 1 -250 150 -1 5 -0 --3.5730 0.0000 --3.5043 0.0000 --3.4357 0.0000 --3.3670 0.0000 --3.2984 0.0000 --3.2298 0.0000 --3.1611 0.0000 --3.0925 0.0000 --3.0239 0.0000 --2.9552 0.0000 --2.8866 0.0001 --2.8180 0.0001 --2.7493 0.0002 --2.6807 0.0003 --2.6121 0.0005 --2.5434 0.0009 --2.4748 0.0015 --2.4062 0.0024 --2.3375 0.0037 --2.2689 0.0058 --2.2003 0.0087 --2.1316 0.0130 --2.0630 0.0190 --1.9943 0.0273 --1.9257 0.0384 --1.8571 0.0532 --1.7884 0.0722 --1.7198 0.0963 --1.6512 0.1260 --1.5825 0.1620 --1.5139 0.2043 --1.4453 0.2531 --1.3766 0.3078 --1.3080 0.3674 --1.2394 0.4305 --1.1707 0.4954 --1.1021 0.5595 --1.0335 0.6205 --0.9648 0.6755 --0.8962 0.7219 --0.8276 0.7575 --0.7589 0.7803 --0.6903 0.7891 --0.6216 0.7834 --0.5530 0.7635 --0.4844 0.7306 --0.4157 0.6863 --0.3471 0.6330 --0.2785 0.5731 --0.2098 0.5094 --0.1412 0.4445 --0.0726 0.3808 --0.0039 0.3203 -0.0647 0.2644 -0.1333 0.2144 -0.2020 0.1706 -0.2706 0.1333 -0.3392 0.1022 -0.4079 0.0770 -0.4765 0.0569 -0.5451 0.0413 -0.6138 0.0294 -0.6824 0.0206 -0.7511 0.0141 -0.8197 0.0095 -0.8883 0.0063 -0.9570 0.0041 -1.0256 0.0026 -1.0942 0.0016 -1.1629 0.0010 -1.2315 0.0006 -1.3001 0.0004 -1.3688 0.0002 -1.4374 0.0001 -1.5060 0.0001 -1.5747 0.0000 -1.6433 0.0000 -1.7119 0.0000 -1.7806 0.0000 -1.8492 0.0000 -1.9178 0.0000 -1.9865 0.0000 -2.0551 0.0000 -2.1238 0.0000 -2.1924 0.0000 -2.2610 0.0000 -2.3297 0.0000 -2.3983 0.0000 -2.4669 0.0000 -2.5356 0.0000 -2.6042 0.0000 -2.6728 0.0000 -2.7415 0.0000 -2.8101 0.0000 -2.8787 0.0000 -2.9474 0.0000 -3.0160 0.0000 -3.0846 0.0000 -3.1533 0.0000 -3.2219 0.0000 -3.2905 0.0000 -TraitA_T1 1 -250 150 -1 5 -2 9 10 -1.5029 1.0000 -TraitB_T2 1 -250 150 -2 5 8 -1 10 --3.6634 0.0000 --3.5878 0.0000 --3.5122 0.0000 --3.4365 0.0000 --3.3609 0.0000 --3.2853 0.0000 --3.2097 0.0000 --3.1340 0.0000 --3.0584 0.0000 --2.9828 0.0000 --2.9072 0.0000 --2.8315 0.0000 --2.7559 0.0000 --2.6803 0.0000 --2.6046 0.0000 --2.5290 0.0000 --2.4534 0.0000 --2.3778 0.0000 --2.3021 0.0001 --2.2265 0.0001 --2.1509 0.0002 --2.0753 0.0003 --1.9996 0.0005 --1.9240 0.0007 --1.8484 0.0011 --1.7727 0.0016 --1.6971 0.0024 --1.6215 0.0035 --1.5459 0.0050 --1.4702 0.0071 --1.3946 0.0099 --1.3190 0.0136 --1.2434 0.0185 --1.1677 0.0249 --1.0921 0.0330 --1.0165 0.0432 --0.9408 0.0558 --0.8652 0.0712 --0.7896 0.0896 --0.7140 0.1112 --0.6383 0.1364 --0.5627 0.1650 --0.4871 0.1971 --0.4115 0.2323 --0.3358 0.2702 --0.2602 0.3103 --0.1846 0.3517 --0.1089 0.3935 --0.0333 0.4345 -0.0423 0.4735 -0.1179 0.5094 -0.1936 0.5408 -0.2692 0.5667 -0.3448 0.5862 -0.4205 0.5985 -0.4961 0.6030 -0.5717 0.5998 -0.6473 0.5888 -0.7230 0.5704 -0.7986 0.5455 -0.8742 0.5149 -0.9498 0.4797 -1.0255 0.4411 -1.1011 0.4004 -1.1767 0.3587 -1.2524 0.3171 -1.3280 0.2768 -1.4036 0.2384 -1.4792 0.2027 -1.5549 0.1701 -1.6305 0.1409 -1.7061 0.1152 -1.7817 0.0929 -1.8574 0.0740 -1.9330 0.0582 -2.0086 0.0451 -2.0843 0.0346 -2.1599 0.0261 -2.2355 0.0195 -2.3111 0.0144 -2.3868 0.0104 -2.4624 0.0075 -2.5380 0.0053 -2.6136 0.0037 -2.6893 0.0026 -2.7649 0.0017 -2.8405 0.0012 -2.9162 0.0008 -2.9918 0.0005 -3.0674 0.0003 -3.1430 0.0002 -3.2187 0.0001 -3.2943 0.0001 -3.3699 0.0001 -3.4455 0.0000 -3.5212 0.0000 -3.5968 0.0000 -3.6724 0.0000 -3.7481 0.0000 -3.8237 0.0000 -3.8993 0.0000 -TraitC_T3 1 -250 150 -2 8 9 -0 --4.6954 0.0000 --4.6103 0.0000 --4.5253 0.0000 --4.4402 0.0000 --4.3551 0.0000 --4.2701 0.0000 --4.1850 0.0000 --4.1000 0.0000 --4.0149 0.0000 --3.9298 0.0000 --3.8448 0.0000 --3.7597 0.0000 --3.6746 0.0000 --3.5896 0.0000 --3.5045 0.0000 --3.4195 0.0000 --3.3344 0.0000 --3.2493 0.0000 --3.1643 0.0000 --3.0792 0.0000 --2.9942 0.0000 --2.9091 0.0000 --2.8240 0.0000 --2.7390 0.0000 --2.6539 0.0000 --2.5688 0.0000 --2.4838 0.0000 --2.3987 0.0000 --2.3137 0.0000 --2.2286 0.0000 --2.1435 0.0000 --2.0585 0.0000 --1.9734 0.0000 --1.8884 0.0000 --1.8033 0.0000 --1.7182 0.0000 --1.6332 0.0000 --1.5481 0.0000 --1.4630 0.0000 --1.3780 0.0000 --1.2929 0.0000 --1.2079 0.0000 --1.1228 0.0000 --1.0377 0.0000 --0.9527 0.0000 --0.8676 0.0000 --0.7825 0.0001 --0.6975 0.0001 --0.6124 0.0003 --0.5274 0.0006 --0.4423 0.0013 --0.3572 0.0026 --0.2722 0.0049 --0.1871 0.0090 --0.1021 0.0158 --0.0170 0.0268 -0.0681 0.0438 -0.1531 0.0690 -0.2382 0.1047 -0.3233 0.1533 -0.4083 0.2161 -0.4934 0.2937 -0.5784 0.3846 -0.6635 0.4853 -0.7486 0.5902 -0.8336 0.6917 -0.9187 0.7812 -1.0038 0.8502 -1.0888 0.8917 -1.1739 0.9013 -1.2589 0.8779 -1.3440 0.8241 -1.4291 0.7455 -1.5141 0.6498 -1.5992 0.5459 -1.6842 0.4419 -1.7693 0.3448 -1.8544 0.2592 -1.9394 0.1878 -2.0245 0.1311 -2.1096 0.0882 -2.1946 0.0572 -2.2797 0.0358 -2.3647 0.0215 -2.4498 0.0125 -2.5349 0.0070 -2.6199 0.0038 -2.7050 0.0020 -2.7900 0.0010 -2.8751 0.0005 -2.9602 0.0002 -3.0452 0.0001 -3.1303 0.0000 -3.2154 0.0000 -3.3004 0.0000 -3.3855 0.0000 -3.4705 0.0000 -3.5556 0.0000 -3.6407 0.0000 -3.7257 0.0000 -3.8108 0.0000 diff --git a/sourcecodes/data/example_time_series/TEbnlevels.txt b/sourcecodes/data/example_time_series/TEbnlevels.txt deleted file mode 100644 index 714e56bd..00000000 --- a/sourcecodes/data/example_time_series/TEbnlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype 1 2 - diff --git a/sourcecodes/data/example_time_series/TEbnnode.txt b/sourcecodes/data/example_time_series/TEbnnode.txt deleted file mode 100644 index f599e28b..00000000 --- a/sourcecodes/data/example_time_series/TEbnnode.txt +++ /dev/null @@ -1 +0,0 @@ -10 diff --git a/sourcecodes/data/example_time_series/TEbnrows.txt b/sourcecodes/data/example_time_series/TEbnrows.txt deleted file mode 100644 index c15fb720..00000000 --- a/sourcecodes/data/example_time_series/TEbnrows.txt +++ /dev/null @@ -1 +0,0 @@ -501 diff --git a/sourcecodes/data/example_time_series/TEbparameters.txt b/sourcecodes/data/example_time_series/TEbparameters.txt deleted file mode 100644 index 14ddb1ac..00000000 --- a/sourcecodes/data/example_time_series/TEbparameters.txt +++ /dev/null @@ -1,41 +0,0 @@ -Genotype -Discrete node with 2 states -1 0.5380 -2 0.4620 - -TraitA_T1 -Continuous node -0.0372 1.3165 - -TraitA_T2 -Continuous node --0.0611 1.3146 - -TraitA_T3 -Continuous node --0.0834 1.1837 - -TraitB_T1 -Continuous node --0.0563 0.9366 - -TraitB_T2 -Continuous node --0.0453 1.0389 - -TraitB_T3 -Continuous node -0.0122 0.9485 - -TraitC_T1 -Continuous node --0.0016 0.9150 - -TraitC_T2 -Continuous node -0.0917 0.9311 - -TraitC_T3 -Continuous node -0.0177 1.0392 - diff --git a/sourcecodes/data/example_time_series/TEbparent.txt b/sourcecodes/data/example_time_series/TEbparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example_time_series/TEbparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example_time_series/TEbstructure_old.txt b/sourcecodes/data/example_time_series/TEbstructure_old.txt deleted file mode 100644 index 2d164e66..00000000 --- a/sourcecodes/data/example_time_series/TEbstructure_old.txt +++ /dev/null @@ -1,6 +0,0 @@ -Genotype 0.5380 0.4620 -TraitA_T1 0.0000 0.0000 0.0000 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0005 0.0007 0.0009 0.0011 0.0015 0.0019 0.0024 0.0030 0.0039 0.0048 0.0060 0.0075 0.0093 0.0114 0.0139 0.0168 0.0203 0.0243 0.0290 0.0344 0.0406 0.0475 0.0554 0.0642 0.0740 0.0848 0.0965 0.1093 0.1231 0.1378 0.1534 0.1698 0.1869 0.2044 0.2224 0.2406 0.2587 0.2767 0.2941 0.3109 0.3268 0.3415 0.3548 0.3666 0.3765 0.3845 0.3905 0.3942 0.3957 0.3950 0.3920 0.3868 0.3794 0.3701 0.3590 0.3461 0.3319 0.3164 0.2999 0.2826 0.2648 0.2467 0.2285 0.2105 0.1927 0.1755 0.1588 0.1430 0.1280 0.1139 0.1007 0.0886 0.0775 0.0674 0.0583 0.0501 0.0428 0.0364 0.0307 0.0258 0.0216 0.0179 0.0148 0.0122 0.0099 0.0081 0.0065 0.0052 0.0042 0.0033 0.0026 -TraitA_T2 0.0007 0.0009 0.0012 0.0015 0.0019 0.0023 0.0029 0.0036 0.0044 0.0054 0.0066 0.0079 0.0096 0.0115 0.0138 0.0164 0.0194 0.0229 0.0269 0.0314 0.0365 0.0423 0.0487 0.0559 0.0638 0.0725 0.0820 0.0923 0.1035 0.1154 0.1281 0.1416 0.1558 0.1705 0.1859 0.2016 0.2177 0.2340 0.2503 0.2666 0.2825 0.2981 0.3131 0.3272 0.3405 0.3526 0.3635 0.3730 0.3810 0.3873 0.3919 0.3948 0.3958 0.3950 0.3923 0.3879 0.3818 0.3740 0.3647 0.3539 0.3419 0.3288 0.3147 0.2998 0.2844 0.2684 0.2522 0.2359 0.2196 0.2034 0.1876 0.1723 0.1574 0.1432 0.1296 0.1168 0.1048 0.0936 0.0832 0.0736 0.0648 0.0568 0.0495 0.0430 0.0372 0.0320 0.0274 0.0233 0.0198 0.0167 0.0141 0.0118 0.0098 0.0081 0.0067 0.0055 0.0045 0.0037 0.0030 0.0024 0.0019 -TraitA_T3 0.0007 0.0008 0.0011 0.0013 0.0017 0.0021 0.0027 0.0033 0.0041 0.0050 0.0062 0.0075 0.0092 0.0111 0.0133 0.0159 0.0189 0.0224 0.0264 0.0310 0.0362 0.0421 0.0486 0.0559 0.0641 0.0730 0.0828 0.0934 0.1049 0.1172 0.1304 0.1443 0.1589 0.1742 0.1900 0.2062 0.2227 0.2394 0.2561 0.2727 0.2889 0.3046 0.3195 0.3336 0.3467 0.3585 0.3688 0.3777 0.3849 0.3903 0.3939 0.3956 0.3954 0.3933 0.3893 0.3834 0.3759 0.3666 0.3559 0.3438 0.3306 0.3162 0.3011 0.2853 0.2690 0.2524 0.2357 0.2190 0.2025 0.1864 0.1707 0.1556 0.1411 0.1273 0.1144 0.1022 0.0909 0.0805 0.0709 0.0622 0.0542 0.0471 0.0407 0.0350 0.0299 0.0255 0.0216 0.0182 0.0153 0.0128 0.0106 0.0088 0.0072 0.0059 0.0048 0.0039 0.0032 0.0025 0.0020 0.0016 0.0013 -TraitB_T2 0.0006 0.0008 0.0010 0.0013 0.0017 0.0021 0.0027 0.0034 0.0043 0.0053 0.0066 0.0081 0.0100 0.0122 0.0148 0.0178 0.0214 0.0255 0.0302 0.0357 0.0419 0.0489 0.0568 0.0655 0.0752 0.0858 0.0975 0.1100 0.1235 0.1379 0.1532 0.1692 0.1858 0.2029 0.2204 0.2381 0.2557 0.2732 0.2902 0.3066 0.3222 0.3366 0.3498 0.3615 0.3715 0.3797 0.3859 0.3901 0.3921 0.3920 0.3897 0.3853 0.3788 0.3704 0.3602 0.3483 0.3350 0.3204 0.3047 0.2882 0.2711 0.2536 0.2359 0.2183 0.2008 0.1838 0.1672 0.1513 0.1362 0.1219 0.1085 0.0960 0.0845 0.0740 0.0644 0.0558 0.0480 0.0411 0.0350 0.0296 0.0250 0.0209 0.0174 0.0144 0.0119 0.0097 0.0079 0.0064 0.0052 0.0041 0.0033 0.0026 0.0021 0.0016 0.0013 0.0010 0.0008 0.0006 0.0004 0.0003 0.0003 -TraitC_T3 0.0000 0.0000 0.0000 0.0000 0.0000 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0005 0.0006 0.0008 0.0011 0.0015 0.0019 0.0025 0.0033 0.0042 0.0054 0.0069 0.0087 0.0109 0.0135 0.0167 0.0205 0.0250 0.0303 0.0364 0.0435 0.0516 0.0608 0.0711 0.0826 0.0953 0.1091 0.1242 0.1403 0.1575 0.1755 0.1943 0.2136 0.2331 0.2527 0.2721 0.2910 0.3090 0.3259 0.3413 0.3550 0.3667 0.3762 0.3833 0.3878 0.3897 0.3889 0.3854 0.3793 0.3708 0.3599 0.3470 0.3322 0.3159 0.2983 0.2797 0.2605 0.2410 0.2214 0.2019 0.1829 0.1646 0.1471 0.1305 0.1150 0.1007 0.0875 0.0755 0.0648 0.0551 0.0466 0.0391 0.0326 0.0270 0.0222 0.0182 0.0147 0.0119 0.0095 0.0075 0.0060 0.0047 0.0036 0.0028 0.0022 0.0016 0.0012 0.0009 0.0007 0.0005 0.0004 diff --git a/sourcecodes/data/example_time_series/TEbthr.txt b/sourcecodes/data/example_time_series/TEbthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example_time_series/TEbthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example_time_series/TEbtier.txt b/sourcecodes/data/example_time_series/TEbtier.txt deleted file mode 100644 index 29aafcbe..00000000 --- a/sourcecodes/data/example_time_series/TEbtier.txt +++ /dev/null @@ -1 +0,0 @@ -4,Tier1,1,Genotype,Tier2,3,TraitA_T1,TraitB_T1,TraitC_T1,Tier3,3,TraitA_T2,TraitB_T2,TraitC_T2,Tier4,3,TraitA_T3,TraitB_T3,TraitC_T3, \ No newline at end of file diff --git a/sourcecodes/data/example_time_series/TEbtype.txt b/sourcecodes/data/example_time_series/TEbtype.txt deleted file mode 100644 index e4d7d174..00000000 --- a/sourcecodes/data/example_time_series/TEbtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype TraitA_T1 TraitA_T2 TraitA_T3 TraitB_T1 TraitB_T2 TraitB_T3 TraitC_T1 TraitC_T2 TraitC_T3 -2 1 1 1 1 1 1 1 1 1 diff --git a/sourcecodes/data/example_time_series/TEbvar.txt b/sourcecodes/data/example_time_series/TEbvar.txt deleted file mode 100644 index 301160a9..00000000 --- a/sourcecodes/data/example_time_series/TEbvar.txt +++ /dev/null @@ -1 +0,0 @@ -8 \ No newline at end of file diff --git a/sourcecodes/data/example_time_series/TEbvardata.txt b/sourcecodes/data/example_time_series/TEbvardata.txt deleted file mode 100644 index f36841a7..00000000 --- a/sourcecodes/data/example_time_series/TEbvardata.txt +++ /dev/null @@ -1 +0,0 @@ -1.5028501775188 \ No newline at end of file diff --git a/sourcecodes/data/example_time_series/TEbvarname.txt b/sourcecodes/data/example_time_series/TEbvarname.txt deleted file mode 100644 index aa23daa0..00000000 --- a/sourcecodes/data/example_time_series/TEbvarname.txt +++ /dev/null @@ -1 +0,0 @@ -TraitA_T1 \ No newline at end of file diff --git a/sourcecodes/data/example_time_series/TEbwhite.txt b/sourcecodes/data/example_time_series/TEbwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example_time_series/TEbwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example_time_series/old/TEbrun_evidencemodified.sh b/sourcecodes/data/example_time_series/old/TEbrun_evidencemodified.sh deleted file mode 100644 index ff2eafcd..00000000 --- a/sourcecodes/data/example_time_series/old/TEbrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified TEb -fi -exit diff --git a/sourcecodes/data/example_time_series/old/TEbrun_initialstructure.sh b/sourcecodes/data/example_time_series/old/TEbrun_initialstructure.sh deleted file mode 100644 index 3417deda..00000000 --- a/sourcecodes/data/example_time_series/old/TEbrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure TEb -fi -exit diff --git a/sourcecodes/data/examplecar15node/MtXcontinuous_input.txt b/sourcecodes/data/examplecar15node/MtXcontinuous_input.txt deleted file mode 100644 index 0d55f02c..00000000 --- a/sourcecodes/data/examplecar15node/MtXcontinuous_input.txt +++ /dev/null @@ -1,1005 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor -3 2 3 3 2 3 2 3 2 2 3 3 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 1 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 2 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 2 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1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 1 1 2 2 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 3 2 2 3 1 1 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 2 1 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 2 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 2 2 1 2 1 1 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 1 2 1 2 3 1 2 2 2 2 2 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 2 2 1 2 3 1 2 2 2 2 2 2 2 2 -1 2 2 1 2 3 1 3 2 2 3 2 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 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2 3 1 1 2 1 1 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 3 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 2 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 3 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 3 2 2 3 1 1 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 1 2 2 2 2 3 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 2 2 2 3 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 1 2 2 2 2 2 2 2 2 -1 2 3 1 2 3 1 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 2 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 1 1 2 3 1 1 2 1 1 1 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 1 2 2 2 2 3 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -3 1 2 2 2 2 1 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 2 2 1 2 2 2 -2 2 3 2 2 3 2 3 2 2 3 2 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 2 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 2 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -2 2 2 1 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 3 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 - - - diff --git a/sourcecodes/data/examplecar15node/MtXgraphviz.txt b/sourcecodes/data/examplecar15node/MtXgraphviz.txt deleted file mode 100644 index 56dcd027..00000000 --- a/sourcecodes/data/examplecar15node/MtXgraphviz.txt +++ /dev/null @@ -1,20 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Voltage_at_plug -> Spark_quality; -Car_cranks -> Car_starts; -Spark_plugs -> Spark_quality; -Spark_quality -> Car_starts; -Distributer -> Voltage_at_plug; -Distributer -> Spark_timing; -Spark_timing -> Car_starts; -Alternator -> Charging_system; -Charging_system -> Battery_voltage; -Battery_voltage -> Voltage_at_plug; -Battery_voltage -> Headlights; -Battery_age -> Battery_voltage; -Main_fuse -> Voltage_at_plug; -Main_fuse -> Starter_system; -Starter_system -> Car_cranks; -Starter_motor -> Starter_system; -} \ No newline at end of file diff --git a/sourcecodes/data/examplecar15node/MtXmap.txt b/sourcecodes/data/examplecar15node/MtXmap.txt deleted file mode 100644 index 8099a6e7..00000000 --- a/sourcecodes/data/examplecar15node/MtXmap.txt +++ /dev/null @@ -1,15 +0,0 @@ -Voltage_at_plug 0.827795 2.021000 -Car_cranks 0.500234 1.504000 -Spark_plugs 0.820310 2.042000 -Spark_quality 0.816376 2.014000 -Distributer 0.500241 1.497000 -Spark_timing 0.810222 2.014000 -Car_starts 0.500054 1.486000 -Headlights 0.810946 2.032000 -Alternator 0.500214 1.494000 -Charging_system 0.500234 1.496000 -Battery_voltage 0.806400 2.037000 -Battery_age 0.561294 1.708000 -Main_fuse 0.500150 1.490000 -Starter_system 0.499674 1.476000 -Starter_motor 0.500201 1.493000 diff --git a/sourcecodes/data/examplecar15node/MtXmapdata.txt b/sourcecodes/data/examplecar15node/MtXmapdata.txt deleted file mode 100644 index 67939bd1..00000000 --- a/sourcecodes/data/examplecar15node/MtXmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Starter_motor Main_fuse Starter_system Car_cranks Battery_age Alternator Charging_system Battery_voltage Headlights Distributer Spark_timing Voltage_at_plug Spark_plugs Spark_quality Car_starts diff --git a/sourcecodes/data/examplecar15node/MtXname.txt b/sourcecodes/data/examplecar15node/MtXname.txt deleted file mode 100644 index 2957eff7..00000000 --- a/sourcecodes/data/examplecar15node/MtXname.txt +++ /dev/null @@ -1 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor diff --git a/sourcecodes/data/examplecar15node/MtXnet_figure.txt b/sourcecodes/data/examplecar15node/MtXnet_figure.txt deleted file mode 100644 index 5a5a3bb9..00000000 --- a/sourcecodes/data/examplecar15node/MtXnet_figure.txt +++ /dev/null @@ -1,114 +0,0 @@ -15 -1800 1200 -Starter_motor 0 0 -Main_fuse 257 0 -Starter_system 373 171 -Car_cranks 343 343 -Battery_age 514 0 -Alternator 771 0 -Charging_system 823 171 -Battery_voltage 943 343 -Headlights 523 514 -Distributer 1029 0 -Spark_timing 1273 171 -Voltage_at_plug 1123 514 -Spark_plugs 1286 0 -Spark_quality 643 686 -Car_starts 823 857 -Starter_motor 2 -250 150 -0 -1 3 -1 0.5070 -2 0.4930 -Main_fuse 2 -250 150 -0 -2 3 12 -1 0.5100 -2 0.4900 -Starter_system 2 -250 150 -2 1 2 -1 4 -1 0.5238 -2 0.4762 -Car_cranks 2 -250 150 -1 3 -1 15 -1 0.4960 -2 0.5040 -Battery_age 3 -250 150 -0 -1 8 -1 0.3460 -2 0.6000 -3 0.0540 -Alternator 2 -250 150 -0 -1 7 -1 0.5060 -2 0.4940 -Charging_system 2 -250 150 -1 6 -1 8 -1 0.5040 -2 0.4960 -Battery_voltage 3 -250 150 -2 5 7 -2 9 12 -1 0.3072 -2 0.3486 -3 0.3442 -Headlights 3 -250 150 -1 8 -0 -1 0.3130 -2 0.3420 -3 0.3450 -Distributer 2 -250 150 -0 -2 11 12 -1 0.5030 -2 0.4970 -Spark_timing 3 -250 150 -1 10 -1 15 -1 0.3210 -2 0.3440 -3 0.3350 -Voltage_at_plug 3 -250 150 -3 2 8 10 -1 14 -1 0.3315 -2 0.3153 -3 0.3532 -Spark_plugs 3 -250 150 -0 -1 14 -1 0.3160 -2 0.3260 -3 0.3580 -Spark_quality 3 -250 150 -2 12 13 -1 15 -1 0.3266 -2 0.3334 -3 0.3400 -Car_starts 2 -250 150 -3 4 11 14 -0 -1 0.5158 -2 0.4842 diff --git a/sourcecodes/data/examplecar15node/MtXnnode.txt b/sourcecodes/data/examplecar15node/MtXnnode.txt deleted file mode 100644 index 60d3b2f4..00000000 --- a/sourcecodes/data/examplecar15node/MtXnnode.txt +++ /dev/null @@ -1 +0,0 @@ -15 diff --git a/sourcecodes/data/examplecar15node/MtXstructure_input.txt b/sourcecodes/data/examplecar15node/MtXstructure_input.txt deleted file mode 100644 index 549070d3..00000000 --- a/sourcecodes/data/examplecar15node/MtXstructure_input.txt +++ /dev/null @@ -1,17 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor -0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 -1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 - diff --git a/sourcecodes/data/examplecar15node/MtXstructure_old.txt b/sourcecodes/data/examplecar15node/MtXstructure_old.txt deleted file mode 100644 index cad36b88..00000000 --- a/sourcecodes/data/examplecar15node/MtXstructure_old.txt +++ /dev/null @@ -1,15 +0,0 @@ -Voltage_at_plug 0.3315 0.3153 0.3532 -Spark_quality 0.3266 0.3334 0.3400 -Car_cranks 0.4960 0.5040 -Car_starts 0.5158 0.4842 -Spark_plugs 0.3160 0.3260 0.3580 -Distributer 0.5030 0.4970 -Spark_timing 0.3210 0.3440 0.3350 -Alternator 0.5060 0.4940 -Charging_system 0.5040 0.4960 -Battery_voltage 0.3072 0.3486 0.3442 -Headlights 0.3130 0.3420 0.3450 -Battery_age 0.3460 0.6000 0.0540 -Main_fuse 0.5100 0.4900 -Starter_system 0.5238 0.4762 -Starter_motor 0.5070 0.4930 diff --git a/sourcecodes/data/examplecar15node/MtXtype.txt b/sourcecodes/data/examplecar15node/MtXtype.txt deleted file mode 100644 index 75ee3397..00000000 --- a/sourcecodes/data/examplecar15node/MtXtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor -3 2 3 3 2 3 2 3 2 2 3 3 2 2 2 diff --git a/sourcecodes/data/examplecar15node/eIAcontinuous_input.txt b/sourcecodes/data/examplecar15node/eIAcontinuous_input.txt deleted file mode 100644 index 66dddb9f..00000000 --- a/sourcecodes/data/examplecar15node/eIAcontinuous_input.txt +++ /dev/null @@ -1,1003 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor -3 2 3 3 2 3 2 3 2 2 3 3 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 1 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 2 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 2 2 1 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 1 1 2 3 1 2 2 2 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 3 2 1 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 2 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -2 2 3 2 2 3 2 2 2 2 2 2 2 2 2 -2 1 1 1 2 3 1 2 2 1 2 1 2 1 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 2 1 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 1 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 1 1 2 2 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 3 2 2 3 1 1 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 2 1 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 2 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 2 2 1 2 1 1 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 1 2 1 2 3 1 2 2 2 2 2 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 2 2 1 2 3 1 2 2 2 2 2 2 2 2 -1 2 2 1 2 3 1 3 2 2 3 2 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 2 1 2 3 1 1 2 1 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 3 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -2 2 1 1 2 3 1 3 2 2 3 2 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 1 1 2 3 1 2 2 1 2 1 2 2 2 -2 2 2 1 2 3 1 3 2 2 3 2 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 1 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 2 2 1 2 1 1 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -1 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1 3 3 2 2 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 1 2 2 2 2 2 2 2 -2 2 1 1 2 2 1 2 2 1 2 1 2 2 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 2 2 3 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 2 2 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 2 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 2 2 2 2 -2 1 3 2 2 3 1 2 2 2 2 1 2 1 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -2 1 2 1 2 3 1 2 2 1 2 1 2 2 2 -3 2 2 2 2 2 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 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2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 3 2 2 3 1 2 2 2 -2 2 2 1 2 3 1 2 2 1 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 2 1 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 2 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 2 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 1 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 2 1 3 2 2 3 1 1 1 2 -1 1 1 1 2 3 1 1 2 1 1 2 2 1 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 1 2 -1 1 3 1 2 3 1 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 2 1 2 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -2 2 3 2 2 3 1 2 2 1 2 2 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 2 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 1 2 2 3 2 3 2 2 3 2 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 2 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -3 2 1 2 2 3 2 3 2 1 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 3 2 1 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 1 1 2 3 1 1 2 1 1 1 1 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 2 2 2 2 2 2 1 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 1 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 2 1 2 2 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 2 2 3 2 2 3 2 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 3 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -2 2 3 2 2 3 1 2 2 2 2 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -2 2 1 1 2 3 1 2 2 2 2 1 2 2 2 -3 1 2 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 1 2 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 1 1 1 2 3 1 3 2 2 3 1 2 2 2 -1 2 3 1 2 2 1 1 2 1 1 1 2 1 2 -1 2 1 1 2 3 1 1 2 1 1 2 2 2 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 1 1 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -2 2 3 2 2 3 1 2 2 1 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -2 1 3 2 2 3 1 1 2 1 2 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 2 2 2 3 2 1 2 2 3 1 2 2 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 1 2 1 2 2 2 -2 1 1 1 2 3 1 2 2 2 2 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 1 2 -1 1 3 1 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 1 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 1 1 2 2 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -2 1 3 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 1 2 2 1 2 1 2 2 2 -2 2 3 2 2 3 1 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 2 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 2 2 2 2 -2 2 3 2 2 3 2 1 2 2 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 1 3 2 2 3 1 2 2 1 2 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 2 2 1 2 -1 2 1 1 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 1 2 2 2 2 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 3 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 2 2 2 2 -2 2 3 2 2 3 2 2 2 1 2 2 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 2 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 2 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 3 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 2 2 3 2 2 3 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 3 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 1 2 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 3 2 2 3 1 1 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 2 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 1 2 2 2 2 3 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 3 3 2 3 2 2 2 2 3 1 2 1 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 1 2 2 2 2 2 2 2 2 -1 2 3 1 2 3 1 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 2 2 1 2 -1 1 3 1 2 3 1 1 2 2 1 2 2 1 2 -3 1 3 3 2 3 1 3 2 2 3 1 2 2 2 -3 2 1 2 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 2 2 3 2 2 3 1 2 2 2 -1 2 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 1 1 2 3 1 1 2 1 1 1 2 2 2 -3 2 1 2 2 3 1 3 2 2 3 1 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 1 2 2 2 2 3 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 2 2 2 3 1 3 2 2 3 1 2 2 2 -3 1 2 2 2 2 1 3 2 2 3 1 2 2 2 -2 2 1 1 2 3 1 2 2 2 2 1 2 2 2 -2 2 3 2 2 3 2 3 2 2 3 2 2 2 2 -1 1 2 1 2 3 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -1 1 3 1 2 2 1 1 2 1 1 1 2 1 2 -3 1 1 2 2 3 1 3 2 2 3 1 2 2 2 -2 2 3 2 2 3 2 2 2 2 2 2 2 2 2 -1 1 3 1 2 3 1 1 2 2 1 1 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -3 2 3 3 2 3 2 3 2 2 3 2 2 2 2 -2 2 2 1 2 3 1 3 2 2 3 1 2 2 2 -1 1 3 1 2 2 1 1 2 1 1 3 2 1 2 -3 2 3 3 2 3 2 3 2 2 3 1 2 2 2 -1 1 1 1 2 3 1 1 2 1 1 1 2 1 2 -2 2 3 2 2 3 2 2 2 2 2 1 2 2 2 -1 1 3 1 2 3 1 1 2 1 1 1 2 1 2 -1 2 3 1 2 3 1 3 2 2 3 1 2 2 2 - diff --git a/sourcecodes/data/examplecar15node/eIAgraphviz.txt b/sourcecodes/data/examplecar15node/eIAgraphviz.txt deleted file mode 100644 index 56dcd027..00000000 --- a/sourcecodes/data/examplecar15node/eIAgraphviz.txt +++ /dev/null @@ -1,20 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Voltage_at_plug -> Spark_quality; -Car_cranks -> Car_starts; -Spark_plugs -> Spark_quality; -Spark_quality -> Car_starts; -Distributer -> Voltage_at_plug; -Distributer -> Spark_timing; -Spark_timing -> Car_starts; -Alternator -> Charging_system; -Charging_system -> Battery_voltage; -Battery_voltage -> Voltage_at_plug; -Battery_voltage -> Headlights; -Battery_age -> Battery_voltage; -Main_fuse -> Voltage_at_plug; -Main_fuse -> Starter_system; -Starter_system -> Car_cranks; -Starter_motor -> Starter_system; -} \ No newline at end of file diff --git a/sourcecodes/data/examplecar15node/eIAmap.txt b/sourcecodes/data/examplecar15node/eIAmap.txt deleted file mode 100644 index 9f705391..00000000 --- a/sourcecodes/data/examplecar15node/eIAmap.txt +++ /dev/null @@ -1,15 +0,0 @@ -Voltage_at_plug 0.908185 1.905000 -Car_cranks 0.500106 1.488000 -Spark_plugs 0.778947 2.543000 -Spark_quality 0.853627 1.757000 -Distributer 0.099549 1.990000 -Spark_timing 0.357390 2.880000 -Car_starts 0.469352 1.327000 -Headlights 0.917301 1.951000 -Alternator 0.044699 1.998000 -Charging_system 0.500246 1.502000 -Battery_voltage 0.915330 2.003000 -Battery_age 0.500554 1.236000 -Main_fuse 0.121613 1.985000 -Starter_system 0.494126 1.578000 -Starter_motor 0.063151 1.996000 diff --git a/sourcecodes/data/examplecar15node/eIAmapdata.txt b/sourcecodes/data/examplecar15node/eIAmapdata.txt deleted file mode 100644 index 67939bd1..00000000 --- a/sourcecodes/data/examplecar15node/eIAmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Starter_motor Main_fuse Starter_system Car_cranks Battery_age Alternator Charging_system Battery_voltage Headlights Distributer Spark_timing Voltage_at_plug Spark_plugs Spark_quality Car_starts diff --git a/sourcecodes/data/examplecar15node/eIAname.txt b/sourcecodes/data/examplecar15node/eIAname.txt deleted file mode 100644 index 2957eff7..00000000 --- a/sourcecodes/data/examplecar15node/eIAname.txt +++ /dev/null @@ -1 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor diff --git a/sourcecodes/data/examplecar15node/eIAnet_figure.txt b/sourcecodes/data/examplecar15node/eIAnet_figure.txt deleted file mode 100644 index 29896806..00000000 --- a/sourcecodes/data/examplecar15node/eIAnet_figure.txt +++ /dev/null @@ -1,114 +0,0 @@ -15 -1800 1200 -Starter_motor 0 0 -Main_fuse 257 0 -Starter_system 373 171 -Car_cranks 343 343 -Battery_age 514 0 -Alternator 771 0 -Charging_system 823 171 -Battery_voltage 943 343 -Headlights 523 514 -Distributer 1029 0 -Spark_timing 1273 171 -Voltage_at_plug 1123 514 -Spark_plugs 1286 0 -Spark_quality 643 686 -Car_starts 823 857 -Starter_motor 2 -250 150 -0 -1 3 -1 0.0039 -2 0.9961 -Main_fuse 2 -250 150 -0 -2 3 12 -1 0.0149 -2 0.9851 -Starter_system 2 -250 150 -2 1 2 -1 4 -1 0.4211 -2 0.5789 -Car_cranks 2 -250 150 -1 3 -1 15 -1 0.5109 -2 0.4891 -Battery_age 3 -250 150 -0 -1 8 -1 0.7989 -2 0.1661 -3 0.0350 -Alternator 2 -250 150 -0 -1 7 -1 0.0020 -2 0.9980 -Charging_system 2 -250 150 -1 6 -1 8 -1 0.4988 -2 0.5012 -Battery_voltage 3 -250 150 -2 5 7 -2 9 12 -1 0.4181 -2 0.1633 -3 0.4186 -Headlights 3 -250 150 -1 8 -0 -1 0.4470 -2 0.1573 -3 0.3957 -Distributer 2 -250 150 -0 -2 11 12 -1 0.0098 -2 0.9902 -Spark_timing 3 -250 150 -1 10 -1 15 -1 0.0088 -2 0.0982 -3 0.8930 -Voltage_at_plug 3 -250 150 -3 2 8 10 -1 14 -1 0.4646 -2 0.1681 -3 0.3674 -Spark_plugs 3 -250 150 -0 -1 14 -1 0.1791 -2 0.0990 -3 0.7219 -Spark_quality 3 -250 150 -2 12 13 -1 15 -1 0.5114 -2 0.2233 -3 0.2652 -Car_starts 2 -250 150 -3 4 11 14 -0 -1 0.7903 -2 0.2097 diff --git a/sourcecodes/data/examplecar15node/eIAnlevels.txt b/sourcecodes/data/examplecar15node/eIAnlevels.txt deleted file mode 100644 index 7ccbca8e..00000000 --- a/sourcecodes/data/examplecar15node/eIAnlevels.txt +++ /dev/null @@ -1,15 +0,0 @@ -Voltage_at_plug 1 2 3 -Car_cranks 1 2 -Spark_plugs 1 2 3 -Spark_quality 1 2 3 -Distributer 1 2 -Spark_timing 1 2 3 -Car_starts 1 2 -Headlights 1 2 3 -Alternator 1 2 -Charging_system 1 2 -Battery_voltage 1 2 3 -Battery_age 1 2 3 -Main_fuse 1 2 -Starter_system 1 2 -Starter_motor 1 2 diff --git a/sourcecodes/data/examplecar15node/eIAnnode.txt b/sourcecodes/data/examplecar15node/eIAnnode.txt deleted file mode 100644 index 60d3b2f4..00000000 --- a/sourcecodes/data/examplecar15node/eIAnnode.txt +++ /dev/null @@ -1 +0,0 @@ -15 diff --git a/sourcecodes/data/examplecar15node/eIAparameters.txt b/sourcecodes/data/examplecar15node/eIAparameters.txt deleted file mode 100644 index 57373374..00000000 --- a/sourcecodes/data/examplecar15node/eIAparameters.txt +++ /dev/null @@ -1,82 +0,0 @@ -Voltage_at_plug -Discrete node with 3 states -1 0.4646 -2 0.1681 -3 0.3674 - -Car_cranks -Discrete node with 2 states -1 0.5109 -2 0.4891 - -Spark_plugs -Discrete node with 3 states -1 0.1791 -2 0.0990 -3 0.7219 - -Spark_quality -Discrete node with 3 states -1 0.5114 -2 0.2233 -3 0.2652 - -Distributer -Discrete node with 2 states -1 0.0098 -2 0.9902 - -Spark_timing -Discrete node with 3 states -1 0.0088 -2 0.0982 -3 0.8930 - -Car_starts -Discrete node with 2 states -1 0.7903 -2 0.2097 - -Headlights -Discrete node with 3 states -1 0.4470 -2 0.1573 -3 0.3957 - -Alternator -Discrete node with 2 states -1 0.0020 -2 0.9980 - -Charging_system -Discrete node with 2 states -1 0.4988 -2 0.5012 - -Battery_voltage -Discrete node with 3 states -1 0.4181 -2 0.1633 -3 0.4186 - -Battery_age -Discrete node with 3 states -1 0.7989 -2 0.1661 -3 0.0350 - -Main_fuse -Discrete node with 2 states -1 0.0149 -2 0.9851 - -Starter_system -Discrete node with 2 states -1 0.4211 -2 0.5789 - -Starter_motor -Discrete node with 2 states -1 0.0039 -2 0.9961 - diff --git a/sourcecodes/data/examplecar15node/eIAstructure_old.txt b/sourcecodes/data/examplecar15node/eIAstructure_old.txt deleted file mode 100644 index 774a14fe..00000000 --- a/sourcecodes/data/examplecar15node/eIAstructure_old.txt +++ /dev/null @@ -1,15 +0,0 @@ -Voltage_at_plug 0.4646 0.1681 0.3674 -Spark_quality 0.5114 0.2233 0.2652 -Car_cranks 0.5109 0.4891 -Car_starts 0.7903 0.2097 -Spark_plugs 0.1791 0.0990 0.7219 -Distributer 0.0098 0.9902 -Spark_timing 0.0088 0.0982 0.8930 -Alternator 0.0020 0.9980 -Charging_system 0.4988 0.5012 -Battery_voltage 0.4181 0.1633 0.4186 -Headlights 0.4470 0.1573 0.3957 -Battery_age 0.7989 0.1661 0.0350 -Main_fuse 0.0149 0.9851 -Starter_system 0.4211 0.5789 -Starter_motor 0.0039 0.9961 diff --git a/sourcecodes/data/examplecar15node/eIAtype.txt b/sourcecodes/data/examplecar15node/eIAtype.txt deleted file mode 100644 index 75ee3397..00000000 --- a/sourcecodes/data/examplecar15node/eIAtype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Voltage_at_plug Car_cranks Spark_plugs Spark_quality Distributer Spark_timing Car_starts Headlights Alternator Charging_system Battery_voltage Battery_age Main_fuse Starter_system Starter_motor -3 2 3 3 2 3 2 3 2 2 3 3 2 2 2 diff --git a/sourcecodes/data/examplecar15node/old/MtXrun_initialstructure.sh b/sourcecodes/data/examplecar15node/old/MtXrun_initialstructure.sh deleted file mode 100644 index 8012f054..00000000 --- a/sourcecodes/data/examplecar15node/old/MtXrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure MtX -fi -exit diff --git a/sourcecodes/data/sample_network.json b/sourcecodes/data/sample_network.json new file mode 100644 index 00000000..7ee3b56f --- /dev/null +++ b/sourcecodes/data/sample_network.json @@ -0,0 +1,10 @@ +{ + "nodes": [ + { + "data": { + "id": "1", + "label": "Node1" + } + } + ] +} diff --git a/sourcecodes/k-best/index.html b/sourcecodes/k-best/index.html deleted file mode 100644 index 59912a77..00000000 --- a/sourcecodes/k-best/index.html +++ /dev/null @@ -1,6 +0,0 @@ -<html> -<head> -<title>Bayesian Network Web Server</title> -<meta HTTP-EQUIV="REFRESH" content="0; url=http://compbio.uthsc.edu/BNW_1.1/sourcecodes/home.php"> -</head> -</html> diff --git a/sourcecodes/k-best/src/GenerateGraphs.sh b/sourcecodes/k-best/src/GenerateGraphs.sh deleted file mode 100644 index 3427eb4d..00000000 --- a/sourcecodes/k-best/src/GenerateGraphs.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash -k=100 -rdir=./../iris3/resdir -for (( i = 0 ; i < k; i++ )) -do - dot ${rdir}/dot_$i -Tps -o ${rdir}/dotRes_$i.ps -done \ No newline at end of file diff --git a/sourcecodes/k-best/src/Model.h b/sourcecodes/k-best/src/Model.h deleted file mode 100644 index 1ba7a0dd..00000000 --- a/sourcecodes/k-best/src/Model.h +++ /dev/null @@ -1,1002 +0,0 @@ -#ifndef MODEL_H -#define MODEL_H - -#include<stdio.h> -#include<stdlib.h> - -#include<iostream> -#include<vector> -#include<deque> -#include<string> -#include<fstream> -#include<math.h> - -#include"Arguments.h" - -using namespace std; - -#include"UpdateHR2.h" - -#define MAX_COUNT 1000 -#define MAX_RQ 8*10000 -static double lr[MAX_RQ][MAX_COUNT]; -static double lr2[MAX_RQ][MAX_COUNT]; - -//ofstream totalOf1("debugModelTotal1.txt"); - -double log_gammaratio(int a, int z){ - if(z >= MAX_COUNT || a >= MAX_RQ){ -// if(z >= MAX_COUNT){ -// cerr << " Counts larger than " << MAX_COUNT << " occured. " << endl; -// cerr << " Increase MAX_COUNT. Exit now.\n"; -// -// } -// else if(a >= MAX_RQ ){ -// cerr << " a larger than " << MAX_RQ << " occured. " << endl; -// cerr << " Increase MAX_RQ. Exit now.\n"; -// } -// -// exit(1); - - double log_gam_res = 0; - //seperate 2 cases: - //if only z >= MAX_COUNT but a < MAX_RQ - if(a < MAX_RQ){ - //can compute it faster based on lr - log_gam_res += lr[a][MAX_COUNT - 1]; - for(int k = MAX_COUNT - 1; k <= z-1; k++){ - log_gam_res += log(1.0/a + k); - } - - } - //o.w.: start from the beginning - else{ - for(int k = 0; k <= z-1; k++){ - log_gam_res += log(1.0/a + k); - } - } - -// totalOf1 << "log_gam_res = " << log_gam_res << endl << endl; - return log_gam_res; - - } - else if (z < MAX_COUNT && a > 0){ - return lr[a][z]; - } - else if (z < MAX_COUNT && a < 0){ - return lr2[-a][z]; - } - else{ - cerr << "Error: a = 0" << endl; - exit(1); - } -} - - -double log_gammaratio(double z){ - return 0.50 * log(M_PI) + (z - 0.50) * log(z) - z + 1.0 / (12 * z); -} - -template<class T> void printvec(ostream& f, const vector<T>& v){ - int size= v.size(); - int i; - for(i=0; i<size; i++){ - f<<v.at(i)<<" "; - } - f<<endl; -} -template<class T> void printvecs(ostream& f, const vector<vector<T> >& v){ - int size= v.size(); - int i; - for(i=0; i<size; i++){ - printvec(f, v.at(i)); - } -} - - -void print_nodes(ostream& f, int *V, int n){ - for (int j = 0; j < n; j ++){ - f<<" "<<V[j]; - } -} - -void print_nodes(ostream& f, int T, int *V, int n){ - int j = 0; - while (T > 0){ - if (T & 1){ - f<<" "<<V[j]; - } - j ++; - - T >>= 1; - } -} -void print_set(ostream& f, int T){ - int j = 0; - while (T > 0){ - if (T & 1){ - f<<" "<<j; - } - j ++; - T >>= 1; - } -} - - -// Reads and stores data. -class Data{ -public: - Data(){} - ~Data(){} - void init(){ - read_data(); - downcode(); - } - void read_data(){ - ifstream ifs(Arguments::datafile, ios::in); - if (!ifs){ - fprintf(stderr, " Cannot read file %s.\n", Arguments::datafile); - exit(1); - } - fprintf(stderr, " Reading file %s...\n", Arguments::datafile); - - char* buffer= new char[10000]; - ifs.getline(buffer, 10000); - char* pch= strtok(buffer,", \t"); - while (pch != NULL){ - string tempstring(pch); - //cerr << "Node = "<< tempstring << endl; - heads.push_back(tempstring); - pch = strtok(NULL, ", \t"); - } - numattributes = heads.size(); - - fprintf(stderr, " Heading read: %d attributes.\n", numattributes); - - dm.clear(); - vector<int> temp; - while (true){ - temp.clear(); - ifs.getline(buffer, 10000); - pch = strtok(buffer,", \t"); - while (pch != NULL){ - temp.push_back(atoi(pch)); - pch = strtok(NULL, ", \t"); - } - if ((int)temp.size() != numattributes) break; - - dm.push_back(temp); - - if ((int)dm.size() >= atoi(Arguments::maxnumrecords)) break; - } - numrecords = dm.size(); - fprintf(stderr, " Data read: %d lines.\n", numrecords); - delete [] buffer; - } - void downcode(){ - //fprintf(stderr, "downcode() starts. \n"); - - int inuse[4096][256]; - for (int v = 0; v < 255; v ++){ - for (int i = 0; i < numattributes; i ++){ - inuse[v][i] = -1; - } - } - //Purpose: For each i attribute, - for (int t = 0; t < numrecords; t ++){ - for (int i = 0; i < numattributes; i ++){ - inuse[dm[t][i]][i] = 1; - } - } - - //ofstream of1("debugDowncode.txt"); - //of1 << "\n inuse check" << endl; - for (int v = 0; v < 30; v ++){ - - -// for (int i = 0; i < numattributes; i++){ -// of1 << " inuse[" << v << "][" << i << "] =" << inuse[v][i] << endl; -// } -// of1 << "\n"; - - - /* - FILE * fp1 = fopen("debug1.txt", "w"); - fprintf(fp1, "\n inuse check\n"); - for (int i = 0; i < numattributes; i++){ - fprintf(fp1, " inuse[%d][%d] = %d\n", v, i, inuse[v][i]); - } - fclose(fp1); - */ - - - /* - fprintf(stderr, "\n inuse check\n"); - for (int i = 0; i < numattributes; i++){ - fprintf(stderr, " inuse[%d][%d]=%d\n", v, i, inuse[v][i]); - } - fprintf(stderr, "\n"); - */ - } - - arities.clear(); - - maxarity = 0; - - for (int i = 0; i < numattributes; i ++){ - int count = 0; - for (int v = 0; v < 255; v ++){ - if (inuse[v][i] == 1){ - inuse[v][i] = count ++; - } - } - arities.push_back(count); - if (count > maxarity) maxarity = count; - } - -// of1 << "maxarity = " << maxarity << endl; -// printvec(of1, arities); - - for (int t = 0; t < numrecords; t ++){ - for (int i = 0; i < numattributes; i ++){ - dm[t][i] = inuse[dm[t][i]][i]; - - } - } - }//end downcode() - - - int get_index(string s){ - int i = 0; - while (i < (int)heads.size() && heads[i] != s){ i ++; } - return i; - } - void print_data(ostream & f){ - for (int i = 0; i < numattributes; i ++){ - f << " " << heads[i]; - } - f << endl; - for (int t = 0; t < numrecords; t ++){ - for (int i = 0; i < numattributes; i ++){ - f << " " << dm[t][i]; - } - f << endl; - } - } - - vector<string> heads; - - vector< vector<int> > dm; - - vector<int> arities; - - int numattributes; - - int numrecords; - - int maxarity; -}; - - -// NOTE: We assume that children come first, that is, -// V[0] is the grandest child and V[n-1] is the grandest parent. -// Layers respectively from 0 to numlayers. -// Note that this is reverse to the input ordering. -class Layering{ -public: - Layering(){} - ~Layering(){ delete [] V;} - - void init(Data & data){ - set_layers(data); - - //print_layers(); - - } - void set_layers(Data & data){ - -// ofstream of1("debugSet_layers.txt"); - - V = new int[data.numattributes]; - int j = 0; - cnh.clear(); nh.clear(); cnh.clear(); - - if (Arguments::layeringfile[0] == '%'){ - numlayers = 1; - int layersize = data.numattributes; - nh.push_back(layersize); - cnh.push_back(j); - - for (int l = 0; l < layersize; l ++){ - int i = j; - V[j++] = i; - } - - edgeswithin.clear(); - edgeswithin.push_back(true); - - return; - } - - parselayeringfile(Arguments::layeringfile, true); - numlayers = nodesinlayers.size(); - - for (int h = numlayers-1; h >= 0; h --){ - int layersize = nodesinlayers[h].size(); - nh.push_back(layersize); - cnh.push_back(j); - for (int l = 0; l < layersize; l ++){ - int i = data.get_index(nodesinlayers[h][l]); - V[j++] = i; - } - } - - } - void print_layers(){ - for (int h = 0; h < numlayers; h ++){ - cerr<<"Layer "<<h<<":"; - for (int j = 0; j < nh[h]; j ++){ - cerr<<" "<<V[cnh[h] + j]; - } - cerr<<endl; - } - } - bool edges_within(int h){ - return edgeswithin[numlayers - h - 1]; - } - void parselayeringfile(char *layerfilename, bool verbose){ - - ifstream ifs(layerfilename, ios::in); - if( !ifs){ - cerr<<"ERROR: The file '"<<layerfilename<<"' could not be opened\n"; - cerr<<"Exiting\n"; - exit(1); - } - if(verbose){ - cerr<<"Reading layer file: '"<<layerfilename<<"'\n"; - } - - char* buffer= new char[10000]; - char* pch; - int i; - char tempchar; - while(true){ - ifs.getline(buffer,10000); - pch = strtok(buffer, ", \t"); - vector<string> tempstringvec; //will hold the tokenized line - while(pch != NULL){ - string tempstring(pch); - tempstringvec.push_back(tempstring); - pch = strtok(NULL, ", \t"); - } - - if(tempstringvec.size() < 3){ - cerr<<" ERROR: in reading file '"<<layerfilename<<"'"<<endl; - cerr<<" each line must be of the form:"<<endl; - cerr<<" layername\t1/0\tn1 ... nn"<<endl; - cerr<<" EXITING"<<endl; - exit(1); - } - - layernames.push_back(tempstringvec.at(0)); - if(tempstringvec.at(1) == "0"){ - edgeswithin.push_back(0); - } - else if( tempstringvec.at(1) == "1"){ - edgeswithin.push_back(1); - } - else{ - cerr<<" ERROR: in reading file '"<<layerfilename<<"'"<<endl; - cerr<<" the values in the second column can either be '1' or '0'"<<endl; - cerr<<" EXITING"<<endl; - exit(1); - } - - vector<string> tempnodesinlayer; - for(i = 2; i < (int)tempstringvec.size();i ++){ - tempnodesinlayer.push_back(tempstringvec.at(i)); - } - nodesinlayers.push_back(tempnodesinlayer); - - ifs>>tempchar; - ifs.putback(tempchar); - if(ifs.eof()){ - break; - } - } - delete [] buffer; - buffer = 0; - pch = 0; - cerr.width(13); - cerr<<"Layer Name"; - cerr.width(24); - cerr<<"Edges Within Allowed"; - cerr.width(14); - cerr<<"Node Names"<<endl; - for(i = 0; i < (int)layernames.size(); i ++){ - cerr.width(13); - cerr<<layernames.at(i); - cerr.width(15); - if(edgeswithin.at(i)){ - cerr<<"true"; - } - else{ - cerr<<"false"; - } - cerr<<" "; - printvec(cerr, nodesinlayers.at(i)); - } - } - - - vector<string> layernames; - vector<bool> edgeswithin; - vector<vector<string> > nodesinlayers; - int *V; - int numlayers; - vector<int> nh; - vector<int> cnh; -}; - - - -// Blocks for computing sufficient statistics. -class Tnode{ -public: - double pseudocount; - short int arity; - short int count; - short int depth; - Tnode** children; - - Tnode(const int a, const int d){ - pseudocount = 1; - arity = a; - count = 0; - depth = d; - children = new Tnode*[arity]; - for(int v = 0; v < arity; v ++){ - children[v] = NULL; - } - } - ~Tnode(){ - for(int v = 0; v < arity; v ++){ - if (children[v] != NULL){ - delete children[v]; - } - } - delete [] children; - //free_memory(); - } - void free_memory(){ - //cerr<<" Deleting d="<<depth<<" c="<<count<<endl; - - for(int v = 0; v < arity; v ++){ - if (children[v] != NULL){ - children[v]->free_memory(); - delete children[v]; - } - } - //delete [] children; - } - // Note: Actually S is not needed. - void update(vector<int> & S, vector<int> & u){ - if (u.size() > 0){ - //int j = S[u.size()-1]; - int v = u[u.size()-1]; - - u.pop_back(); - if (children[v] == NULL){ - //cerr<<" Creating d="<<depth<<" c="<<count<<endl; - - children[v] = new Tnode(arity, depth+1); - } - children[v]->update(S, u); - } - count ++; - } - void print(ostream & f){ - f << "(" << count << ")" << endl; - for (int v = 0; v < arity; v ++){ - if (children[v] != NULL){ - for (int d = 0; d < depth; d ++) f << " "; - f << " " << v << " "; - children[v]->print(f); - } - } - } - - double evaluate(int d, int a, int r){ - double sum = 0; - - //if no parent, directly log[gamma(1+count) / gamma(1) ] (1/a = 1/1 = 1) - if (depth == d){ - sum = log_gammaratio(a, count); - //cerr << "count1: " << count << endl; - - } - else if (depth <= d - 1){ - for (int v = 0; v < arity; v ++){ - if (children[v] != NULL){ - double value = children[v]->evaluate(d, a, r); - sum += value; - } - } - if (depth == d - 1){ - sum -= log_gammaratio(r, count); - //cerr << "count2: " << count << endl; - - } - } - return sum; - } - - - double evaluateHR(int d, int alpha_v_pa, int r){ - //cerr << "start: root.evaluateHR(d =" - //<< d << ", alpha_v_pa=" << alpha_v_pa << ", r=" << r << ")" << endl; - double sum = 0; - - //if no parent, directly log[gamma(1+count) / gamma(1) ] (1/a = 1/1 = 1) - if (depth == d){ - //sum = log_gammaratio(a, count); - sum = log_gammaratio(alpha_v_pa, count); - //cerr << "count1: " << count << endl; - - } - else if (depth <= d - 1){ - for (int v = 0; v < arity; v ++){ - if (children[v] != NULL){ - double value = children[v]->evaluateHR(d, alpha_v_pa, r); - sum += value; - } - } - if (depth == d - 1){ - int alpha_pa = alpha_v_pa / r; - - sum -= log_gammaratio(alpha_pa, count); -// totalOf1 << "\nalpha_pa: " << alpha_pa << endl; -// totalOf1 << "count2: " << count << endl; -// totalOf1 << "-log_gammaratio(alpha_pa, count) = " << -log_gammaratio(alpha_pa, count) << endl; - //cerr << "count2: " << count << endl; - - } - } - return sum; - } - -}; - - -class Model{ -public: - Model(){} - ~Model(){} - - void makeADTree(vector< vector<int> > & dm, vector<int> & arities){ - //Create dmIndex from dm, dmIndex stroes {0, 1, R-1} - vector<int> dmIndex; -// cout << "dm.size() = " << dm.size() << endl; - for(int i = 0; i < (int) dm.size(); i++){ - dmIndex.push_back(i); - } -// cout << "dmIndex:" << endl; -// for(int i = 0; i < (int) dm.size(); i++){ -// cout << "dmIndex[" << i << "] = "<< dmIndex[i] << endl; -// } - - // M: the num of attr -// int M = dm[0].size(); -// cout << "M = " << M << endl; - - //cout << "Start MakeADTree()" << endl; - //ADTreeNode * ADTreeNodeP1 = MakeADTree(0, dmIndex, dm, arities); - ADTreeNodeP1 = MakeADTree(0, dmIndex, dm, arities); - //cout << "End MakeADTree()" << endl; - - //cout << "Start PrintADTreeNode()" << endl; - //PrintADTreeNode(ADTreeNodeP1, 0, M, arities); - //cout << "End PrintADTreeNode()" << endl; - - } - - void makeADTree(){ - makeADTree(data.dm, data.arities); - } - - void freeADTree(vector< vector<int> > & dm, vector<int> & arities){ - int M = dm[0].size(); - //cout << "M = " << M << endl; - //cout << "Start FreeADTreeNode()" << endl; - FreeADTreeNode(ADTreeNodeP1, M, arities); - //cout << "End FreeADTreeNode()" << endl; - - } - - void freeADTree(){ - freeADTree(data.dm, data.arities); - } - - - void MakeADContiTable(vector< vector<int> > & dm, vector<int> & arities){ - cout << "\nStart MakeADContiTable(vector< vector<int> > & dm, vector<int> & arities)" << endl; - // M: the num of attr - int M = dm[0].size(); - cout << "M = " << M << endl; - - deque<int> inquiryAttrs; - - for(int i = 0; i < (int) inquiryAttrs.size(); i++){ - cout << "inquiryAttrs[" << i << "] = " << inquiryAttrs[i] << endl; - } - - vector<int> givenAttrs; - - vector<int> givenVals; - - cout << "Call MakeContab() " << endl; - CondiContiTable resultTable = MakeContab(inquiryAttrs, ADTreeNodeP1, givenAttrs, givenVals, arities); - cout << "Return MakeContab() " << endl; - for(unsigned int i = 0; i < resultTable.contiTableCounts.size(); i++){ - cout << "resultTable.contiTableCounts[" << i << "] = " << resultTable.contiTableCounts[i] << endl; - } - - cout << "End MakeADContiTable(vector< vector<int> > & dm, vector<int> & arities)" << endl; - - - } //end void MakeADContiTable() - - void MakeADContiTable(){ - MakeADContiTable(data.dm, data.arities); - } - - vector<int> MakeADContiTable(deque<int> inquiryAttrs, vector< vector<int> > & dm, vector<int> & arities){ - //cout << "\nStart MakeADContiTable(vector< vector<int> > & dm, vector<int> & arities)" << endl; - // M: the num of attr - //int M = dm[0].size(); - //cout << "M = " << M << endl; - - //deque<int> inquiryAttrs; - - //Full inquiry -// for(int i = 0; i < M; i++){ -// inquiryAttrs.push_back(i); -// } - - -// for(int i = 0; i < (int) inquiryAttrs.size(); i++){ -// cout << "inquiryAttrs[" << i << "] = " << inquiryAttrs[i] << endl; -// } - - vector<int> givenAttrs; - - vector<int> givenVals; - - //cout << "Call MakeContab() " << endl; - CondiContiTable resultTable = MakeContab(inquiryAttrs, ADTreeNodeP1, givenAttrs, givenVals, arities); - //cout << "Return MakeContab() " << endl; -// -// for(unsigned int i = 0; i < resultTable.contiTableCounts.size(); i++){ -// cout << "resultTable.contiTableCounts[" << i << "] = " << resultTable.contiTableCounts[i] << endl; -// } -// -// cout << "End MakeADContiTable(vector< vector<int> > & dm, vector<int> & arities)" << endl; - return resultTable.contiTableCounts; - - } //end vector<int> MakeADContiTable() - - - - void init(){ - data.init(); - m = data.numrecords; - n = data.numattributes; - - layering.init(data); - - for (int a = 1; a < MAX_RQ; a ++){ - double aa = 1.0 / a; - lr[a][0] = 0; lr2[a][0] = 0; - - for (int k = 1; k < MAX_COUNT; k ++){ - lr[a][k] = lr[a][k-1] + log(aa + k - 1); - lr2[a][k] = lr2[a][k-1] + log(a + k - 1); - } - } - - } - - - - - - - - void test(){ - for (int i = 0; i < 1; i ++){ - vector<int> T; - T.clear(); - T.push_back(1); - T.push_back(2); - - } - exit(1); - } - - - void testHR(){ - for (int i = 0; i < 1; i ++){ - vector<int> T; - T.clear(); - T.push_back(1); - T.push_back(2); - T.push_back(3); - T.push_back(4); - - } - } //end void testHR() - - - void testHR_ADtree(){ - for (int i = 0; i < 1; i ++){ - deque<int> T; - T.clear(); - T.push_back(1); - T.push_back(2); - T.push_back(3); - T.push_back(4); - - } - } //end void testHR_ADtree() - - - - //--- Interface functions --- below ---------- - // - // Log of local conditional probability, log p(xi | xS). - double log_lcp(int i, vector<int> & T){ - - return log_lcp_mult(i, T); - } - double log_lcp(int i, int *T, int d){ - vector<int> TT; - for (int j = 0; j < d; j ++) TT.push_back(T[j]); - return log_lcp_mult(i, TT); - } - - - double log_lcpHR(int i, vector<int> & T){ - - return log_lcp_multHR(i, T); - } - - double log_lcpHR(int i, int *T, int d){ - vector<int> TT; - for (int j = 0; j < d; j ++) TT.push_back(T[j]); - //cerr << "start log_lcp_multHR(i, TT)" << endl; - double result = log_lcp_multHR(i, TT); - return result; - } - - - double log_lcpHR_ADtree(int i, int *T, int d){ - deque<int> TT; - for (int j = 0; j < d; j ++) TT.push_back(T[j]); - double result = log_lcp_multHR_ADtree(i, TT); - return result; - } - - - double log_prior(int i, int *T, int d){ - return lr[1][d] + lr[1][n-1-d] - lr[1][n-1]; - } - int num_layers(){ - return layering.numlayers; - } - void layer(int h, int** Vh, int* nh){ - *Vh = &(layering.V[layering.cnh[h]]); - *nh = layering.nh[h]; - } - void upper_layers(int h, int** Vu, int* nu){//similar to above but upper means parent - if (h < layering.numlayers){ - *Vu = &(layering.V[layering.cnh[h+1]]); - *nu = n - layering.cnh[h+1]; - } - else{ *Vu = NULL; *nu = 0;} - } - void lower_layers(int h, int **Vl, int *nl){//similar to above but lower means children - if (h > 0){ - *Vl = layering.V; - *nl = layering.cnh[h]; - } - else{ *Vl = NULL; *nl = 0;} - } - int max_indegree(){ - return atoi(Arguments::maxindegree); - } - bool edges_within(int h){ - return layering.edges_within(h); - } - int num_nodes(){ - return n; - } - - void print_edge_prob(ostream& f, int i, int j, double p){ - //f<<data.heads[i]<<" -> "<<data.heads[j]<<" "<<p<<endl; - f<<data.heads[i]<<" -> "<<data.heads[j]<<" \t" <<p <<endl; - } - - // - //--- Interface functions --- above ---------- - - -private: - // Dirichlet-multinomial model - double log_lcp_mult(int i, vector<int> & T){ - vector<int> S; - - S.push_back(i); - - for (int k = 0; k < (int)T.size(); k ++){ - S.push_back(T[k]); - } - - //cerr << " Evaluation yields: " << evaluate(S) << " , log_gammaratio(1, 2) = " - // << log_gammaratio(1, 2) << " , a = " << data.arities[S[0]] << endl; - - return evaluate(S); - } - - double evaluate(vector<int> & S){ - - Tnode root(data.maxarity+1, 0); - vector<int> u; - - //for each record t - for (int t = 0; t < m; t ++){ - u.clear(); - for (int k = 0; k < (int)S.size(); k ++){ - int j = S[k]; - u.push_back(data.dm[t][j]); - } - //cerr << t+1 << "th update: "; - - root.update(S, u); - //cerr << endl; - - } - //root.print(cerr); - - - return root.evaluate(S.size(), 1, -data.arities[S[0]]); - - } - - - double log_lcp_multHR(int i, vector<int> & T){ - vector<int> S; - - S.push_back(i); - - for (int k = 0; k < (int)T.size(); k ++){ - S.push_back(T[k]); - } - - //cerr << " Evaluation yields: " << evaluate(S) << " , log_gammaratio(1, 2) = " - // << log_gammaratio(1, 2) << " , a = " << data.arities[S[0]] << endl; - double result = evaluateHR(S); - return result; - - - }//end log_lcp_multHR() - - - double log_lcp_multHR_ADtree(int i, deque<int> & T){ - //totalOf1 << "Inside log_lcp_multHR()" << endl; - - double result2 = evaluateHR_ADtree(T); - - int insertIndex = -1; - for(int k = 0; k < (int)T.size(); k++){ - if(i < T[k]){ - insertIndex = k; - break; - } - } - if(insertIndex == -1){ - insertIndex = (int)T.size(); - } - - deque<int> S; - - for(int k = 0; k <= insertIndex - 1; k++){ - S.push_back(T[k]); - } - S.push_back(i); - for(int k = insertIndex; k < (int)T.size(); k++){ - S.push_back(T[k]); - } - - double result1 = evaluateHR_ADtree(S); - - //cerr << " Evaluation yields: " << evaluate(S) << " , log_gammaratio(1, 2) = " - // << log_gammaratio(1, 2) << " , a = " << data.arities[S[0]] << endl; - double result = result1 - result2; - return result; - - } - - - // Dirichlet-multinomial model - double evaluateHR(vector<int> & S){ - Tnode * root = new Tnode (data.maxarity+1, 0); - vector<int> u; - - //for each record t - for (int t = 0; t < m; t ++){ - u.clear(); - for (int k = 0; k < (int)S.size(); k ++){ - int j = S[k]; - u.push_back(data.dm[t][j]); - } - //cerr << t+1 << "th update: "; - - (*root).update(S, u); - // - //cerr << endl; - - } - //root.print(cerr); - - int alpha_v_pa = 1; - for(int index = 0; index < (int)S.size(); index++){ - alpha_v_pa *= data.arities[S[index]]; - } - int r = data.arities[S[0]]; - //return root.evaluateHR(S.size(), alpha_v_pa, r); - - double result = (*root).evaluateHR(S.size(), alpha_v_pa, r); - //totalOf1 << " result of root.evaluateHR(" << S.size() <<", " - // << alpha_v_pa << ", " << r << ") = " << result << endl; - delete root; - return result; - - } //end double evaluateHR(vector<int> & S) - - - double evaluateHR_ADtree(deque<int> & S){ - - int alpha = 1; - for(int index = 0; index < (int)S.size(); index++){ - alpha *= data.arities[S[index]]; - } - - vector<int> countVec = MakeADContiTable(S, data.dm, data.arities); - - double sum = 0; - for(int i = 0; i < (int) countVec.size(); i++){ - //totalOf1 << "countVec[" << i <<" ]" << countVec[i] << endl; - sum += log_gammaratio(alpha, countVec[i]); - } - -// totalOf1 << "evaluateHR_ADtree(deque<int> & S) ends" << endl; - - return sum; - - } //end double evaluateHR_ADtree() - - - Data data; - int n; - int m; - Layering layering; - - ADTreeNode * ADTreeNodeP1; - -}; //end of class Model - - - - - -#endif diff --git a/sourcecodes/k-best/src/UpdateHR.h b/sourcecodes/k-best/src/UpdateHR.h deleted file mode 100644 index 19b93c1d..00000000 --- a/sourcecodes/k-best/src/UpdateHR.h +++ /dev/null @@ -1,1652 +0,0 @@ -#include<stdio.h> -#include<stdlib.h> -#include"math.h" - -#include"Arguments.h" -#include"Model.h" -#include"Engine.h" - - -#define LOGADD_NEW(logA, logB) if(logA == MARK) logA = logB; else if (logA == LOG_ZERO) logA = logB; else if (logB == LOG_ZERO) logA = logA; else logA = logA + log(1+exp(logB-logA)); - -//#define LOGMINUS(la,lb) if(la>8e99||lb-la>100) la=lb;else la+=log(1-exp(lb-la)); - -#define LOGMINUS_NEW(logA, logB) if(logA == MARK) logA = logB; else if (logA == LOG_ZERO) logA = logB; else if (logB == LOG_ZERO) logA = logA; else logA = logA + log(1-exp(logB-logA)); - -#define epsilon 1.0e5 - -bool logSpecValEquals(double logX, double logSpecVal){ - return (logX >= logSpecVal - epsilon && logX <= logSpecVal + epsilon); -} - -//call by reference to the original value -//the log sum result is stored in logA -//replace LOGADD_NEW(logA, logB) -//Pre: if neither logA nor logB is MARK/LOG_ZERO, then logA < 0 && logB < 0 -void logAdd_New(double & logA, double & logB){ - //if(logA == MARK){ - if(logSpecValEquals(logA, MARK)){ - logA = logB; - } - //else if (logA == LOG_ZERO){ - else if (logSpecValEquals(logA, LOG_ZERO)){ - logA = logB; - } - //else if(logB == MARK){ - else if(logSpecValEquals(logB, MARK)){ - logA = logA; - } - //else if(logB == LOG_ZERO){ - else if(logSpecValEquals(logB, LOG_ZERO)){ - logA = logA; - } - //Nither logA nor logB is MARK/LOG_ZERO - //logA < 0 && logB < 0 - else{ - //1.1 - //Gaurd logB-logA <= 100 to avoid that exp(logB-logA) go to inf - if(logB - logA <= 100 ){ - logA = logA + log( 1 + exp(logB-logA) ); - - } - //1.2 - //if logB - logA > 100, then logB > 100 + logA so that B is much bigger than A (B > e^100 * A) - // So (A + B) almost = B - else{ - //logA = logB; - //The following is the real formula,; but it is almost same as //logA = logB; - logA = logB + log( exp(logA - logB) + 1); - } - - } -}// end of void logAdd_New(double & logA, double & logB) - -//Pre: -// (logA != MARK) and (if logB != LOG_ZERO then logA !=LOG_ZERO) and (logA < 0); (i.e. logA has been assigned some value) -// if logB != MARK/LOG_ZERO, then logA >= logB - -void logMinus_New(double & logA, double & logB){ - //if(logA == MARK){ - if(logSpecValEquals(logA, MARK)){ - cerr << "Error: logMinus_New(double & logA, double & logB): logA == MARK\n"; - exit(1); - } - //else if (logA == LOG_ZERO && logB != LOG_ZERO){ - else if (logSpecValEquals(logA, LOG_ZERO) && ! logSpecValEquals(logB, LOG_ZERO)){ - cerr << "Error: logMinus_New(double & logA, double & logB): logA == LOG_ZERO && logB != LOG_ZERO\n"; - exit(1); - } - //else if(logB == MARK){ - else if(logSpecValEquals(logB, MARK)){ - logA = logA; - } - //else if(logB == LOG_ZERO){ - else if(logSpecValEquals(logB, LOG_ZERO)){ - logA = logA; - } - //Nither logA nor logB is MARK/LOG_ZERO - //logA >= logB - else{ - if(logA == logB){ - logA = LOG_ZERO; - } - //logA > logB - else{ - if(logA > logB){ - logA = logA + log(1 - exp(logB-logA)); - } - //if logA < logB - //Note: this is the case which only occurs in - // sub_h_Fast_Details() and sub_RR_Fast_Details() for the testing; it should not happen generally - else{ - cerr << "Warning: logMinus_New(double & logA, double & logB): logA < logB" << endl; - logA = -( logB + log(1 - exp(logA-logB)) ); - } - - - } - - } -} // end of void logMinus_New(double & logA, double & logB) - - -//Add: modified from void logMinus_New(double & logA, double & logB) - -//Only for void sub_RR_Fast_TSize() and void sub_h_Fast_TSize() -//Pre: -// (logA != MARK) and -// (logB != MARK) and -// both logA >= logB and logA < logB are allowed -// Post: -// if logA < logB, then return LOG_ZERO bound -// ow, return the correctly exact answer -void logMinus_New_NonnegRes(double & logA, double & logB){ - //if(logA == MARK){ - if(logSpecValEquals(logA, MARK)){ - cerr << "Error: logMinus_New_NonnegRes(double & logA, double & logB): logA == MARK\n"; - exit(1); - } - //else if(logB == MARK){ - else if(logSpecValEquals(logB, MARK)){ - cerr << "Error: logMinus_New_NonnegRes(double & logA, double & logB): logB == MARK\n"; - exit(1); - } - //else if(logB == LOG_ZERO){ - else if(logSpecValEquals(logB, LOG_ZERO)){ - logA = logA; - } - //Nither logA nor logB is MARK/LOG_ZERO - //logA >= logB - else{ - if(logA == logB){ - logA = LOG_ZERO; - } - //logA > logB - else{ - if(logA > logB){ - logA = logA + log(1 - exp(logB-logA)); - } - //if logA < logB, return LOG_ZERO as the bound - //Note: this is the case which only occurs in - // sub_h_Fast_TSize() and sub_RR_Fast_TSize(); - else{ - logA = LOG_ZERO; - } - - } - - } -} // end of void logMinus_New_NonnegRes(double & logA, double & logB) - - -//call by reference to the original value -//the log sum result is stored in logA -void logAddComp(double & logA, double & logB){ - - //if(logA == MARK){ - if(logSpecValEquals(logA, MARK)){ - logA = logB; - } - //else if (logA == LOG_ZERO){ - else if (logSpecValEquals(logA, LOG_ZERO)){ - logA = logB; - } - //else if(logB == MARK){ - else if(logSpecValEquals(logB, MARK)){ - logA = logA; - } - //else if(logB == LOG_ZERO){ - else if(logSpecValEquals(logB, LOG_ZERO)){ - logA = logA; - } - - - //Nither logA nor logB is MARK/LOG_ZERO - else{ - //1 - if(logA < 0 && logB < 0 ){ - //1.1 - //Gaurd logB-logA <= 100 to avoid that exp(logB-logA) go to inf - if(logB - logA <= 100 ){ - logA = logA + log( 1 + exp(logB-logA) ); - - } - //1.2 - //if logB - logA > 100, then logB > 100 + logA so that B is much bigger than A (B > e^100 * A) - // So (A + B) almost = B - else{ - //logA = logB; - //The following is the real formula,; but it is almost same as //logA = logB; - logA = logB + log( exp(logA - logB) + 1); - } - } - - //2 - else if(logA > 0 && logB > 0){ - //always make exp(.): . > 0 - if(-logB + logA <= 100){ - //2.1 - logA = -( -logA + log( 1 + exp(-logB+logA) ) ); - } - else{ - //2.2 - logA = -( -logB + log( 1 + exp(-logA+logB) ) ); - } - - } - //3 - else if(logA < 0 && logB > 0){ - //3.1 - if(logA + logB > 0){ - if(logA + logB <= 100){ - //3.1.2 - logA = -logB + log( exp(logA + logB) - 1 ); - } - else{ - //3.1.1 - logA = logA + log( 1 - exp(-logB-logA) ); - } - - } - //3.2 - else if(logA + logB < 0){ - if(-logA - logB <= 100){ - //3.2.2 - logA = -( logA + log( exp(-logB-logA) - 1) ); - } - else{ - //3.2.1 - logA = - ( -logB + log(1 - exp(logA+logB) ) ); - } - - } - //3.3 - else{ - logA = LOG_ZERO; - } - } - //4 - else if(logA > 0 && logB < 0){ - //4.1 - if(logA + logB > 0){ - if(logA + logB <= 100){ - //4.1.2 - logA = -logA + log( exp(logB+logA) - 1); - } - else{ - //4.1.1 - logA = logB + log( 1 - exp(-logA-logB) ); - } - - } - //4.2 - else if(logA + logB < 0){ - if(-logA-logB <= 100){ - //4.2.2 - logA = -( logB + log( exp(-logA-logB) - 1) ); - } - else{ - //4.2.1 - logA = -( -logA + log(1 - exp(logB+logA)) ); - } - - } - //4.3 - else{ - logA = LOG_ZERO; - } - } - - } - -} // end of void logAddComp(double & logA, double & logB) - - - -//#include <vector> - -//forward -double * hFunc; -double * hFuncNume; - - -//backward -//AA_S = new double [S+1]; -double * AA_S; - -double * RRFunc; -double * RRFuncNume; - - -//mixIndegree -double * Eta_U; -double ** KFunc; - -//In_Out -double * RRFuncInOut; - -//ofstream totalOfMixEta("debugEngineMixForEta_U.txt"); - -void printIntArr(int * TSet, int leng){ - for(int ind = 0; ind < leng; ind++){ - cout << "Set[" << ind << "]=" << TSet[ind] << endl; - } -} - - -int binIntLen(int S){ - int SSetLen = 0; - - while(S > 0){ - if(S & 1){ - SSetLen++; - - } - S >>= 1; - } - return SSetLen; - -} - - -void binIntToDecIntArr(int S, int ones, int *SSet){ - int posFromLeft = 0; - int ind = 0; - while(S > 0){ - if(S & 1){ - SSet[ind++] = posFromLeft; - - } - S >>= 1; - posFromLeft++; - } - //printIntArr(SSet, ones); - -} - - - -//HR: Compute F(S, T) -double compute_f(int nh, int S, int T, int sizeofT, int *TSet, double * h, double ** alpha){ - - - double result_f = MARK; - double result_h = h[S-T]; - //LOGADD(result_f, result_h); - result_f = result_h; - if (result_f == LOG_ZERO){ - return result_f; - } - - - for(int index = 0; index < sizeofT; index++){ - int j = TSet[index]; - double result_A = alpha[j][S-T]; - //result_f += result_A; - if (result_A == LOG_ZERO){ - return LOG_ZERO; - } - else{ - result_f += result_A; - } - } - return result_f; -} - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} F(S,T) -void rec_compute_sum_F_S_T( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * h, - double ** alpha, - double & sumOdd, - double & sumEven) -{ - - if(d < nh){ - rec_compute_sum_F_S_T(d+1, nh, S, ones, SSet, T, sizeofT, TSet, h, alpha, sumOdd, sumEven); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_F_S_T(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, h, alpha, sumOdd, sumEven); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - else{ - double result_F = compute_f(nh, S, T, sizeofT, TSet, h, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, result_F); - //LOGADD_NEW(sumOdd, result_F); - } - else{ - logAdd_New(sumEven, result_F); - //LOGADD_NEW(sumEven, result_F); - } - - } - - } -} // end rec_compute_sum_F_S_T() - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} F(S,T) -void compute_sum_F_S_T(int nh, int S, int ones, int * SSet, double * h, double ** alpha, double & sumOdd, double & sumEven){ - //TSet's length is set to be SSet's length: it is fine since each TSetLen is set accordingly to each subset T; - int * TSet = new int[ones]; - rec_compute_sum_F_S_T(0, nh, S, ones, SSet, 0, 0, TSet, h, alpha, sumOdd, sumEven); - delete[] TSet; - -} // end compute_sum_F_S_T() - - -void sub_h_Fast(int d, int nh, int S, int ones, int * SSet, double * h, double ** alpha){ - if(d < nh){ - - //this kind of ordering in the recursion is crucial; - //it guarantee when you want to compute one S, all its subsets have already been computed - sub_h_Fast(d+1, nh, S, ones, SSet, h, alpha); - - SSet[ones] = d; - sub_h_Fast(d+1, nh, S|(1<<d), (ones+1), SSet, h, alpha); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - h[0] = 0; //log(1) = 0; - //cout << "h[0] = 0" << endl; - //cout << endl; - return; - - } - - //if S > 0 - double sumOdd = MARK; - double sumEven = MARK; - - - compute_sum_F_S_T(nh, S, ones, SSet, h, alpha, sumOdd, sumEven); - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - h[S] = sumOdd; - //cout << "h[" << S << "] = " << h[S] << endl; - //cout << endl; - - } -} // end sub_h_Fast() - - -//HR: -// Compute h -void compute_h_Fast(int nh, double * h, double ** alpha){ - int * SSet = new int[nh]; - - sub_h_Fast(0, nh, 0, 0, SSet, h, alpha); - - delete [] SSet; - -} // end compute_h_Fast() - - - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} F(S,T) -void compute_sum_F_S_T_Iter(int nh, int S, double * h, double ** alpha, double & sumOdd, double & sumEven){ - - //all the subsets T of S, expect that T = 0 (empty set) - for(int T = 1; T <= S; T++){ - //if T is the subset of S - if((S|T) == S){ - - int TSetLen = binIntLen(T); - int * TSet = new int[TSetLen]; - binIntToDecIntArr(T, TSetLen, TSet); - - double result_F = compute_f(nh, S, T, TSetLen, TSet, h, alpha); - //sizeofT is odd - if(TSetLen % 2 == 1){ - logAdd_New(sumOdd, result_F); - //LOGADD_NEW(sumOdd, result_F); - } - else{ - logAdd_New(sumEven, result_F); - //LOGADD_NEW(sumEven, result_F); - } - - delete[] TSet; - - } - - } - -} - - -//HR: -// Compute h by iteration instead of recursion -void compute_h_Iter(int nh, double * h, double ** alpha){ - - // - h[0] = 0; - - //h[S]: S: from 1 to (1<<nh)-1 - for(int S = 1; S < (1<<nh); S++){ - - double sumOdd = MARK; - double sumEven = MARK; - - //int ones = binIntLen(S); - //cout << "\nones = " << ones << endl; - //int * SSet = new int[ones]; - //binIntToDecIntArr(S, ones, SSet); - //compute_sum_F_S_T(nh, S, ones, SSet, h, alpha, sumOdd, sumEven); - compute_sum_F_S_T_Iter(nh, S, h, alpha, sumOdd, sumEven); - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - h[S] = sumOdd; - } - -} - - -void rec_compute_AA_S( - int d, - int nh, - int S, - int ones, //leng of SSet - int * SSet, - int T, - int sizeofT, - int * TSet, - double * AA_S, - double ** alpha -){ - - if(d < nh){ - rec_compute_AA_S(d+1, nh, S, ones, SSet, T, sizeofT, TSet, AA_S, alpha); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_AA_S(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, AA_S, alpha); - } - } - else{ - if(T == 0){ - //cout << "\nT == 0" << endl; - - AA_S[T] = 0; - - //cout << "AA_S[" << T << "]=" << AA_S[T] << endl; - //cout << endl; - } - else{ - //TSet[0]: the right most element - //T - (1<<TSet[0]): the binary repre of the the left most biggest - // subset of T (including all the elements of T except the right most element) - //(1<<nh) - 1 - S: V - S - //AA_S[T - (1<<TSet[0])] must have been computed - - //cout << "\nT = " << T << endl; - //cout << "sizeofT = " << sizeofT << endl; - //printIntArr(TSet, sizeofT); - //cout << "alpha[" << TSet[0] << "][" << (1<<nh) - 1 - S << "] = " - // << alpha[TSet[0]][(1<<nh) - 1 - S] << endl; - //cout << "AA_S[" << T - (1<<TSet[0]) << "] = " << AA_S[T - (1<<TSet[0])] << endl; - - //AA_S[T] = alpha[TSet[0]][(1<<nh) - 1 - S] + AA_S[T - (1<<TSet[0])]; - - if(alpha[TSet[0]][(1<<nh) - 1 - S] == LOG_ZERO){ - AA_S[T] = LOG_ZERO; - } - else{ - AA_S[T] = alpha[TSet[0]][(1<<nh) - 1 - S] + AA_S[T - (1<<TSet[0])]; - } - - - //cout << "AA_S[" << T << "]=" << AA_S[T] << endl; - //cout << endl; - } - - } - - -} - - - -// Given S \subset V, -// Compute all T \subset S: AA_S(T) at one time -void compute_AA_S( - int nh, - int S, - int ones, //leng of SSet - int * SSet, - double * AA_S, - double ** alpha -){ - int * TSet = new int[ones]; - rec_compute_AA_S(0, nh, S, ones, SSet, 0, 0, TSet, AA_S, alpha); - delete[] TSet; - -} - - -// Given S \subset V, -// Compute all T \subset S: AA_S(T) at one time -void compute_AA_S_Iter( - int nh, - int S, - //int ones, //leng of SSet - //int * SSet, - double * AA_S, - double ** alpha -){ - - AA_S[0] = 0; - - //all the subsets T of S, expect that T = 0 (empty set) - for(int T = 1; T <= S; T++){ - //if T is the subset of S - if((S|T) == S){ - - int TSetLen = binIntLen(T); - int * TSet = new int[TSetLen]; - binIntToDecIntArr(T, TSetLen, TSet); - - //TSet[TSetLen-1]: the left most element - //T - (1<<TSet[TSetLen-1]): the binary repre of the the right most biggest - // subset of T (including all the elements of T except the left most element) - //(1<<nh) - 1 - S: V - S - //AA_S[T - (1<<TSet[TSetLen-1])] must have been computed - - AA_S[T] = alpha[TSet[TSetLen-1]][(1<<nh) - 1 - S] + AA_S[T - (1<<TSet[TSetLen-1])]; - - delete[] TSet; - - } - - } - -} - - - - -//HR: Compute RF(S, T) -double compute_RF(int nh, int S, int T, int sizeofT, int *TSet, double * RR, double ** alpha){ - - double result_RF = MARK; - double result_RR = RR[S-T]; - //LOGADD(result_f, result_h); - result_RF = result_RR; - if (result_RF == LOG_ZERO){ - return result_RF; - } - - //AA_S has been computed - if(AA_S[T] == LOG_ZERO){ - return LOG_ZERO; - } - else{ - result_RF += AA_S[T]; - } - - return result_RF; -} - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} RF(S,T) -void rec_compute_sum_RF_S_T( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * RR, - double ** alpha, - double & sumOdd, - double & sumEven) -{ - - if(d < nh){ - rec_compute_sum_RF_S_T(d+1, nh, S, ones, SSet, T, sizeofT, TSet, RR, alpha, sumOdd, sumEven); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_RF_S_T(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, RR, alpha, sumOdd, sumEven); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - else{ - double result_RF = compute_RF(nh, S, T, sizeofT, TSet, RR, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, result_RF); - //LOGADD_NEW(sumOdd, result_RF); - } - else{ - logAdd_New(sumEven, result_RF); - //LOGADD_NEW(sumEven, result_RF); - } - - } - - } -} // end rec_compute_sum_RF_S_T() - - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} RF(S,T) -void compute_sum_RF_S_T(int nh, int S, int ones, int * SSet, double * RR, double ** alpha, double & sumOdd, double & sumEven){ - - int * TSet = new int[ones]; - rec_compute_sum_RF_S_T(0, nh, S, ones, SSet, 0, 0, TSet, RR, alpha, sumOdd, sumEven); - delete[] TSet; - -} // end compute_sum_RF_S_T() - - -void sub_RR_Fast(int d, int nh, int S, int ones, int * SSet, double * RR, double ** alpha){ - if(d < nh){ - sub_RR_Fast(d+1, nh, S, ones, SSet, RR, alpha); - - SSet[ones] = d; - sub_RR_Fast(d+1, nh, S|(1<<d), (ones+1), SSet, RR, alpha); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - RR[0] = 0; //log(1) = 0; - //cout << "R[0] = 0" << endl; - //cout << endl; - return; - - } - - //For given S, for all T \subset S, Compute AA_S[T] - AA_S = new double [S+1]; - compute_AA_S(nh, S, ones, SSet, AA_S, alpha); - //compute_AA_S_Iter(nh, S, AA_S, alpha); - - double sumOdd = MARK; - double sumEven = MARK; - - - compute_sum_RF_S_T(nh, S, ones, SSet, RR, alpha, sumOdd, sumEven); - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - RR[S] = sumOdd; - delete[] AA_S; - - } -} // end sub_RR_Fast() - - - - - - - -//HR: -// Compute RR -void compute_RR_Fast(int nh, double * RR, double ** alpha){ - int * SSet = new int[nh]; - - sub_RR_Fast(0, nh, 0, 0, SSet, RR, alpha); - - delete[] SSet; - -} // end compute_RR_Fast() - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} RF(S,T) -void rec_compute_sum_RF_S_T_TSize( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * RR, - double ** alpha, - double & sumOdd, - double & sumEven, - int TSize) -{ - - if(d < nh){ - rec_compute_sum_RF_S_T_TSize(d+1, nh, S, ones, SSet, T, sizeofT, TSet, RR, alpha, sumOdd, sumEven, TSize); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_RF_S_T_TSize(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, RR, alpha, sumOdd, sumEven, TSize); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - //HR: new for *_TSize - else if(sizeofT <= TSize){ - //else{ - double result_RF = compute_RF(nh, S, T, sizeofT, TSet, RR, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, result_RF); - //LOGADD_NEW(sumOdd, result_RF); - } - else{ - logAdd_New(sumEven, result_RF); - //LOGADD_NEW(sumEven, result_RF); - } - - } - - } -} // end rec_compute_sum_RF_S_T_TSize() - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} RF(S,T) -void compute_sum_RF_S_T_TSize(int nh, int S, int ones, int * SSet, double * RR, double ** alpha, double & sumOdd, double & sumEven, int TSize){ - - int * TSet = new int[ones]; - rec_compute_sum_RF_S_T_TSize(0, nh, S, ones, SSet, 0, 0, TSet, RR, alpha, sumOdd, sumEven, TSize); - delete[] TSet; - - -}// end compute_sum_RF_S_T_TSize() - - - -void sub_RR_Fast_TSize(int d, int nh, int S, int ones, int * SSet, double * RR, double ** alpha, int TSize){ - if(d < nh){ - sub_RR_Fast_TSize(d+1, nh, S, ones, SSet, RR, alpha, TSize); - - SSet[ones] = d; - sub_RR_Fast_TSize(d+1, nh, S|(1<<d), (ones+1), SSet, RR, alpha, TSize); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - RR[0] = 0; //log(1) = 0; - //cout << "R[0] = 0" << endl; - //cout << endl; - return; - - } - - //For given S, for all T \subset S, Compute AA_S[T] - AA_S = new double [S+1]; - compute_AA_S(nh, S, ones, SSet, AA_S, alpha); - //compute_AA_S_Iter(nh, S, AA_S, alpha); - - double sumOdd = MARK; - double sumEven = MARK; - - - compute_sum_RF_S_T_TSize(nh, S, ones, SSet, RR, alpha, sumOdd, sumEven, TSize); - - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New_NonnegRes(sumOdd, sumEven); - //logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - RR[S] = sumOdd; - delete[] AA_S; - - } -}// end sub_RR_Fast_TSize() - - -//HR: -// Compute RR -void compute_RR_Fast_TSize(int nh, double * RR, double ** alpha, int TSize){ - int * SSet = new int[nh]; - - sub_RR_Fast_TSize(0, nh, 0, 0, SSet, RR, alpha, TSize); - - delete[] SSet; - -} // end compute_RR_Fast_TSize() - - - -void rec_compute_sum_F_S_T_Details( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * h, - double ** alpha, - double & sumOdd, - double & sumEven, - double * FSum) -{ - - if(d < nh){ - rec_compute_sum_F_S_T_Details(d+1, nh, S, ones, SSet, T, sizeofT, TSet, h, alpha, sumOdd, sumEven, FSum); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_F_S_T_Details(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, h, alpha, sumOdd, sumEven, FSum); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - else{ - double result_F = compute_f(nh, S, T, sizeofT, TSet, h, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, result_F); - //LOGADD_NEW(sumOdd, result_F); - - } - else{ - logAdd_New(sumEven, result_F); - //LOGADD_NEW(sumEven, result_F); - } - - //FSum[sizeofT - 1] stores the sum_{T \subset S, |T| = sizeofT} F(S,T) - logAdd_New(FSum[sizeofT - 1], result_F); - //LOGADD_NEW(sumEven, result_F); - - - - } - - } -} - - - -void compute_sum_F_S_T_Details(int nh, int S, int ones, int * SSet, double * h, double ** alpha, double & sumOdd, double & sumEven, double * FSum){ - //TSet's length is set to be SSet's length: it is fine since each TSetLen is set accordingly to each subset T; - int * TSet = new int[ones]; - rec_compute_sum_F_S_T_Details(0, nh, S, ones, SSet, 0, 0, TSet, h, alpha, sumOdd, sumEven, FSum); - delete[] TSet; - - -} - - -void sub_h_Fast_Details(int d, int nh, int S, int ones, int * SSet, double * h, double ** alpha, double * FSum){ - if(d < nh){ - - //this kind of ordering in the recursion is crucial; - //it guarantee when you want to compute one S, all its subsets have already been computed - sub_h_Fast_Details(d+1, nh, S, ones, SSet, h, alpha, FSum); - - SSet[ones] = d; - sub_h_Fast_Details(d+1, nh, S|(1<<d), (ones+1), SSet, h, alpha, FSum); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - h[0] = 0; //log(1) = 0; - //cout << "h[0] = 0" << endl; - //cout << endl; - return; - - } - - //if S > 0 - double sumOdd = MARK; - double sumEven = MARK; - - if(S < (1 << nh) - 1 ){ - compute_sum_F_S_T(nh, S, ones, SSet, h, alpha, sumOdd, sumEven); - } - //S == (1 << nh) - 1 - else{ - compute_sum_F_S_T_Details(nh, S, ones, SSet, h, alpha, sumOdd, sumEven, FSum); - } - - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - h[S] = sumOdd; - //cout << "h[" << S << "] = " << h[S] << endl; - //cout << endl; - - } -} - - -void compute_h_Fast_Details(int nh, double * h, double ** alpha, double * FSum){ - int * SSet = new int[nh]; - - sub_h_Fast_Details(0, nh, 0, 0, SSet, h, alpha, FSum); - - delete [] SSet; - -} - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} F(S,T) -void rec_compute_sum_F_S_T_TSize( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * h, - double ** alpha, - double & sumOdd, - double & sumEven, - int TSize) -{ - - if(d < nh){ - rec_compute_sum_F_S_T_TSize(d+1, nh, S, ones, SSet, T, sizeofT, TSet, h, alpha, sumOdd, sumEven, TSize); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_F_S_T_TSize(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, h, alpha, sumOdd, sumEven, TSize); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - //else { - //HR: new for *_TSize - else if(sizeofT <= TSize){ - double result_F = compute_f(nh, S, T, sizeofT, TSet, h, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - //if(sizeofT % 2 == 1 && sizeofT <= TSize){ - logAdd_New(sumOdd, result_F); - //LOGADD_NEW(sumOdd, result_F); - } - else{ - //else if(sizeofT % 2 == 0 && sizeofT <= TSize){ - logAdd_New(sumEven, result_F); - //LOGADD_NEW(sumEven, result_F); - } - - } - - } -} // end rec_compute_sum_F_S_T_TSize() - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} F(S,T) -void compute_sum_F_S_T_TSize(int nh, int S, int ones, int * SSet, double * h, double ** alpha, double & sumOdd, double & sumEven, int TSize){ - //TSet's length is set to be SSet's length: it is fine since each TSetLen is set accordingly to each subset T; - int * TSet = new int[ones]; - rec_compute_sum_F_S_T_TSize(0, nh, S, ones, SSet, 0, 0, TSet, h, alpha, sumOdd, sumEven, TSize); - delete[] TSet; - - -} - - -void sub_h_Fast_TSize(int d, int nh, int S, int ones, int * SSet, double * h, double ** alpha, int TSize){ - if(d < nh){ - - //this kind of ordering in the recursion is crucial; - //it guarantee when you want to compute one S, all its subsets have already been computed - sub_h_Fast_TSize(d+1, nh, S, ones, SSet, h, alpha, TSize); - - SSet[ones] = d; - sub_h_Fast_TSize(d+1, nh, S|(1<<d), (ones+1), SSet, h, alpha, TSize); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - h[0] = 0; //log(1) = 0; - //cout << "h[0] = 0" << endl; - //cout << endl; - return; - - } - - //if S > 0 - double sumOdd = MARK; - double sumEven = MARK; - - - compute_sum_F_S_T_TSize(nh, S, ones, SSet, h, alpha, sumOdd, sumEven, TSize); - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New_NonnegRes(sumOdd, sumEven); - //logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - h[S] = sumOdd; - //cout << "h[" << S << "] = " << h[S] << endl; - //cout << endl; - - } -} // end sub_h_Fast_TSize() - - -//HR: -// Compute h - -void compute_h_Fast_TSize(int nh, double * h, double ** alpha, int TSize){ - int * SSet = new int[nh]; - - sub_h_Fast_TSize(0, nh, 0, 0, SSet, h, alpha, TSize); - - delete [] SSet; - -} // end compute_h_Fast_TSize() - - - - -void rec_compute_sum_RF_S_T_Details( - int d, - int nh, - int S, - int ones, - int * SSet, - int T, - int sizeofT, - int * TSet, - double * RR, - double ** alpha, - double & sumOdd, - double & sumEven, - double * RFSum) -{ - - if(d < nh){ - rec_compute_sum_RF_S_T_Details(d+1, nh, S, ones, SSet, T, sizeofT, TSet, RR, alpha, sumOdd, sumEven, RFSum); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((S>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_sum_RF_S_T_Details(d+1, nh, S, ones, SSet, (T | (1<<d)), (sizeofT + 1), TSet, RR, alpha, sumOdd, sumEven, RFSum); - } - } - else{ - if(sizeofT == 0){ - //|T| == 0 does not count - return; - - } - else{ - double result_RF = compute_RF(nh, S, T, sizeofT, TSet, RR, alpha); - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, result_RF); - //LOGADD_NEW(sumOdd, result_RF); - } - else{ - logAdd_New(sumEven, result_RF); - //LOGADD_NEW(sumEven, result_RF); - } - //RFSum[sizeofT - 1] stores the sum_{T \subset S, |T| = sizeofT} RF(S,T) - logAdd_New(RFSum[sizeofT - 1], result_RF); - //LOGADD_NEW(RFSum[sizeofT - 1], result_RF); - - } - - } -} - - - -void compute_sum_RF_S_T_Details(int nh, int S, int ones, int * SSet, double * RR, double ** alpha, double & sumOdd, double & sumEven, double * RFSum){ - - int * TSet = new int[ones]; - rec_compute_sum_RF_S_T_Details(0, nh, S, ones, SSet, 0, 0, TSet, RR, alpha, sumOdd, sumEven, RFSum); - delete[] TSet; - - -} - - - -void sub_RR_Fast_Details(int d, int nh, int S, int ones, int * SSet, double * RR, double ** alpha, double * RFSum){ - if(d < nh){ - sub_RR_Fast_Details(d+1, nh, S, ones, SSet, RR, alpha, RFSum); - - SSet[ones] = d; - sub_RR_Fast_Details(d+1, nh, S|(1<<d), (ones+1), SSet, RR, alpha, RFSum); - } - //d == nh - else{ - //S = 0 means that S is the empty set; - if(S == 0){ - RR[0] = 0; //log(1) = 0; - //cout << "R[0] = 0" << endl; - //cout << endl; - return; - - } - - //For given S, for all T \subset S, Compute AA_S[T] - AA_S = new double [S+1]; - compute_AA_S(nh, S, ones, SSet, AA_S, alpha); - //compute_AA_S_Iter(nh, S, AA_S, alpha); - - double sumOdd = MARK; - double sumEven = MARK; - - if(S < (1 << nh) - 1 ){ - compute_sum_RF_S_T(nh, S, ones, SSet, RR, alpha, sumOdd, sumEven); - } - //if S == (1 << nh) - 1 - else{ - compute_sum_RF_S_T_Details(nh, S, ones, SSet, RR, alpha, sumOdd, sumEven, RFSum); - } - - - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - RR[S] = sumOdd; - delete[] AA_S; - - } -} - - - - -void compute_RR_Fast_Details(int nh, double * RR, double ** alpha, double * RFSum){ - int * SSet = new int[nh]; - - sub_RR_Fast_Details(0, nh, 0, 0, SSet, RR, alpha, RFSum); - - delete[] SSet; - -} - - - - - - - - -//HR: Compute: \sum_{k=1}^{|S|} (-1)^{k+1} \sum{T \subset S, |T|=k} RF(S,T) -void compute_sum_RF_S_T_Iter(int nh, int S, double * RR, double ** alpha, double & sumOdd, double & sumEven){ - - //all the subsets T of S, expect that T = 0 (empty set) - for(int T = 1; T <= S; T++){ - //if T is the subset of S - if((S|T) == S){ - - int TSetLen = binIntLen(T); - int * TSet = new int[TSetLen]; - binIntToDecIntArr(T, TSetLen, TSet); - - double result_RF = compute_RF(nh, S, T, TSetLen, TSet, RR, alpha); - //sizeofT is odd - if(TSetLen % 2 == 1){ - logAdd_New(sumOdd, result_RF); - //LOGADD_NEW(sumOdd, result_RF); - } - else{ - logAdd_New(sumEven, result_RF); - //LOGADD_NEW(sumEven, result_RF); - } - - delete[] TSet; - } - - } - -} - -//HR: -// Compute RR -void compute_RR_Iter(int nh, double * RR, double ** alpha){ - - - RR[0] = 0; //log(1) = 0; - - //RR[S]: S: from 1 to (1<<nh)-1 - for(int S = 1; S < (1<<nh); S++){ - //For given S, for all T \subset S, Compute AA_S[T] - AA_S = new double [S+1]; - //compute_AA_S(nh, S, ones, SSet, AA_S, alpha); - compute_AA_S_Iter(nh, S, AA_S, alpha); - - double sumOdd = MARK; - double sumEven = MARK; - - compute_sum_RF_S_T_Iter(nh, S, RR, alpha, sumOdd, sumEven); - - //if sumEven has been assigned some value instead of MARK - if(sumEven != MARK){ - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - } - - RR[S] = sumOdd; - //cout << "RR[" << S << "] = " << h[S] << endl; - //cout << endl; - - delete[] AA_S; - - } - -} - - - - -// Given v \in V, given U \subset V-{v}, -// Compute all T \subset (V-{v}-U) = TMax: Eta_U(T) at one time -void rec_compute_Eta_U( - int d, - int nh, - int TMax, - int TMaxSetLen, //leng of SSet - int * TMaxSet, - int U, - int T, - int sizeofT, - int * TSet, - double * Eta_U, - double ** alpha -){ - - if(d < nh){ - rec_compute_Eta_U(d+1, nh, TMax, TMaxSetLen, TMaxSet, U, T, sizeofT, TSet, Eta_U, alpha); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((TMax>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_Eta_U(d+1, nh, TMax, TMaxSetLen, TMaxSet, U, (T | (1<<d)), (sizeofT + 1), TSet, Eta_U, alpha); - } - } - else{ - if(T == 0){ - //cout << "\nT == 0" << endl; - - Eta_U[T] = 0; - - //cout << "AA_S[" << T << "]=" << AA_S[T] << endl; - //cout << endl; - } - else{ - - Eta_U[T] = alpha[TSet[0]][U] + Eta_U[T - (1<<TSet[0])]; - - } - - } - - -} - - -// Given v \in V, given U \subset V-{v}, -// Compute all T \subset (V-{v}-U) = TMax: Eta_U(T) at one time -void compute_Eta_U( - int nh, - int TMax, - int TMaxSetLen, - int * TMaxSet, - int U, - double * Eta_U, - double ** alpha -){ - int * TSet = new int[TMaxSetLen]; - rec_compute_Eta_U(0, nh, TMax, TMaxSetLen, TMaxSet, U, 0, 0, TSet, Eta_U, alpha); - delete[] TSet; - -} - - -// Given v \in V, given U \subset V-{v}, -// Compute K_v(U) -void rec_compute_K_v( - int d, - int nh, - int TMax, - int TMaxSetLen, //leng of SSet - int * TMaxSet, - int U, - int T, - int sizeofT, - int * TSet, - double * Eta_U, - double * K_v, - double ** alpha, - double & sumOdd, - double & sumEven -){ - if(d < nh){ - rec_compute_K_v(d+1, nh, TMax, TMaxSetLen, TMaxSet, U, T, sizeofT, TSet, Eta_U, K_v, alpha, sumOdd, sumEven); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((TMax>>d) & 1) == 1){ - TSet[sizeofT] = d; - rec_compute_K_v(d+1, nh, TMax, TMaxSetLen, TMaxSet, U, (T | (1<<d)), (sizeofT + 1), TSet, Eta_U, K_v, alpha, sumOdd, sumEven); - } - } - else{ - double abs_result = RRFunc[TMax - T] + Eta_U[T]; - //sizeofT is odd - if(sizeofT % 2 == 1){ - logAdd_New(sumOdd, abs_result); - //LOGADD_NEW(sumOdd, abs_result); - } - else{ - logAdd_New(sumEven, abs_result); - //LOGADD_NEW(sumEven, abs_result); - } - - } - -} - - - -// Given v \in V, given U \subset V-{v}, -// Compute K_v(U) -void compute_K_v( - int nh, - double * K_v, - int v, - int U, - int USetLen, - int * USet, - double * Eta_U, - double ** alpha -) - - -{ - //TMax = V - {v} - U - int TMax = (1 << nh) - 1 - (1 << v) - U; - int TMaxSetLen = nh - 1 - USetLen; - int * TMaxSet = new int[TMaxSetLen]; - binIntToDecIntArr(TMax, TMaxSetLen, TMaxSet); - - //compute Eta_U - Eta_U = new double [TMax+1]; - compute_Eta_U(nh, TMax, TMaxSetLen, TMaxSet, U, Eta_U, alpha); - -// totalOfMixEta << "\nEta_U U == " << U << ":" << endl; -// for(int index = 0; index < TMax+1; index++){ -// totalOfMixEta << "Eta_U[" << index << "] = " << Eta_U[index] << endl; -// } - - - - double result_K_v; - - double sumOdd = MARK; - double sumEven = MARK; - - int * TSet = new int[TMaxSetLen]; - rec_compute_K_v(0, nh, TMax, TMaxSetLen, TMaxSet, U, 0, 0, TSet, Eta_U, K_v, alpha, sumOdd, sumEven); - - - - // sum of itmes of Even sizeofT must have been assigned some value, since |T| = 0 must exist - // sum of itmes of odd sizeofT must have been assigned some value could be not assigned so that it is still MARK - if(sumOdd == MARK){ - result_K_v = sumEven; - } - else{ - //if sum of itmes of Even sizeofT > sum of itmes of odd sizeofT, so that log(sumEven) > log(sumOdd) - if(sumEven > sumOdd){ - logMinus_New(sumEven, sumOdd); - //LOGMINUS_NEW(sumEven, sumOdd); - //result_K_v is log(prob) < 0 - result_K_v = sumEven; - } - else if(sumEven == sumOdd){ - //cerr<<"\n******Original K_v is zero!" << endl; - result_K_v = LOG_ZERO; - } - else{ - //cerr<<"\n******Original K_v is negetive!" << endl; - logMinus_New(sumOdd, sumEven); - //LOGMINUS_NEW(sumOdd, sumEven); - //use result_K_v > 0 to represent negative prob - result_K_v = - sumOdd; - //cerr<<"K_v[" << U << "]" << result_K_v << endl; - } - } - K_v[U] = result_K_v; - - delete[] TSet; - - delete[] Eta_U; - - -} - - -void init_all_K_v(int d, int S, double * K_v, double value, int ones, int nh){ - //cerr<<" d: "<<d<<endl; - - if (d < nh){ - init_all_K_v(d+1, S, K_v, value, ones, nh); - - //HR: ones means the num of 1 bits, represeting the num of parents - //HR: S | (1 << d) reprents the S could have 1 bit in the d'th if current S does not have - //HR: if (ones < k) - init_all_K_v(d+1, S | (1 << d), K_v, value, ones+1, nh); - } - else{ - K_v[S] = value; - - } -} - - -void rec_compute_all_K_v( - int d, - int nh, - int UMax, - int UMaxSetLen, //leng of SSet - int * UMaxSet, - int U, - int USetLen, - int * USet, - double * K_v, - int v, - double ** alpha -){ - if(d < nh){ - rec_compute_all_K_v(d+1, nh, UMax, UMaxSetLen, UMaxSet, U, USetLen, USet, K_v, v, alpha); - - //the binary repre of S has 1 in d'th position (starting from 0) from right - if(((UMax>>d) & 1) == 1){ - USet[USetLen] = d; - rec_compute_all_K_v(d+1, nh, UMax, UMaxSetLen, UMaxSet, (U | (1<<d)), (USetLen + 1), USet, K_v, v, alpha); - } - } - else{ - compute_K_v(nh, K_v, v, U, USetLen, USet, Eta_U, alpha); - - } - -} - - -void compute_all_K_v( - int nh, - double * K_v, - int v, - double ** alpha -){ - - init_all_K_v(0, 0, K_v, LOG_ZERO, 0, nh); - - //UMax = V - {v} - int UMax = (1 << nh) - 1 - (1 << v); - int UMaxSetLen = nh - 1; - int * UMaxSet = new int[UMaxSetLen]; - binIntToDecIntArr(UMax, UMaxSetLen, UMaxSet); - - int * USet = new int[UMaxSetLen]; - rec_compute_all_K_v(0, nh, UMax, UMaxSetLen, UMaxSet, 0, 0, USet, K_v, v, alpha); - - delete[] USet; - -} - - diff --git a/sourcecodes/k-best/src/UpdateHR2.h b/sourcecodes/k-best/src/UpdateHR2.h deleted file mode 100644 index c7deefe8..00000000 --- a/sourcecodes/k-best/src/UpdateHR2.h +++ /dev/null @@ -1,511 +0,0 @@ -#include<stdio.h> -#include<stdlib.h> - -#include<iostream> -#include<vector> -#include<deque> -#include<string> -#include<fstream> -#include<math.h> - -#include"Arguments.h" -#include"Model.h" - -using namespace std; - - -struct ADTreenode{ - int count; - - //i.e. start attr which = *; - int startVaryNodeInd; - - //struct ADVarynode * ADVaryNodePs[]; - struct ADVarynode ** ADVaryNodePs; -}; - -typedef struct ADTreenode ADTreeNode; - -struct ADVarynode{ - //Represent Vary Index - int index; - - int mcv; - - //struct ADTreenode * ADTreeNodePs[]; - struct ADTreenode ** ADTreeNodePs; - -}; - -typedef struct ADVarynode ADVaryNode; - - -typedef struct { - //the count for each arrangment of contiTableAttrs - //contiTableCounts.size() == the product of the arity of each element in contiTableAttrs - //do not explicitly record the whole contiTable - vector<int> contiTableCounts; - - //invariant: in the decreasing order - vector<int> contiTableAttrs; - - //condiAttrs.size() == condiVals.size() - //invariant: in the increasing order - vector<int> condiAttrs; - vector<int> condiVals; - - //invariant: contiTableAttrs.size() + condiAttrs.size() == the whole original inquiry length - // finally: condiAttrs.size() == 0 -} CondiContiTable; - - - - - -ADTreeNode * MakeADTree(int, vector<int> &, vector< vector<int> > &, vector<int> &); -ADVaryNode * MakeVaryNode(int, vector<int> &, vector< vector<int> > &, vector<int> &); -void PrintADTreeNode(ADTreeNode *, int, const int, vector<int> &); -void PrintADVaryNode(ADVaryNode *, int, const int, vector<int> &); -void FreeADTreeNode(ADTreeNode *, const int, vector<int> &); -void FreeADVaryNode(ADVaryNode *, const int, vector<int> &); - - -CondiContiTable MakeContab(deque<int>, ADTreeNode *, - vector<int> &, vector<int> &, const vector<int> &); - -void MinusContab(CondiContiTable &, CondiContiTable *, int, int); - -void ConcatContab(CondiContiTable *, int, int, CondiContiTable &); - - - - - -//HR: -// a_i is in {0, ..., M-1} -// dm: the data matrix: R * M -// dmIndex: initially stores {0, 1, ..., R - 1}, it is just the light-weight index for dm -// arities: stores the arity of each attr -// could use vector<int> & dmIndex instead of vector<int> dmIndex -ADTreeNode * MakeADTree(int a_i, vector<int> & dmIndex, vector< vector<int> > & dm, vector<int> & arities){ - //M = num of attr - int M = dm[0].size(); - - ADTreeNode * ADTreeNodeP1 = (ADTreeNode *) malloc(sizeof(ADTreeNode)); - ADTreeNodeP1->count = dmIndex.size(); - ADTreeNodeP1->startVaryNodeInd = a_i; - //base - if(a_i >= M){ - ADTreeNodeP1->ADVaryNodePs = NULL; - } - else{ - ADTreeNodeP1->ADVaryNodePs = (ADVaryNode **) malloc(sizeof(ADVaryNode*) * - (M - 1 - a_i + 1)); - } - for(int a_j = a_i; a_j <= M-1; a_j++){ - ADTreeNodeP1->ADVaryNodePs[a_j - a_i] = MakeVaryNode(a_j, dmIndex, dm, arities); - } - return ADTreeNodeP1; - -}//end ADTreeNode * MakeADTree() - - - -//HR: -// a_i is in {0, ..., M-1} -// dm: the data matrix: R * M -// dmIndex: initially stores {0, 1, ..., R - 1} -// arities: stores the arity of each attr -// could use vector<int> & dmIndex instead of vector<int> dmIndex -ADVaryNode * MakeVaryNode(int a_i, vector<int> & dmIndex, vector< vector<int> > & dm, vector<int> & arities){ - ADVaryNode * ADVaryNodeP1 = (ADVaryNode *) malloc(sizeof(ADVaryNode)); - ADVaryNodeP1->index = a_i; - int n_i = arities[a_i];//may be used as global var - ADVaryNodeP1->ADTreeNodePs = (ADTreeNode **) malloc(sizeof(ADTreeNode *) * n_i); - vector<int> dmIndexSub[n_i]; - for(unsigned int j = 0; j <= dmIndex.size() - 1; j++){ - int v = dm[dmIndex[j]][a_i]; - dmIndexSub[v].push_back(dmIndex[j]); - } - ADVaryNodeP1->mcv = 0; - int maxCount = dmIndexSub[0].size(); - for(int j = 1; j <= n_i - 1; j++){ - if((int) dmIndexSub[j].size() > maxCount){ - maxCount = dmIndexSub[j].size(); - ADVaryNodeP1->mcv = j; - } - } - for(int j = 0; j <= n_i - 1; j++){ - if(dmIndexSub[j].size() == 0 || j == ADVaryNodeP1->mcv){ - ADVaryNodeP1->ADTreeNodePs[j] = NULL; - } - else{ - ADVaryNodeP1->ADTreeNodePs[j] = MakeADTree(a_i+1, dmIndexSub[j], dm, arities); - } - } - //not necessary in fact - //dmIndex.clear(); - //HR: Neither necessary nor correct - //delete dmIndex; - return ADVaryNodeP1; - - -}//end ADVaryNode * MakeVaryNode() - - -//HR: -// ADTreeNodeP1: pointers to the ADTreeNode -// level: starting from 0 -// M: the num of attr -// arities: stores the arity of each attr -// initial call: PrintADTreeNode(ADTreeNodeP1, 0, M, arities) in Model.h -// pre-order to print the ADtree -void PrintADTreeNode(ADTreeNode * ADTreeNodeP1, int level, const int M, vector<int> & arities){ - string strSpace = ""; - for(int i = 0; i < level; i++){ - strSpace += " "; - } - cout << strSpace << "ADTreeNode" << endl; - cout << strSpace << "Count = " << ADTreeNodeP1->count << endl; - cout << strSpace << "startVaryNodeInd = " << ADTreeNodeP1->startVaryNodeInd << endl; - if(ADTreeNodeP1->ADVaryNodePs == NULL){ - return; - } - else{ - for(int i = 0; i < M - 1 - ADTreeNodeP1->startVaryNodeInd + 1; i++){ - PrintADVaryNode(ADTreeNodeP1->ADVaryNodePs[i], level+1, M, arities); - } - } -} //end void PrintADTreeNode() - - -//HR: -// ADVaryNodeP1: pointers to the ADVaryNode -// level: starting from 0 -// M: the num of attr -// arities: stores the arity of each attr -// pre-order to print the ADtree -void PrintADVaryNode(ADVaryNode * ADVaryNodeP1, int level, const int M, vector<int> & arities){ - string strSpace = ""; - for(int i = 0; i < level; i++){ - strSpace += " "; - } - cout << strSpace << "ADVaryNode" << endl; - cout << strSpace << "index = " << ADVaryNodeP1->index << endl; - cout << strSpace << "mcv = " << ADVaryNodeP1->mcv << endl; - int n_i = arities[ADVaryNodeP1->index]; //may be changed to global var - for(int j = 0; j <= n_i - 1; j++){ - if(j == ADVaryNodeP1->mcv){ - cout << strSpace << " mcv" << endl; - } - else if(ADVaryNodeP1->ADTreeNodePs[j] == NULL){ - cout << strSpace << " NULL" << endl; - } - else{ - PrintADTreeNode(ADVaryNodeP1->ADTreeNodePs[j], level+1, M, arities); - } - } - -}//end void PrintADVaryNode() - - - -//HR: -// ADTreeNodeP1: pointers to the ADTreeNode -// M: the num of attr -// arities: stores the arity of each attr -// initial call: FreeADTreeNode(ADTreeNodeP1, M, arities) in Model.h -// pre-order to free the ADtree -void FreeADTreeNode(ADTreeNode * ADTreeNodeP1, const int M, vector<int> & arities){ - - if(ADTreeNodeP1->ADVaryNodePs != NULL){ - for(int i = 0; i < M - 1 - ADTreeNodeP1->startVaryNodeInd + 1; i++){ - FreeADVaryNode(ADTreeNodeP1->ADVaryNodePs[i], M, arities); - } - free(ADTreeNodeP1->ADVaryNodePs); - } - - free(ADTreeNodeP1); -} //end void FreeADTreeNode() - - -//HR: -// ADVaryNodeP1: pointers to the ADVaryNode -// M: the num of attr -// arities: stores the arity of each attr -// pre-order to free the ADtree -void FreeADVaryNode(ADVaryNode * ADVaryNodeP1, const int M, vector<int> & arities){ - - int n_i = arities[ADVaryNodeP1->index]; //may be changed to global var - for(int j = 0; j <= n_i - 1; j++){ - if(j == ADVaryNodeP1->mcv){ - ; - } - else if(ADVaryNodeP1->ADTreeNodePs[j] == NULL){ - ; - } - else{ - FreeADTreeNode(ADVaryNodeP1->ADTreeNodePs[j], M, arities); - } - } - free(ADVaryNodeP1->ADTreeNodePs); - free(ADVaryNodeP1); - -}//end void FreeADVaryNode() - - - -//Error: if use ofstream of1 instead of ofstream & of1 -//In file included from Model.h:19, -// from main.cc:6: -//UpdateHR2.h: In copy constructor `std::basic_ios<char, std::char_traits<char> >::basic_ios(const std::basic_ios<char, std::char_traits<char> >&)': -///usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/bits/ios_base.h:781: error: `std::ios_base::ios_base(const std::ios_base&)' is private -//UpdateHR2.h:220: error: within this context -//UpdateHR2.h: In copy constructor `std::basic_filebuf<char, std::char_traits<char> >::basic_filebuf(const std::basic_filebuf<char, std::char_traits<char> >&)': -///usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/streambuf:769: error: `std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char, _Traits = std::char_traits<char>]' is private -//UpdateHR2.h:220: error: within this context -//UpdateHR2.h: In function `void print_CondiContiTable(CondiContiTable&, std::ofstream)': -//UpdateHR2.h:220: error: initializing argument 2 of `void print_vec(std::vector<int, std::allocator<int> >, std::ofstream)' - - -void print_vec(vector<int> & vec1, ofstream & of1){ - for(int i = 0; i < (int) vec1.size(); i++){ - of1 << vec1[i] << " "; - } - of1 << endl; -} - -void print_deque(deque<int> & v1, ofstream & of1){ - for(int i = 0; i < (int) v1.size(); i++){ - of1 << v1[i] << " "; - } - of1 << endl; -} - -void print_CondiContiTable(CondiContiTable & ccTable1, ofstream & of1){ - of1 << "ccTable1.contiTableCounts: " << endl; - print_vec(ccTable1.contiTableCounts, of1); - - of1 << "ccTable1.contiTableAttrs: " << endl; - print_vec(ccTable1.contiTableAttrs, of1); - - of1 << "ccTable1.condiAttrs: " << endl; - print_vec(ccTable1.condiAttrs, of1); - - of1 << "ccTable1.condiVals: " << endl; - print_vec(ccTable1.condiVals, of1); - -} - - - -void print_vec(vector<int> & vec1){ - for(int i = 0; i < (int) vec1.size(); i++){ - cout << vec1[i] << " "; - } - cout << endl; -} - - -void print_deque(deque<int> & v1){ - for(int i = 0; i < (int) v1.size(); i++){ - cout << v1[i] << " "; - } - cout << endl; -} - -void print_CondiContiTable(CondiContiTable & ccTable1){ - cout << "ccTable1.contiTableCounts: " << endl; - print_vec(ccTable1.contiTableCounts); - - cout << "ccTable1.contiTableAttrs: " << endl; - print_vec(ccTable1.contiTableAttrs); - - cout << "ccTable1.condiAttrs: " << endl; - print_vec(ccTable1.condiAttrs); - - cout << "ccTable1.condiVals: " << endl; - print_vec(ccTable1.condiVals); - -} - - - -//HR: -// inquiryAttrs: {a_i_1, ..., a_i_n} -// ADNP: The current pointer to ADTreeNode -// givenAttrs, givenVals explicilty record the meaning of ADNP -// {b_i_1, ..., b_i_m} = {value_b_i_1, .. value_b_i_m} -// pre: -// inquiryAttrs is in the increasing order -// givenAttrs is in the increasing order -CondiContiTable MakeContab(deque<int> inquiryAttrs, ADTreeNode * ADNP, - vector<int> & givenAttrs, vector<int> & givenVals, const vector<int> & arities){ - -// cout << "\nMakeContab()" << endl; -// cout << "inquiryAttrs" << endl; -// print_deque(inquiryAttrs); -// cout << "givenAttrs" << endl; -// print_vec(givenAttrs); -// cout << "givenVals" << endl; -// print_vec(givenVals); - - - - - //base 1 - if(ADNP == NULL){ - CondiContiTable bottomTable; - - //base 1.1 - //if(inquiryAttrs.size() == 0){ - if(inquiryAttrs.empty()){ - bottomTable.contiTableCounts.push_back(0); - //bottomTable.contiTableAttrs is empty - bottomTable.condiAttrs = givenAttrs; - bottomTable.condiVals = givenVals; - - //cout << "//base 1.1: if(ADNP == NULL) and if(inquiryAttrs.empty())" << endl; - //print_CondiContiTable(bottomTable); - - } - //base 1.2 - //if(inquiryAttrs.size() > 0) - else{ - int rowNum = 1; - for(unsigned int i = 0; i < inquiryAttrs.size(); i++){ - //Note: I explicitly write inquiryAttrs[inquiryAttrs.size() - 1 - i ] instead of - // inquiryAttrs[i] because this is really the ordering to create the whole contiTable - int lastAttr = inquiryAttrs[inquiryAttrs.size() - 1 - i ]; - rowNum *= arities[lastAttr]; - - bottomTable.contiTableAttrs.push_back(lastAttr); - } - bottomTable.condiAttrs = givenAttrs; - bottomTable.condiVals = givenVals; - - for(int i = 0; i < rowNum; i++){ - bottomTable.contiTableCounts.push_back(0); - } - - //cout << "//base 1.2: if(ADNP == NULL) and if(!inquiryAttrs.empty())" << endl; - //print_CondiContiTable(bottomTable); - } - - - - return bottomTable; - - }// end if(ADNP == NULL) - - //base 2 - else if (inquiryAttrs.empty()){ - CondiContiTable bottomTable; - bottomTable.contiTableCounts.push_back(ADNP->count); - //bottomTable.contiTableAttrs is empty - bottomTable.condiAttrs = givenAttrs; - bottomTable.condiVals = givenVals; - - //cout << "//base 2: if(ADNP != NULL) and if(inquiryAttrs.empty())" << endl; - //print_CondiContiTable(bottomTable); - - return bottomTable; - } - else{ - int a_i_1 = inquiryAttrs.front(); - int VNIndex = a_i_1 - ADNP->startVaryNodeInd; - ADVaryNode * VNP = ADNP->ADVaryNodePs[VNIndex]; - int mcv = VNP->mcv; - int n_i_1 = arities[a_i_1]; - CondiContiTable CTs[n_i_1]; - - //delete the 1st element a_i_1 of inquiryAtts, will never use the 1st element a_i_1 again - //but does not allow the sub_program to delete more elements, so use deque<int> inquiryAttrs instead of deque<int> & inquiryAttrs - //vector<int> & givenAttrs, vector<int> & givenVals can be used because the sub_program will change but then restore it - inquiryAttrs.pop_front(); - - for(int k = 0; k < n_i_1; k++){ - if(k != mcv){ - ADTreeNode * ADNP_k = VNP -> ADTreeNodePs[k]; - - vector<int> newGivenAttrs = givenAttrs; - newGivenAttrs.push_back(a_i_1); - vector<int> newGivenVals = givenVals; - newGivenVals.push_back(k); - CTs[k] = MakeContab(inquiryAttrs, ADNP_k, newGivenAttrs, newGivenVals, arities); - - } - } - CondiContiTable sumCTs = MakeContab(inquiryAttrs, ADNP, givenAttrs, givenVals, arities); - MinusContab(sumCTs, CTs, n_i_1, mcv); - - CondiContiTable result; - ConcatContab(CTs, n_i_1, a_i_1, result); - - //cout << "//non-base: " << endl; - //print_CondiContiTable(result); - - return result; - } - -}// end CondiContiTable MakeContab() - - -void MinusContab(CondiContiTable & sumCTs, CondiContiTable * CTs, int n_i_1, int mcv){ - CTs[mcv].contiTableCounts = sumCTs.contiTableCounts; - CTs[mcv].contiTableAttrs = sumCTs.contiTableAttrs; - for(unsigned int i = 0; i < CTs[mcv].contiTableCounts.size(); i++){ - for(int k = 0; k < n_i_1; k++){ - if(k != mcv){ - CTs[mcv].contiTableCounts[i] -= CTs[k].contiTableCounts[i]; - } - } - } - //assume arities of each attr >=2 - if(mcv != 0){ - CTs[mcv].condiAttrs = CTs[0].condiAttrs; - CTs[mcv].condiVals = CTs[0].condiVals; - } - else{ - CTs[mcv].condiAttrs = CTs[1].condiAttrs; - CTs[mcv].condiVals = CTs[1].condiVals; - } - CTs[mcv].condiVals.pop_back(); - CTs[mcv].condiVals.push_back(mcv); - -} //end void MinusContab() - - -void ConcatContab(CondiContiTable * CTs, int n_i_1, int a_i_1, CondiContiTable & concatedTable){ - for(int i = 0; i < n_i_1; i++){ - //for each i, CTs[i].contiTableCounts.size() is the same - for(unsigned int j = 0; j < CTs[i].contiTableCounts.size(); j++){ - concatedTable.contiTableCounts.push_back(CTs[i].contiTableCounts[j]); - } - } - - //check: a_i_1 == CTs[0].condiAttrs.back(); - if(a_i_1 != CTs[0].condiAttrs.back()){ - cout << "Error: a_i_1 != CTs[0].condiAttrs.back()" << endl; - cout << "a_i_1 = " << a_i_1 << endl; - cout << "CTs[0].condiAttrs.back() = " << CTs[0].condiAttrs.back() << endl; - } - - //move a_i_1 from the end of CTs[0].condiAttrs to the end of concatedTable.contiTableAttrs - concatedTable.contiTableAttrs = CTs[0].contiTableAttrs; - concatedTable.contiTableAttrs.push_back(a_i_1); - - concatedTable.condiAttrs = CTs[0].condiAttrs; - concatedTable.condiAttrs.pop_back(); - - concatedTable.condiVals = CTs[0].condiVals; - concatedTable.condiVals.pop_back(); - -} //end void ContatContab() - - - - - - - diff --git a/sourcecodes/k-best/src/arcToNet.cc b/sourcecodes/k-best/src/arcToNet.cc deleted file mode 100644 index b071baab..00000000 --- a/sourcecodes/k-best/src/arcToNet.cc +++ /dev/null @@ -1,233 +0,0 @@ -#include <iostream> -#include <fstream> -#include <iomanip> -//#include "varpar.h" -#include <stdlib.h> -#include <math.h> -#include <list> -#include <stdio.h> -#include <vector> -//#include "cfg.h" -#include <string.h> -#include <cmath> -//HR -//#define EPSILON 0.001 -#define EPSILON 0.00001 - - -//HR: Add for hash_set -#if __GNUC__ < 3 && __GNUC__ >= 2 && __GNUC_MINOR__ >= 95 -# include <hash_set> -# include <functional> -# define gnu_namespace std -#elif __GNUC__ >= 3 -# include <ext/hash_set> -# if __GNUC_MINOR__ == 0 -# include <functional> -# define gnu_namespace std -# else -# include <ext/functional> -# define gnu_namespace __gnu_cxx -# endif -#else -# include <hash_set.h> -# include <functional.h> -# define gnu_namespace std -#endif -using namespace gnu_namespace; -#include <set> -// - - -using namespace std; - - -//HR: add from Engine.h in BayesNw -#define MARK 9e99 -#define LOG_ZERO -1e101 -//#define LOGMINUS_NEW(logA, logB) if(logA == MARK) logA = logB; else if (logA == LOG_ZERO) logA = logB; else if (logB == LOG_ZERO) logA = logA; else logA = logA + log(1-exp(logB-logA)); -//HR: add from UpdateHR.h in BayesNw to deal with the problem in sum = 0 in comp_post() -//call by reference to the original value -//the log sum result is stored in logA -//may change double into long double; no, use double -void logAddComp(double & logA, double & logB){ - if(logA == MARK){ - logA = logB; - } - else if (logA == LOG_ZERO){ - logA = logB; - } - else if(logB == MARK){ - logA = logA; - } - else if(logB == LOG_ZERO){ - logA = logA; - } - //Nither logA nor logB is MARK/LOG_ZERO - else{ - //1 - if(logA < 0 && logB < 0 ){ - logA = logA + log( 1 + exp(logB-logA) ); - } - //2 - else if(logA > 0 && logB > 0){ - //always make exp(.): . > 0 - //2.1 - if(logA >= logB){ - logA = -( -logA + log( 1 + exp(-logB+logA) ) ); - } - //2.2 - else{ - logA = -( -logB + log( 1 + exp(-logA+logB) ) ); - } - - } - //3 - else if(logA < 0 && logB > 0){ - //3.1 - if(logA + logB > 0){ - //logA = logA + log( 1 - exp(-logB-logA) ); - logA = -logB + log( exp(logA + logB) - 1 ); - - } - //3.2 - else if(logA + logB < 0){ - logA = -( logA + log( exp(-logB-logA) - 1) ); - } - //3.3 - else{ - logA = LOG_ZERO; - } - } - //4 - else if(logA > 0 && logB < 0){ - //4.1 - if(logA + logB > 0){ - logA = -logA + log( exp(logB+logA) - 1); - } - //4.2 - else if(logA + logB < 0){ - //logA = -( -logA + log(1 - exp(logB+logA)) ); - logA = -( logB + log( exp(-logA-logB) - 1) ); - - } - //4.3 - else{ - logA = LOG_ZERO; - } - } - - } - -} - - -//HR: Add -//Will be used for checking edges-based feasure for Engineer in BayesNW -void arcToNet(char * inFeasFileName, char* outFeasFileName){ - - cout << "inFeasFileName: " << inFeasFileName << endl; - - cout << "outFeasFileName: " << outFeasFileName << endl; - - int MAX_VAR_NUM = 32; - - int inFeatureEdges[MAX_VAR_NUM]; - for(int i = 0; i < MAX_VAR_NUM; i++){ - inFeatureEdges[i] = 0; - } - - string str; - str.assign(inFeasFileName); - - - FILE* fp = fopen(str.c_str(), "r"); - - int fromNode; - int toNode; - //int i=0; - while(!feof(fp)){ - char c; - fromNode = -1; - toNode = -1; - - fscanf(fp,"%d",&fromNode); - fscanf(fp,"%d",&toNode); - fscanf(fp,"%c",&c); - - cout << "fromNode = "<< fromNode << endl; - cout << "toNode = "<< toNode << endl; - - inFeatureEdges[toNode] += (1 << fromNode); - - - - } - fclose(fp); - int no_var = toNode; - - for(int i = 0; i < MAX_VAR_NUM; i++){ - cout << "inFeatureEdges[" << i << "] " << inFeatureEdges[i] << endl; - } - - - int outFeatureEdges[MAX_VAR_NUM]; - for(int i = 0; i < MAX_VAR_NUM; i++){ - outFeatureEdges[i] = 0; - } - - string str2; - str2.assign(outFeasFileName); - - - fp=fopen(str2.c_str(), "r"); - - //int fromNode; - //int toNode; - //int i=0; - while(!feof(fp)){ - char c; - fromNode = -1; - toNode = -1; - - fscanf(fp,"%d",&fromNode); - fscanf(fp,"%d",&toNode); - fscanf(fp,"%c",&c); - - cout << "fromNode = "<< fromNode << endl; - cout << "toNode = "<< toNode << endl; - - outFeatureEdges[toNode] += (1 << fromNode); - - - - } - fclose(fp); - //int no_var = toNode; - - - for(int i = 0; i < MAX_VAR_NUM; i++){ - cout << "outFeatureEdges[" << i << "] " << outFeatureEdges[i] << endl; - } - - - - -} - - - -//HR:F -int main(int argc, char* argv[]){ - - if (argc!=3){ - cout << "Please type the correct format: arcToNet inFeatureFileName outFeatureFileName\n" << endl; - return 1; - } - - arcToNet(argv[1], argv[2]); - -} - - - diff --git a/sourcecodes/k-best/src/arcs2dot.c b/sourcecodes/k-best/src/arcs2dot.c deleted file mode 100644 index 12f48158..00000000 --- a/sourcecodes/k-best/src/arcs2dot.c +++ /dev/null @@ -1,60 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#define BUFSIZE (1024) - -void arcs2dot(char* vdfile, char* arcfile, char* dotfile) -{ - char buffer[BUFSIZE]; - FILE* dotf = strcmp(dotfile,"-") ? fopen(dotfile, "w") : stdout; - - fprintf(dotf, "digraph Bene {\n"); - fprintf(dotf, " /*@@@BEFORE_ALL@@@*/\n"); - - {/* read vdfile to get names of variables */ - - FILE* vdf = fopen(vdfile, "r"); - int v; - fprintf(dotf, " /*@@@BEFORE_NODES@@@*/\n"); - for(v=0; NULL != fgets(buffer, BUFSIZE, vdf); ++v){ - char* token = strtok(buffer, "\t\r\n"); - fprintf(dotf, " V%d [label=\"%s\" /*@@@NODE_ATTS@@@*/];\n", v, token); - } - fprintf(dotf, " /*@@@AFTER_NODES@@@*/\n"); - fclose(vdf); - } - - { - - int from, to; - FILE* arcf = strcmp(arcfile,"-") ? fopen(arcfile, "r") : stdin; - - fprintf(dotf, " /*@@@BEFORE_EDGES@@@*/\n"); - while(2 == fscanf(arcf, "%d %d", &from, &to)){ - fprintf(dotf, " V%d -> V%d /*@@@EDGE_ATTS@@@*/;\n", from, to); - } - fprintf(dotf, " /*@@@AFTER_EDGES@@@*/\n"); - - fclose(arcf); - } - - fprintf(dotf, " /*@@@AFTER_ALL@@@*/\n"); - fprintf(dotf, "}\n"); - fclose(dotf); -} - -int main(int argc, char* argv[]) -{ - - if (argc!=4) { - fprintf(stderr, "Usage: arcs2dot vdfile arcfile dotfile\n"); - return 1; - } - - arcs2dot(argv[1], argv[2], argv[3]); - - return 0; -} diff --git a/sourcecodes/k-best/src/buildk.sh b/sourcecodes/k-best/src/buildk.sh deleted file mode 100644 index 9bd06a3e..00000000 --- a/sourcecodes/k-best/src/buildk.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash - -if [ ${1:-UNIX} == "WIN" ]; then - CC="i586-mingw32msvc-gcc" - EXT=".exe" -else - CC=gcc -fi - -D=g++ - -#CFLAGS="-Wextra -g -ansi -pedantic" -#CFLAGS="-Wall -O3 -g -pg" -CFLAGS="-Wall -O3" - -$CC $CFLAGS -c -o files.o files.c -$CC $CFLAGS -c -o varpar.o varpar.c - -$CC $CFLAGS -o get_local_scores$EXT files.c reg.c ilogi.c ls_XIC.c ls_NML.c ls_BDe.c ls_LOO.c get_local_scores.c -lm -$CC $CFLAGS -o split_local_scores$EXT split_local_scores.c files.o -$CC $CFLAGS -o reverse_local_scores$EXT reverse_local_scores.c files.o -$D -o get_kbest_parents$EXT get_kbest_parents.cc -$D -o get_kbest_nets$EXT get_kbest_nets.cc diff --git a/sourcecodes/k-best/src/buildk_poster.sh b/sourcecodes/k-best/src/buildk_poster.sh deleted file mode 100644 index a9964f8a..00000000 --- a/sourcecodes/k-best/src/buildk_poster.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - - -D=g++ - - -$D -o get_kbest_parents$EXT get_kbest_parents.cc -$D -o get_kbest_nets$EXT get_kbest_nets.cc - diff --git a/sourcecodes/k-best/src/clean.sh b/sourcecodes/k-best/src/clean.sh deleted file mode 100644 index 3db60eb5..00000000 --- a/sourcecodes/k-best/src/clean.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -rm -f get_local_scores split_local_scores reverse_local_scores \ - get_best_parents get_best_sinks get_best_order get_best_net \ - score_net score_nets net2parents parents2arcs arcs2dot \ - *.exe *.o *~ diff --git a/sourcecodes/k-best/src/comp_pHat_D.cc b/sourcecodes/k-best/src/comp_pHat_D.cc deleted file mode 100644 index fc789912..00000000 --- a/sourcecodes/k-best/src/comp_pHat_D.cc +++ /dev/null @@ -1,213 +0,0 @@ -#include <iostream> -#include <fstream> -#include <iomanip> -//#include "varpar.h" -#include <stdlib.h> -#include <math.h> -#include <list> -#include <stdio.h> -#include <vector> -//#include "cfg.h" -#include <string.h> -#include <cmath> -//HR -//#define EPSILON 0.001 -#define EPSILON 0.00001 - - -//HR: Add for hash_set -#if __GNUC__ < 3 && __GNUC__ >= 2 && __GNUC_MINOR__ >= 95 -# include <hash_set> -# include <functional> -# define gnu_namespace std -#elif __GNUC__ >= 3 -# include <ext/hash_set> -# if __GNUC_MINOR__ == 0 -# include <functional> -# define gnu_namespace std -# else -# include <ext/functional> -# define gnu_namespace __gnu_cxx -# endif -#else -# include <hash_set.h> -# include <functional.h> -# define gnu_namespace std -#endif -using namespace gnu_namespace; -#include <set> -// - - -using namespace std; - - -//HR: add from Engine.h in BayesNw -#define MARK 9e99 -#define LOG_ZERO -1e101 -//#define LOGMINUS_NEW(logA, logB) if(logA == MARK) logA = logB; else if (logA == LOG_ZERO) logA = logB; else if (logB == LOG_ZERO) logA = logA; else logA = logA + log(1-exp(logB-logA)); -//HR: add from UpdateHR.h in BayesNw to deal with the problem in sum = 0 in comp_post() -//call by reference to the original value -//the log sum result is stored in logA -//may change double into long double; no, use double -void logAddComp(double & logA, double & logB){ - if(logA == MARK){ - logA = logB; - } - else if (logA == LOG_ZERO){ - logA = logB; - } - else if(logB == MARK){ - logA = logA; - } - else if(logB == LOG_ZERO){ - logA = logA; - } - //Nither logA nor logB is MARK/LOG_ZERO - else{ - //1 - if(logA < 0 && logB < 0 ){ - logA = logA + log( 1 + exp(logB-logA) ); - } - //2 - else if(logA > 0 && logB > 0){ - //always make exp(.): . > 0 - //2.1 - if(logA >= logB){ - logA = -( -logA + log( 1 + exp(-logB+logA) ) ); - } - //2.2 - else{ - logA = -( -logB + log( 1 + exp(-logA+logB) ) ); - } - - } - //3 - else if(logA < 0 && logB > 0){ - //3.1 - if(logA + logB > 0){ - //logA = logA + log( 1 - exp(-logB-logA) ); - logA = -logB + log( exp(logA + logB) - 1 ); - - } - //3.2 - else if(logA + logB < 0){ - logA = -( logA + log( exp(-logB-logA) - 1) ); - } - //3.3 - else{ - logA = LOG_ZERO; - } - } - //4 - else if(logA > 0 && logB < 0){ - //4.1 - if(logA + logB > 0){ - logA = -logA + log( exp(logB+logA) - 1); - } - //4.2 - else if(logA + logB < 0){ - //logA = -( -logA + log(1 - exp(logB+logA)) ); - logA = -( logB + log( exp(-logA-logB) - 1) ); - - } - //4.3 - else{ - logA = LOG_ZERO; - } - } - - } - -} - - -//HR: Add -//Update from comp_post -void comp_pHat(){ - //double logSum = -450.491; //iris - double logSum = -9418.56; //tic - - //double logSum = -637.91; //zoo - - cerr << "logSum = " << logSum << endl; - - //double truelogP = -450.491; //iris - double truelogP = -9418.29; //tic - - //double truelogP = -619.502; //zoo - - cerr << "truelogP = " << truelogP << endl; - - int sampleSize = 1000; - - long double post[sampleSize]; - double relaLogScore[sampleSize]; - - double sumPost[sampleSize]; - - string str; - char str1[32]; - - FILE *fp = fopen("netpost" ,"r"); - int i = 0; - - - - - while(!feof(fp) && i < sampleSize){ - char c; - fscanf(fp,"%Lg",&post[i]); - //cout << " post[" << i << "] = " << post[i] << endl; - fscanf(fp,"%c",&c); - i++; - } - - for(int j = 0; j < sampleSize; j++){ - relaLogScore[j] = log(post[j]) + logSum; - //cout << " relaLogScore[" << i << "] = " << relaLogScore[j] << endl; - } - //cout << " relaLogScore[" << 1 << "] = " << relaLogScore[1] << endl; - //cout << " relaLogScore[" << 2 << "] = " << relaLogScore[2] << endl; - - for(int j = 0; j < sampleSize; j++){ - sumPost[j] = LOG_ZERO; - } - - for(int j = 0; j < sampleSize; j++){ - for(int k = 0; k <= j; k++){ - logAddComp(sumPost[j], relaLogScore[k]); - } - //cout << " sumPost[" << j << "] = " << sumPost[j] << endl; - } - - double DRatio[sampleSize]; - - - for(int j = 0; j < sampleSize; j++){ - DRatio[j] = exp( sumPost[j] - truelogP ) * 100; - //cout << "" << DRatio[j] << endl; - } - - double GRatio[sampleSize]; - for(int j = 0; j < sampleSize; j++){ - GRatio[j] = post[0]/post[j]; - //cout << "" << GRatio[j] << endl; - } - - cout << "\n\nDRatio\t GRatio" << endl; - for(int j = 0; j < sampleSize; j++){ - cout << "" << DRatio[j] << "\t " << GRatio[j] << endl; - } -} - - - -//HR:F -int main(int argc, char* argv[]){ - comp_pHat(); - -} - - - diff --git a/sourcecodes/k-best/src/data.sh b/sourcecodes/k-best/src/data.sh deleted file mode 100644 index d775b92a..00000000 --- a/sourcecodes/k-best/src/data.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -binpath=`dirname $0` - -if [ $# -ne 4 ]; then - echo Usage: data2net.sh vdfile datafile score resultdir 1>&2 - exit 1 -fi - -vdfile=$1; shift -datafile=$1; shift -score=$1; shift -rdir=$1; shift - -mkdir -p $rdir -nof_vars=`cat $vdfile | wc -l` - -START=$(date +%s) -$binpath/get_best_parents $nof_vars ${rdir} -$binpath/get_best_sinks $nof_vars ${rdir} ${rdir}/sinks -$binpath/get_best_order $nof_vars ${rdir}/sinks ${rdir}/ord -$binpath/get_best_net $nof_vars ${rdir} ${rdir}/ord ${rdir}/net -$binpath/score_net ${rdir}/net ${rdir} -END=$(date +%s) -DIFF=$(( $END - $START )) -echo "Best network took $DIFF seconds" - diff --git a/sourcecodes/k-best/src/data2net.sh b/sourcecodes/k-best/src/data2net.sh deleted file mode 100644 index 3bc5d133..00000000 --- a/sourcecodes/k-best/src/data2net.sh +++ /dev/null @@ -1,35 +0,0 @@ -#!/bin/bash - -binpath=`dirname $0` - -if [ $# -ne 4 ]; then - echo Usage: data2net.sh vdfile datafile score resultdir 1>&2 - exit 1 -fi - -vdfile=$1; shift -datafile=$1; shift -score=$1; shift -rdir=$1; shift - -mkdir -p $rdir -nof_vars=`cat $vdfile | wc -l` - -START=$(date +%s) -$binpath/get_local_scores $vdfile $datafile $score 1 0 ${rdir}/res -$binpath/split_local_scores $nof_vars ${rdir} -$binpath/reverse_local_scores $nof_vars ${rdir} -END=$(date +%s) -DIFF=$(( $END - $START )) -echo "Local score took $DIFF seconds" - -START=$(date +%s) -$binpath/get_best_parents $nof_vars ${rdir} -$binpath/get_best_sinks $nof_vars ${rdir} ${rdir}/sinks -$binpath/get_best_order $nof_vars ${rdir}/sinks ${rdir}/ord -$binpath/get_best_net $nof_vars ${rdir} ${rdir}/ord ${rdir}/net -$binpath/score_net ${rdir}/net ${rdir} -END=$(date +%s) -DIFF=$(( $END - $START )) -echo "Best network took $DIFF seconds" - diff --git a/sourcecodes/k-best/src/data2netk.sh b/sourcecodes/k-best/src/data2netk.sh deleted file mode 100644 index e20f12c9..00000000 --- a/sourcecodes/k-best/src/data2netk.sh +++ /dev/null @@ -1,55 +0,0 @@ -#!/bin/bash - -binpath=`dirname $0` - -if [ $# -ne 5 ]; then - echo Usage: data2net.sh vdfile datafile score resultdir k 1>&2 - exit 1 -fi - -vdfile=$1; shift -datafile=$1; shift -score=$1; shift -rdir=$1; shift -k=$1;shift - -mkdir -p $rdir -nof_vars=`cat $vdfile | wc -l` - -START=$(date +%s%N) -$binpath/get_local_scores $vdfile $datafile $score 1 0 ${rdir}/res -#HR -echo "get_local_scores is done." -$binpath/split_local_scores $nof_vars ${rdir} -#HR -echo "split_local_scores is done." -$binpath/reverse_local_scores $nof_vars ${rdir} -#HR -echo "reverse_local_scores is done." -END=$(date +%s%N) -#DIFF=$(( $END - $START )) -DIFF1=$(( $END - $START )) -echo "Local score took $DIFF1 seconds" - -#the above is the same as original bene - -START=$(date +%s%N) -$binpath/get_kbest_parents $nof_vars ${rdir} $k -#HR -END=$(date +%s%N) -#DIFF=$(( $END - $START )) -DIFF2=$(( $END - $START )) -echo "get_kbest_parents is done." -echo "get_kbest_parents took $DIFF2 seconds" - -START=$(date +%s%N) -$binpath/get_kbest_nets $nof_vars ${rdir} $k -#HR -END=$(date +%s%N) -#DIFF=$(( $END - $START )) -DIFF3=$(( $END - $START )) -echo "get_kbest_nets is done." -echo "get_kbest_nets took $DIFF3 seconds" - -DIFF=`expr $DIFF1 + $DIFF2 + $DIFF3` -echo "total process took $DIFF seconds" diff --git a/sourcecodes/k-best/src/data2netk_poster.sh.bk b/sourcecodes/k-best/src/data2netk_poster.sh.bk deleted file mode 100644 index 6b3a34ca..00000000 --- a/sourcecodes/k-best/src/data2netk_poster.sh.bk +++ /dev/null @@ -1,56 +0,0 @@ -#!/bin/bash - -binpath=`dirname $0` - -if [ $# -ne 4 ]; then - echo Usage: data2net.sh datafile resultdir k 1>&2 - exit 1 -fi - -datafile=$1; shift -#score=$1; shift -rdir=$1; shift -k=$1;shift -n=$1;shift - -nof_vars=`head -1 $datafile|wc -w` -echo "The number of variables is $nof_vars." - -#HR: -if [ "$n" -eq 0 ] -then - maxindegree=`expr $nof_vars - 1` -else - maxindegree=$n -fi - -#maxindegree=`expr $nof_vars - 1` -echo "maxindegree is $maxindegree." - -#HR: -nof_instances=`cat $datafile | wc -l` -#delete the header and type -nof_instances=`expr $nof_instances - 2` -echo "The number of instances is $nof_instances." - - -START=$(date +%s%N) -$binpath/get_kbest_parents $nof_vars ${rdir} $k -#HR -END=$(date +%s%N) -#DIFF=$(( $END - $START )) -DIFF2=$(( $END - $START )) -echo "get_kbest_parents is done." -echo "get_kbest_parents took $DIFF2 n-seconds." - -START=$(date +%s%N) -$binpath/get_kbest_nets $nof_vars ${rdir} $k -#HR -END=$(date +%s%N) -#DIFF=$(( $END - $START )) -DIFF3=$(( $END - $START )) -echo "get_kbest_nets is done." -echo "get_kbest_nets took $DIFF3 n-seconds." - -DIFF=`expr $DIFF1 + $DIFF2 + $DIFF3` -echo "The total process took $DIFF n-seconds." diff --git a/sourcecodes/k-best/src/datak.sh b/sourcecodes/k-best/src/datak.sh deleted file mode 100644 index 8ae66439..00000000 --- a/sourcecodes/k-best/src/datak.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash - -binpath=`dirname $0` - -if [ $# -ne 5 ]; then - echo Usage: data2net.sh vdfile datafile score resultdir k 1>&2 - exit 1 -fi - -vdfile=$1; shift -datafile=$1; shift -score=$1; shift -rdir=$1; shift -k=$1; shift - -mkdir -p $rdir -nof_vars=`cat $vdfile | wc -l` -START=$(date +%s) -$binpath/get_kbest_parents $nof_vars ${rdir} $k -$binpath/get_kbest_nets $nof_vars ${rdir} $k -END=$(date +%s) -DIFF=$(( $END - $START )) -echo "Top k took $DIFF seconds" diff --git a/sourcecodes/k-best/src/drawgraph.sh b/sourcecodes/k-best/src/drawgraph.sh deleted file mode 100644 index a0f59c88..00000000 --- a/sourcecodes/k-best/src/drawgraph.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -k=$1 -rdir=$2 -for (( i = 0 ; i < k; i++ )) -do - ${rdir}/../../src/arcs2dot ${rdir}/../iris.vd ${rdir}/$arc$i ${rdir}/dot_$i -done - diff --git a/sourcecodes/k-best/src/files.c b/sourcecodes/k-best/src/files.c deleted file mode 100644 index 3227f63c..00000000 --- a/sourcecodes/k-best/src/files.c +++ /dev/null @@ -1,59 +0,0 @@ -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" - -int nof_digits(int n) -{ - int c=0; - do { - c += 1; - n /= 10; - } while(n); - return c; -} - -int nof_lines(char* filename) { - int nof_lines = 0; - FILE* f = fopen(filename,"r"); - int c = 0; - while(EOF != (c=fgetc(f))) - if(c=='\n') ++nof_lines; - fclose(f); - return nof_lines; -} - -char* create_fn(char* dirname, int i, char* ext) -{ char* fn = malloc((strlen(dirname)+1+nof_digits(i)+strlen(ext)+1) - *sizeof(char)); - sprintf(fn,"%s/%d%s", dirname,i,ext); - return fn; -} - -FILE* open_file(char* dirname, int i, char* ext, char* mode) -{ - FILE* f; - char* fn = create_fn(dirname, i, ext); - sprintf(fn,"%s/%d%s", dirname,i,ext); - f = fopen(fn, mode); - free(fn); - return f; -} - -FILE** open_files(int nof_vars, char* dirname, char* ext, char* mode) -{ - FILE** files = malloc(nof_vars * sizeof(FILE*)); - int i; - for(i=0; i<nof_vars; ++i){ - files[i] = open_file(dirname, i, ext, mode); - } - return files; -} - -void free_files(int nof_vars, FILE** files){ - int i; - for(i=0; i<nof_vars; ++i) fclose(files[i]); - free(files); -} - diff --git a/sourcecodes/k-best/src/get_best_net.c b/sourcecodes/k-best/src/get_best_net.c deleted file mode 100644 index 5ed6ebfb..00000000 --- a/sourcecodes/k-best/src/get_best_net.c +++ /dev/null @@ -1,63 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" -#include "varpar.h" - -void get_best_net(int nof_vars, char* ordfile, FILE** bpsfiles, varset_t* net) -{ - FILE* ordf = fopen(ordfile,"r"); - varset_t parcands = 0; - int i; - for(i=0;i<nof_vars; ++i){ - varset_t parset; - int v; -// printf("Parcands = %u",parcands); - - fscanf(ordf, "%d", &v); - // printf(" v= %d",v); - fseek(bpsfiles[v], varset2parset(v,parcands)*sizeof(varset_t), SEEK_SET); - fread(&parset, sizeof(varset_t), 1, bpsfiles[v]); - // printf("Parset =%u ",parset); - parcands |= 1U<<v; - // printf("Parcands = %u",parcands); - net[v] = parset2varset(v, parset); - // printf("net %d = %u",v,net[v]); - } - fclose(ordf); -} - - -int main(int argc, char* argv[]) -{ - - if (argc!=5) { - fprintf(stderr, "Usage: get_best_net nof_vars dirname ordfile netfile\n"); - return 1; - } - - { - int nof_vars = atoi(argv[1]); - - varset_t* net = malloc(nof_vars*sizeof(varset_t)); - FILE** files = open_files(nof_vars, argv[2],".bps", "rb"); - get_best_net(nof_vars, argv[3], files, net); - free_files(nof_vars, files); - - { - FILE* netf = fopen(argv[4],"w"); - int i; - for (i=0;i<nof_vars;++i){ - fprintf(netf, "%u\n", net[i]); - } - fclose(netf); - } - - free(net); - } - - return 0; -} diff --git a/sourcecodes/k-best/src/get_best_order.c b/sourcecodes/k-best/src/get_best_order.c deleted file mode 100644 index 232956aa..00000000 --- a/sourcecodes/k-best/src/get_best_order.c +++ /dev/null @@ -1,54 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -void get_best_order(int nof_vars, char* sinkfile, char* ord) -{ - FILE* sinkf = fopen(sinkfile, "rb"); - varset_t set = LARGEST_SET(nof_vars); - // printf("\n\n\nset = %u",set); - int i; - for(i=nof_vars-1; i>=0;--i){ - char sink; - // printf("\n\n\n\nset =%u",set); - fseek(sinkf, set, SEEK_SET); - - fread(&sink, sizeof(char), 1, sinkf); -// printf(" sink = %d",sink); - ord[i] = sink; - - set ^= 1U<<sink; - // printf(" new set = %u",set); - } - fclose(sinkf); -} - - -int main(int argc, char* argv[]) -{ - - if (argc!=4) { - fprintf(stderr, "Usage: get_best_net nof_vars sinkfile ordfile\n"); - return 1; - } - - { - int nof_vars = atoi(argv[1]); - char* ord = malloc(nof_vars*sizeof(char)); - - get_best_order(nof_vars, argv[2], ord); - - { - FILE* ordf = fopen(argv[3], "w"); - int i; - for(i=0;i<nof_vars;++i){ - fprintf(ordf, "%d%c", ord[i], i==nof_vars-1 ? '\n' : ' '); - } - fclose(ordf); - } - } - - return 0; -} diff --git a/sourcecodes/k-best/src/get_best_parents.c b/sourcecodes/k-best/src/get_best_parents.c deleted file mode 100644 index 8562a271..00000000 --- a/sourcecodes/k-best/src/get_best_parents.c +++ /dev/null @@ -1,114 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" - - -void get_best_parents(int nof_vars, char* dirname) { -//printf("I'm here!!!"); - - varset_t nof_parsets = 1U<<(nof_vars-1); - int i; -// FILE* fp; - score_t* scores = malloc(nof_parsets*sizeof(score_t)); - varset_t* bsps = malloc(nof_parsets*sizeof(varset_t)); -// fp = fopen("/home/grad/lram/RA stuff/check/src/out.txt","w"); - - for(i=0;i<nof_vars; ++i){ - - { /* READ SCORES FOR i */ - FILE* fin = open_file(dirname, i, "", "rb"); - fread(scores, sizeof(score_t), nof_parsets, fin); - // fp = fopen("out.txt","a"); -// fp = fopen("out.txt","a"); - // fprintf(fp,"\n\nLocal Scores for Var %d:",i); - // for(j=0;j<nof_parsets;j++) - // { - // fprintf(fp,"%8.10f\n ",scores[j]); - // } - - fclose(fin); - } - - - { /* FIND BEST PARENTS AND THEIR SCORES IN EACH SET FOR i */ - - varset_t ps; - - for(ps=0; ps<nof_parsets; ++ps){ - varset_t psel = 1U; - - bsps[ps] = ps; - for(psel=1; psel<nof_parsets; psel <<= 1){ - if (ps & psel){ - varset_t subset = ps^psel; - if (scores[subset] >= scores[ps]){ - scores[ps] = scores[subset]; - bsps[ps] = bsps[subset]; - } - } - } - } - } - - - { /* WRITE BEST PARENTS FOR i */ - - FILE* fout = open_file(dirname, i, ".bps", "wb"); - fwrite(bsps, sizeof(varset_t), nof_parsets, fout); - -//fprintf(fp,"\n\nBest parent sets for var %d",i); - //for(j=0;j<nof_parsets;j++) - // { - // fprintf(fp,"%u ",bsps[j]); - //} - - - - - fclose(fout); - } - - { /* WRITE BEST SCORES FOR i */ - - FILE* fout = open_file(dirname, i, ".bss", "wb"); - fwrite(scores, sizeof(score_t), nof_parsets, fout); - -//fprintf(fp,"\n\nBest score for var %d",i); - //for(j=0;j<nof_parsets;j++) - // { - // fprintf(fp,"%g ",scores[j]); - //} - - - - - fclose(fout); - } - } -//fclose(fp); - free(bsps); - free(scores); -} - - -int main(int argc, char* argv[]) -{ -//FILE *fp=fopen("/home/grad/lram/RA stuff/try/src/kd4.log", "w+"); -//fprintf(stdout, "loose kutty"); -//fclose(fp); - if (argc!=3) { - fprintf(stderr, "Usage: best_parents nof_vars dirname\n"); - return 1; - } - - { - int nof_vars = atoi(argv[1]); - get_best_parents(nof_vars, argv[2]); - } - - return 0; -} diff --git a/sourcecodes/k-best/src/get_best_sinks.c b/sourcecodes/k-best/src/get_best_sinks.c deleted file mode 100644 index 4d83d217..00000000 --- a/sourcecodes/k-best/src/get_best_sinks.c +++ /dev/null @@ -1,78 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" - -void get_best_sinks(int nof_vars, FILE** files, char* sinkfile) -{ - - FILE* sinkf = fopen(sinkfile, "wb"); -FILE *fp = fopen("/home/grad/lram/RA stuff/check/src/sinks.txt","w"); - -score_t* scores = malloc((1U<<nof_vars) * sizeof(score_t)); - score_t best_score = 0.0; - - varset_t varset; - for(varset=0; varset < (1U<<nof_vars); ++varset){ -// printf("\n\n\nVarset %u",varset); - int sink; - char best_sink = -1; - - for(sink=0; sink<nof_vars; ++sink){ /* could use ffs */ - // printf("\nTry Sink %d",sink); - varset_t sinkleton = 1U<<sink; - - if (varset & sinkleton) { -//printf(" True!!"); - score_t new_score = scores[varset & ~sinkleton]; - -//printf("New score = %f + ",new_score); -//printf("Scores[ %d ] +",varset & ~sinkleton); - - score_t par_score; - fread(&par_score, sizeof(score_t), 1, files[sink]); -//printf(" New score + %f",par_score); -//printf(" Score is [%d .bss,???] ",sink); - new_score += par_score; - if (best_sink == -1 || best_score < new_score){ -//printf("This is better than previous"); - best_score = new_score; - best_sink = sink; - - } - } - } - - scores[varset] = best_score; - - fwrite(&best_sink, sizeof(char), 1, sinkf); - -fprintf(fp,"Best score: %f",best_score); -fprintf(fp,"Best sink: %d", best_sink); - } - - free(scores); - fclose(sinkf); -} - - -int main(int argc, char* argv[]) -{ - - if (argc!=4) { - fprintf(stderr, "Usage: get_best_net nof_vars dirname sinkfile\n"); - return 1; - } - - { - int nof_vars = atoi(argv[1]); - FILE** files = open_files(nof_vars, argv[2],".bss", "rb"); - get_best_sinks(nof_vars, files, argv[3]); - free_files(nof_vars, files); - } - - return 0; -} diff --git a/sourcecodes/k-best/src/get_kbest_parents b/sourcecodes/k-best/src/get_kbest_parents deleted file mode 100644 index e79b12b4..00000000 --- a/sourcecodes/k-best/src/get_kbest_parents +++ /dev/null Binary files differdiff --git a/sourcecodes/k-best/src/get_local_scores.h b/sourcecodes/k-best/src/get_local_scores.h deleted file mode 100644 index 3a86d9c9..00000000 --- a/sourcecodes/k-best/src/get_local_scores.h +++ /dev/null @@ -1,15 +0,0 @@ -#ifndef _GET_LOCAL_SCORES_H_ -#define _GET_LOCAL_SCORES_H_ - -#include "cfg.h" - -extern int N; -extern int nof_vars; -extern int* nof_vals; -int* freqmem; /* a working memory to collect the conditional frequences */ - -extern score_t get_nof_cfgs(varset_t vs); -typedef score_t (*scorefun) (int, varset_t, int); -typedef void (*scorefree) (); - -#endif diff --git a/sourcecodes/k-best/src/graph.sh b/sourcecodes/k-best/src/graph.sh deleted file mode 100644 index 12967360..00000000 --- a/sourcecodes/k-best/src/graph.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash -k=10 -rdir=./../iris3/resdir -for (( i = 0 ; i < k; i++ )) -do -#if which dot > /dev/null; then - ${rdir}/../../src/net2parents ${rdir}/${i}net ${rdir}/${i}parent \ - | ${rdir}/../../src/parents2arcs ${rdir}/${i}parent ${rdir}/${i}arc \ - | ${rdir}/../../src/arcs2dot ${rdir}/../iris.vd ${rdir}/${i}arc ${rdir}/dot_$i \ - | dot ${rdir}/dot_$i -Tps -o ${rdir}/dot_res_${i}.ps - echo See $d/resdir/iris.ps for a postscript picture of the net. -#fi -done \ No newline at end of file diff --git a/sourcecodes/k-best/src/ilogi.c b/sourcecodes/k-best/src/ilogi.c deleted file mode 100644 index 50a8e651..00000000 --- a/sourcecodes/k-best/src/ilogi.c +++ /dev/null @@ -1,37 +0,0 @@ -#include <stdlib.h> -#include <math.h> -#include "cfg.h" -#include "ilogi.h" - -score_t* ilogi = NULL; -int len_ilogi = 0; - -static int refcount = 0; - -int ensure_ilogi(int maxi){ - if (maxi >= len_ilogi) - len_ilogi = maxi+1; - - ilogi = (score_t*) realloc(ilogi, len_ilogi * sizeof(score_t)); - ++refcount; - - { - int i; - - if (ilogi) - ilogi[0] = 0.0; - - for(i=1;i<len_ilogi;++i) - ilogi[i] = i*log(i); - } - - return 1; -} - -void free_ilogi(){ - --refcount; - if (!refcount){ - free(ilogi); - ilogi = NULL; - } -} diff --git a/sourcecodes/k-best/src/ilogi.h b/sourcecodes/k-best/src/ilogi.h deleted file mode 100644 index 4fef7a35..00000000 --- a/sourcecodes/k-best/src/ilogi.h +++ /dev/null @@ -1,9 +0,0 @@ -#ifndef _ILOGI_H_ -#define _ILOGI_H_ -#include "cfg.h" - -extern score_t* ilogi; -extern int ensure_ilogi(int maxi); -extern void free_ilogi(); - -#endif diff --git a/sourcecodes/k-best/src/ls_BDe.c b/sourcecodes/k-best/src/ls_BDe.c deleted file mode 100644 index 83865f31..00000000 --- a/sourcecodes/k-best/src/ls_BDe.c +++ /dev/null @@ -1,163 +0,0 @@ -#include <stdlib.h> -#include <string.h> -#include<stdio.h> -#include <math.h> -#include "get_local_scores.h" -#include "ilogi.h" -#include "ls_BDe.h" - -extern int* nof_vals; -extern int N; - -score_t ess; - -int* freq2mem = NULL; -int* freq2mem2 = NULL; -int nof_freq2s; - - -#define BIG_BDE_DATA (1<<10) - -extern double lgamma(double); /* to avoid the warning with ansi-flag */ - -/* BDe */ - -score_t big_bde_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - score_t ess_per_pcc = ess / pcc; - score_t ess_per_cc = ess_per_pcc / vc_v; - - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = nof_freqs * lgamma(ess_per_pcc); - int nof_zeros = 0; - - memset(freq2mem, 0, nof_freq2s*sizeof(int)); /* could reset later */ - memset(freq2mem2, 0, nof_freq2s*sizeof(int)); /* could reset later */ - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - if(freq<nof_freq2s){ - ++freq2mem[freq]; - } else { - res += lgamma(ess_per_cc + freq); - } - } else { - ++ nof_zeros; - } - } - if(pcfreq<nof_freq2s){ - ++freq2mem2[pcfreq]; - } else { - res -= lgamma(ess_per_pcc + pcfreq); - } - } - - res += (nof_zeros - nof_freqs * vc_v) * lgamma(ess_per_cc); - - { - int i; - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem[i]; - if(freq2) res += freq2 * lgamma(ess_per_cc + i); - } - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem2[i]; - if(freq2) res -= freq2 * lgamma(ess_per_pcc + i); - } - - } - - return res > 0.0 ? 0.0 : res; -} - - -score_t bde_score(int i, varset_t psi, int nof_freqs){ -//HR -//printf ("bde score %d, %u %d",i, psi, nof_freqs); - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - score_t ess_per_pcc = ess / pcc; - score_t ess_per_cc = ess_per_pcc / vc_v; - - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = nof_freqs * lgamma(ess_per_pcc); - int nof_zeros = 0; - - memset(freq2mem, 0, nof_freq2s*sizeof(int)); /* could reset later */ - memset(freq2mem2, 0, nof_freq2s*sizeof(int)); /* could reset later */ - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - ++freq2mem[freq]; - } else { - ++ nof_zeros; - } - } - ++freq2mem2[pcfreq]; - } - - res += (nof_zeros - nof_freqs * vc_v) * lgamma(ess_per_cc); - - { - int i; - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem[i]; - if(freq2) res += freq2 * lgamma(ess_per_cc + i); - } - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem2[i]; - if(freq2) res -= freq2 * lgamma(ess_per_pcc + i); - } - - } - - return res > 0.0 ? 0.0 : res; -} - - - -scorefun init_BDe_scorer(char* arg){ - - scorefun sf; - - ess = atof(arg); - - if (N<BIG_BDE_DATA){ - sf = bde_score; - nof_freq2s = N+1; - } else { - sf = big_bde_score; - nof_freq2s = BIG_BDE_DATA; - } - - freq2mem = malloc(nof_freq2s * sizeof(int)); - freq2mem2 = malloc(nof_freq2s * sizeof(int)); - - return sf; -} - -void free_BDe_scorer(){ - if(freq2mem) free(freq2mem); - if(freq2mem2) free(freq2mem2); -} diff --git a/sourcecodes/k-best/src/ls_BDe.h b/sourcecodes/k-best/src/ls_BDe.h deleted file mode 100644 index 01a92fab..00000000 --- a/sourcecodes/k-best/src/ls_BDe.h +++ /dev/null @@ -1,12 +0,0 @@ -#ifndef _LS_BDE_H_ -#define _LS_BDE_H_ - -#include "cfg.h" -#include "get_local_scores.h" - -/* BDe = P(D|G,ess) */ - -extern scorefun init_BDe_scorer(); -extern void free_BDe_scorer(); - -#endif diff --git a/sourcecodes/k-best/src/ls_LOO.c b/sourcecodes/k-best/src/ls_LOO.c deleted file mode 100644 index 57a1fae4..00000000 --- a/sourcecodes/k-best/src/ls_LOO.c +++ /dev/null @@ -1,152 +0,0 @@ -#include <stdlib.h> -#include <string.h> -#include <math.h> -#include "get_local_scores.h" -#include "ls_LOO.h" - -extern int* nof_vals; -extern int N; - -static score_t ess; -static int splitess; - -static int* freq2mem = NULL; -static int* freq2mem2 = NULL; -static int nof_freq2s; - - -#define BIG_LOO_DATA (1<<10) - -/* LOO */ - -score_t big_loo_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - score_t ess_per_pcc = splitess ? (ess / pcc) : (ess*vc_v); - score_t ess_per_cc = splitess ? (ess_per_pcc / vc_v) : ess; - - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = - log(N); - - memset(freq2mem, 0, nof_freq2s*sizeof(int)); /* could reset later */ - memset(freq2mem2, 0, nof_freq2s*sizeof(int)); /* could reset later */ - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - if(freq<nof_freq2s){ - ++freq2mem[freq]; - } else { - res += freq * log(ess_per_cc + freq - 1); - } - } - } - - if(pcfreq<nof_freq2s){ - ++freq2mem2[pcfreq]; - } else { - res -= pcfreq * log(ess_per_pcc + pcfreq); - } - } - - { - int i; - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem[i]; - if(freq2) res += freq2 * i * log(ess_per_cc + i - 1); - } - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem2[i]; - if(freq2) res -= freq2 * i * log(ess_per_pcc + i); - } - - } - - return res > 0.0 ? 0.0 : res; -} - - -score_t loo_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - - score_t ess_per_pcc = splitess ? (ess / pcc) : (ess*vc_v); - score_t ess_per_cc = splitess ? (ess_per_pcc / vc_v) : ess; - - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = -log(N); - - memset(freq2mem, 0, nof_freq2s*sizeof(int)); /* could reset later */ - memset(freq2mem2, 0, nof_freq2s*sizeof(int)); /* could reset later */ - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - ++freq2mem[freq]; - } - } - ++freq2mem2[pcfreq]; - } - - { - int i; - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem[i]; - if(freq2) res += freq2 * i * log(ess_per_cc + i - 1); - } - - for(i=1;i<nof_freq2s;++i){ - int freq2 = freq2mem2[i]; - if(freq2) res -= freq2 * i * log(ess_per_pcc + i); - } - - } - - return res > 0.0 ? 0.0 : res; -} - - - -scorefun init_LOO_scorer(char* arg){ - - scorefun sf; - int arglen = strlen(arg); - - ess = atof(arg); - splitess = arg[arglen-1] == 'l'; - - if (N<BIG_LOO_DATA){ - sf = loo_score; - nof_freq2s = N+1; - } else { - sf = big_loo_score; - nof_freq2s = BIG_LOO_DATA; - } - - freq2mem = malloc(nof_freq2s * sizeof(int)); - freq2mem2 = malloc(nof_freq2s * sizeof(int)); - - return sf; -} - -void free_LOO_scorer(){ - if(freq2mem) free(freq2mem); - if(freq2mem2) free(freq2mem2); -} diff --git a/sourcecodes/k-best/src/ls_LOO.h b/sourcecodes/k-best/src/ls_LOO.h deleted file mode 100644 index a2963832..00000000 --- a/sourcecodes/k-best/src/ls_LOO.h +++ /dev/null @@ -1,10 +0,0 @@ -#ifndef _LS_LOO_H_ -#define _LS_LOO_H_ - -#include "cfg.h" -#include "get_local_scores.h" - -extern scorefun init_LOO_scorer(); -extern void free_LOO_scorer(); - -#endif diff --git a/sourcecodes/k-best/src/ls_NML.c b/sourcecodes/k-best/src/ls_NML.c deleted file mode 100644 index 6c3523a4..00000000 --- a/sourcecodes/k-best/src/ls_NML.c +++ /dev/null @@ -1,77 +0,0 @@ -#include <math.h> -#include "get_local_scores.h" -#include "ilogi.h" -#include "reg.h" -#include "ls_NML.h" - -extern int* nof_vals; -extern int N; - -#define BIG_NML_DATA (1<<16) - -/* NML = log(ML) - log(REGRET) */ - -score_t big_nml_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = 0.0; - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - res += (freq < BIG_NML_DATA) ? ilogi[freq] : freq * log(freq); - } - } - res -= (pcfreq < BIG_NML_DATA) ? ilogi[pcfreq] : pcfreq * log(pcfreq); - res -= log(reg(pcfreq, vc_v)); /* regret */ - } - - return res; -} - -score_t nml_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = 0.0; - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - res += ilogi[freq]; - } - } - res -= ilogi[pcfreq]; - res -= log(reg(pcfreq, vc_v)); /* regret */ - } - - return res; -} - - -scorefun init_NML_scorer(){ - if (N<BIG_NML_DATA){ - ensure_ilogi(N); - return nml_score; - } else { - ensure_ilogi(BIG_NML_DATA); - return big_nml_score; - } -} - -void free_NML_scorer(){ - free_ilogi(); -} diff --git a/sourcecodes/k-best/src/ls_NML.h b/sourcecodes/k-best/src/ls_NML.h deleted file mode 100644 index bd7df9de..00000000 --- a/sourcecodes/k-best/src/ls_NML.h +++ /dev/null @@ -1,12 +0,0 @@ -#ifndef _LS_NML_H_ -#define _LS_NML_H_ - -#include "cfg.h" -#include "get_local_scores.h" - -/* NML = log(ML) - SUM_D log(ML(D)) */ - -extern scorefun init_NML_scorer(); -extern void free_NML_scorer(); - -#endif diff --git a/sourcecodes/k-best/src/ls_XIC.c b/sourcecodes/k-best/src/ls_XIC.c deleted file mode 100644 index 22d51d04..00000000 --- a/sourcecodes/k-best/src/ls_XIC.c +++ /dev/null @@ -1,82 +0,0 @@ -#include <math.h> -#include <string.h> -#include "get_local_scores.h" -#include "ilogi.h" -#include "ls_XIC.h" - -extern int* nof_vals; -extern int N; - -static int bic = 0; - -#define BIG_XIC_DATA (1<<16) - -/* XIC = log(ML) - 0.5*nof_params*log(n) */ - -score_t big_xic_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - score_t nof_params = pcc * (vc_v-1); - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = bic ? (-0.5 * nof_params * log(N)) : nof_params; - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - res += (freq < BIG_XIC_DATA) ? ilogi[freq] : freq * log(freq); - } - } - res -= (pcfreq < BIG_XIC_DATA) ? ilogi[pcfreq] : pcfreq * log(pcfreq); - } - - return res; -} - -score_t xic_score(int i, varset_t psi, int nof_freqs){ - - int vc_v = nof_vals[i]; - score_t pcc = get_nof_cfgs(psi); - score_t nof_params = pcc * (vc_v-1); - int* freqp = freqmem; - int* end_freqp = freqp + nof_freqs * vc_v; - - score_t res = bic ? (-0.5 * nof_params * log(N)) : -nof_params; - - for(;freqp < end_freqp; freqp += vc_v) { - int pcfreq = 0; - int v; - for(v = 0; v<vc_v; ++v) { - int freq = freqp[v]; - if (freq) { - pcfreq += freq; - res += ilogi[freq]; - } - } - res -= ilogi[pcfreq]; - } - - return res; -} - -scorefun init_XIC_scorer(char* essarg){ - bic = strncmp(essarg,"BIC", 3) == 0; - - if (N<BIG_XIC_DATA){ - ensure_ilogi(N); - return xic_score; - } else { - ensure_ilogi(BIG_XIC_DATA); - return big_xic_score; - } -} - -void free_XIC_scorer(){ - free_ilogi(); -} diff --git a/sourcecodes/k-best/src/ls_XIC.h b/sourcecodes/k-best/src/ls_XIC.h deleted file mode 100644 index 773a1d94..00000000 --- a/sourcecodes/k-best/src/ls_XIC.h +++ /dev/null @@ -1,13 +0,0 @@ -#ifndef _LS_XIC_H_ -#define _LS_XIC_H_ - -#include "cfg.h" -#include "get_local_scores.h" - -/* BIC = log(ML) - 0.5*nof_params*log(n) */ -/* AIC = log(ML) - 0.5*nof_params */ - -extern scorefun init_XIC_scorer(char*); -extern void free_XIC_scorer(); - -#endif diff --git a/sourcecodes/k-best/src/main.cc b/sourcecodes/k-best/src/main.cc deleted file mode 100644 index d84af256..00000000 --- a/sourcecodes/k-best/src/main.cc +++ /dev/null @@ -1,51 +0,0 @@ -#include<stdio.h> -#include<stdlib.h> -#include"math.h" - -#include"Arguments.h" -#include"Model.h" -#include"Engine.h" - -void welcome(){ - fprintf(stderr, - " ~~~ Welcome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n"); - fprintf(stderr, - " Poster: The Tool for Computing Posterior \n"); - fprintf(stderr, - " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n"); - -} -void goodbye(){ - fprintf(stderr, - " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n"); -} - - - -int main(int argc, char **argv){ - welcome(); - - Arguments::init(argc, argv); - - Model model; - - model.init(); - - //HR - //model.makeADTree(); - ////model.MakeADContiTable(); - //model.testHR_ADtree(); - //model.freeADTree(); - //return 1; - - //cerr << "Start Engine.h " << endl; - - Engine engine; - - engine.init(&model); - - engine.compute_edge_probabilities(); - - goodbye(); - return 1; -} diff --git a/sourcecodes/k-best/src/net2parents.c b/sourcecodes/k-best/src/net2parents.c deleted file mode 100644 index f12e9f64..00000000 --- a/sourcecodes/k-best/src/net2parents.c +++ /dev/null @@ -1,50 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -void net2parents(char* netfile, char* parfile) -{ - int v; - varset_t varset; -//score_t s; -//FILE *fp=fopen("/home/grad/lram/RA stuff/try/src/kd.log","w+"); - - - FILE* netf = strcmp(netfile,"-") ? fopen(netfile, "r") : stdin; - FILE* parf = strcmp(parfile,"-") ? fopen(parfile, "w") : stdout; -//fprintf(fp, "great one was here"); -//fclose(fp); - -//fscanf(netf,"%f",&s); - for(v=0; 1 == fscanf(netf, "%u", &varset); ++v){ - int p; -//printf("Var %d", v); - - for(p=0; varset; ++p, varset>>=1){ - if(varset & 1) { - fprintf(parf, "%d", p); - if(varset>1)fprintf(parf, " "); - } - } -// printf("Var %d", v); - fprintf(parf,"\n"); - } -//printf("Here"); - fclose(parf); - fclose(netf); -} - -int main(int argc, char* argv[]) -{ - - if (argc!=3) { - fprintf(stderr, "Usage: net2parents netfile parentfile\n"); - return 1; - } - - net2parents(argv[1], argv[2]); - - return 0; -} diff --git a/sourcecodes/k-best/src/parents2arcs.c b/sourcecodes/k-best/src/parents2arcs.c deleted file mode 100644 index 81e8b3b1..00000000 --- a/sourcecodes/k-best/src/parents2arcs.c +++ /dev/null @@ -1,37 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#define BUFSIZE (1024) - -void parents2arcs(char* parfile, char* arcfile) -{ - char buffer[BUFSIZE]; - int v; - FILE* parf = strcmp(parfile,"-") ? fopen(parfile, "r") : stdin; - FILE* arcf = strcmp(arcfile,"-") ? fopen(arcfile, "w") : stdout; - for(v=0; NULL != fgets(buffer, BUFSIZE, parf); ++v){ - /* could check that the last character in buffer is newline */ - char* token; - for(token=strtok(buffer, " \t\r\n"); token; token=strtok(NULL, " \t\r\n")){ - fprintf(arcf, "%d %d\n", atoi(token), v); - } - } - fclose(arcf); - fclose(parf); -} - -int main(int argc, char* argv[]) -{ - - if (argc!=3) { - fprintf(stderr, "Usage: parents2arcs parentfile arcfile\n"); - return 1; - } - - parents2arcs(argv[1], argv[2]); - - return 0; -} diff --git a/sourcecodes/k-best/src/reg.c b/sourcecodes/k-best/src/reg.c deleted file mode 100644 index 311bf59c..00000000 --- a/sourcecodes/k-best/src/reg.c +++ /dev/null @@ -1,320 +0,0 @@ -#include <math.h> -#include "reg.h" - -#define pi 3.1415926535897932384626433832795 - - -static score_t r2_1000[] = { -1.0, 2.0, 2.5, 2.88888888889, 3.21875, 3.5104, 3.77469135802, -4.01813870071, 4.24501800537, 4.45831574489, 4.66021568, -4.85237205074, 5.0360736751, 5.21234791295, 5.38202942438, -5.54580728515, 5.70425824707, 5.8578708208, 6.00706309899, -6.15219620096, 6.293584586, 6.43150408335, 6.56619822786, -6.69788331895, 6.82675250392, 6.95297910625, 7.07671936269, -7.19811469288, 7.31729359534, 7.43437324249, 7.54946083103, -7.66265473218, 7.77404547667, 7.88371660286, 7.99174539033, -8.09820349737, 8.2031575174, 8.30666946646, 8.408797212, -8.50959485133, 8.60911304685, 8.70739932387, 8.80449833604, -8.90045210255, 8.9953002208, 9.08908005739, 9.1818269202, -9.27357421386, 9.36435358028, 9.45419502625, 9.54312703934, -9.63117669346, 9.71836974515, 9.80473072166, 9.89028300153, -9.97504888851, 10.0590496796, 10.1423057273, 10.2248364976, -10.3066606229, 10.3877959509, 10.4682595908, 10.5480679547, -10.627236797, 10.7057812508, 10.7837158615, 10.8610546184, -10.937810984, 11.0139979213, 11.0896279195, 11.1647130175, -11.239264827, 11.3132945527, 11.3868130127, 11.4598306561, -11.5323575813, 11.6044035514, 11.6759780103, 11.7470900966, -11.8177486575, 11.8879622617, 11.9577392113, 12.0270875534, -12.0960150909, 12.1645293929, 12.2326378041, 12.3003474542, -12.3676652666, 12.4345979668, 12.5011520898, 12.5673339879, -12.6331498379, 12.6986056474, 12.7637072616, 12.8284603691, -12.8928705079, 12.9569430709, 13.0206833111, 13.0840963465, -13.1471871653, 13.2099606302, 13.2724214826, 13.3345743473, -13.3964237358, 13.4579740508, 13.5192295895, 13.5801945472, -13.6408730205, 13.7012690107, 13.7613864269, 13.8212290886, -13.8808007292, 13.9401049979, 13.9991454631, 14.0579256142, -14.1164488646, 14.1747185536, 14.2327379487, 14.2905102481, -14.3480385822, 14.405326016, 14.4623755507, 14.5191901259, -14.5757726211, 14.6321258572, 14.6882525988, 14.7441555552, -14.799837382, 14.8553006829, 14.9105480108, 14.9655818692, -15.0204047137, 15.0750189533, 15.1294269511, 15.1836310264, -15.2376334551, 15.291436471, 15.3450422672, 15.3984529967, -15.4516707737, 15.5046976745, 15.5575357382, 15.6101869683, -15.6626533327, 15.7149367651, 15.7670391659, 15.8189624026, -15.870708311, 15.9222786955, 15.9736753304, 16.0248999601, -16.0759543002, 16.1268400377, 16.1775588321, 16.2281123159, -16.2785020951, 16.3287297498, 16.3787968348, 16.4287048805, -16.4784553929, 16.5280498543, 16.5774897242, 16.6267764392, -16.6759114139, 16.7248960413, 16.7737316932, 16.8224197206, -16.8709614543, 16.9193582051, 16.9676112644, 17.0157219046, -17.0636913794, 17.1115209241, 17.1592117562, 17.2067650757, -17.2541820653, 17.3014638909, 17.3486117017, 17.3956266311, -17.4425097961, 17.4892622985, 17.5358852248, 17.5823796464, -17.6287466201, 17.6749871882, 17.721102379, 17.7670932069, -17.8129606726, 17.8587057635, 17.9043294539, 17.9498327054, -17.9952164666, 18.0404816741, 18.0856292522, 18.130660113, -18.1755751573, 18.2203752741, 18.2650613411, 18.309634225, -18.3540947814, 18.3984438554, 18.4426822814, 18.4868108834, -18.5308304754, 18.5747418613, 18.6185458352, 18.6622431813, -18.7058346748, 18.749321081, 18.7927031564, 18.8359816483, -18.8791572952, 18.9222308268, 18.9652029643, 19.0080744204, -19.0508458994, 19.0935180976, 19.136091703, 19.1785673961, -19.2209458492, 19.2632277271, 19.3054136872, 19.3475043792, -19.3895004457, 19.431402522, 19.4732112364, 19.5149272102, -19.5565510578, 19.598083387, 19.6395247987, 19.6808758874, -19.7221372412, 19.7633094418, 19.8043930645, 19.8453886786, -19.8862968473, 19.9271181279, 19.9678530715, 20.0085022239, -20.0490661246, 20.0895453079, 20.1299403023, 20.1702516311, -20.2104798118, 20.250625357, 20.2906887737, 20.3306705641, -20.3705712249, 20.4103912481, 20.4501311206, 20.4897913245, -20.5293723369, 20.5688746305, 20.608298673, 20.6476449276, -20.6869138529, 20.7261059032, 20.7652215281, 20.804261173, -20.843225279, 20.8821142829, 20.9209286172, 20.9596687105, -20.9983349871, 21.0369278674, 21.0754477678, 21.1138951007, -21.1522702748, 21.1905736947, 21.2288057616, 21.2669668728, -21.3050574217, 21.3430777984, 21.3810283893, 21.4189095773, -21.4567217417, 21.4944652585, 21.5321405003, 21.5697478361, -21.6072876319, 21.6447602504, 21.6821660507, 21.7195053891, -21.7567786187, 21.7939860892, 21.8311281476, 21.8682051376, -21.9052174, 21.9421652726, 21.9790490904, 22.0158691853, -22.0526258864, 22.0893195201, 22.1259504099, 22.1625188766, -22.1990252382, 22.2354698102, 22.271852905, 22.3081748329, -22.3444359014, 22.3806364152, 22.4167766768, 22.4528569861, -22.4888776404, 22.5248389346, 22.5607411612, 22.5965846105, -22.63236957, 22.6680963252, 22.7037651592, 22.7393763528, -22.7749301845, 22.8104269307, 22.8458668654, 22.8812502606, -22.9165773859, 22.9518485091, 22.9870638955, 23.0222238086, -23.0573285098, 23.0923782582, 23.1273733112, 23.1623139241, -23.1972003501, 23.2320328405, 23.2668116448, 23.3015370104, -23.3362091828, 23.3708284059, 23.4053949214, 23.4399089693, -23.4743707879, 23.5087806136, 23.5431386809, 23.5774452228, -23.6117004703, 23.6459046528, 23.6800579981, 23.7141607321, -23.7482130793, 23.7822152621, 23.8161675019, 23.8500700178, -23.8839230279, 23.9177267482, 23.9514813936, 23.985187177, -24.0188443102, 24.0524530031, 24.0860134643, 24.1195259009, -24.1529905184, 24.1864075209, 24.2197771112, 24.2530994905, -24.2863748586, 24.3196034138, 24.3527853533, 24.3859208726, -24.4190101661, 24.4520534266, 24.4850508458, 24.5180026138, -24.5509089198, 24.5837699513, 24.6165858946, 24.6493569349, -24.682083256, 24.7147650405, 24.7474024696, 24.7799957236, -24.8125449812, 24.8450504203, 24.8775122172, 24.9099305473, -24.9423055847, 24.9746375025, 25.0069264724, 25.0391726652, -25.0713762504, 25.1035373964, 25.1356562707, 25.1677330394, -25.1997678678, 25.2317609198, 25.2637123586, 25.295622346, -25.3274910431, 25.3593186096, 25.3911052044, 25.4228509853, -25.4545561092, 25.4862207318, 25.517845008, 25.5494290916, -25.5809731355, 25.6124772915, 25.6439417106, 25.6753665429, -25.7067519372, 25.7380980417, 25.7694050037, 25.8006729694, -25.8319020841, 25.8630924924, 25.8942443377, 25.9253577628, -25.9564329095, 25.9874699187, 26.0184689304, 26.0494300839, -26.0803535176, 26.111239369, 26.1420877748, 26.1728988708, -26.2036727921, 26.234409673, 26.2651096468, 26.2957728462, -26.326399403, 26.3569894483, 26.3875431124, 26.4180605247, -26.448541814, 26.4789871082, 26.5093965346, 26.5397702197, -26.5701082891, 26.6004108679, 26.6306780804, 26.66091005, -26.6911068996, 26.7212687513, 26.7513957266, 26.781487946, -26.8115455297, 26.841568597, 26.8715572664, 26.9015116561, -26.9314318831, 26.9613180642, 26.9911703153, 27.0209887518, -27.0507734882, 27.0805246386, 27.1102423164, 27.1399266342, -27.1695777042, 27.1991956378, 27.2287805458, 27.2583325386, -27.2878517257, 27.3173382162, 27.3467921183, 27.3762135401, -27.4056025886, 27.4349593705, 27.4642839918, 27.4935765581, -27.5228371742, 27.5520659444, 27.5812629725, 27.6104283616, -27.6395622145, 27.6686646331, 27.697735719, 27.7267755733, -27.7557842963, 27.7847619879, 27.8137087475, 27.842624674, -27.8715098657, 27.9003644204, 27.9291884353, 27.9579820072, -27.9867452325, 28.0154782067, 28.0441810252, 28.0728537828, -28.1014965736, 28.1301094915, 28.1586926296, 28.1872460809, -28.2157699376, 28.2442642915, 28.2727292341, 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39.2590794966, 39.2794252526, 39.2997602936, -39.3200846366, 39.3403982984, 39.3607012959, 39.3809936458, -39.401275365, 39.4215464701, 39.4418069776, 39.4620569043, -39.4822962667, 39.5025250812, 39.5227433645, 39.5429511329, -39.5631484027, 39.5833351904, 39.6035115122, 39.6236773845, -39.6438328234, 39.6639778451, 39.6841124657, 39.7042367014, -39.7243505682, 39.744454082, 39.7645472589, 39.7846301149, -39.8047026656, 39.8247649272, 39.8448169153, 39.8648586456, -39.884890134, 39.9049113962, 39.9249224477, 39.9449233041, -39.9649139811, 39.9848944942, 40.0048648588, 40.0248250904, -40.0447752044, 40.0647152162, 40.0846451411, 40.1045649944, -40.1244747914, 40.1443745472, 40.164264277, 40.1841439961, -40.2040137194, 40.2238734621, 40.2437232392, 40.2635630656, -40.2833929563, 40.3032129263 -}; - -static score_t reg2(int N){ - if (N<=1000) - return r2_1000[N]; - else - return exp(0.5*log(N*pi/2) - + sqrt(8/(9*N*pi)) - + (1.0/12 - 4/(9*pi))/N); -} - -score_t reg(int N, int K){ - - if (K == 1) - return 1.0 ; - else if (K == 2) - return reg2(N); - else { - int k = 0; - score_t rk_2 = reg(N,1); - score_t rk_1 = reg(N,2); - score_t rk = 0; - for (k=3; k<=K;++k){ - rk = rk_1 + rk_2 /(k-2)*N; - rk_2 = rk_1; - rk_1 = rk; - } - return rk; - } -} - -#ifdef MAIN -#include <stdio.h> -#include <stdlib.h> - - int main(int argc, char* argv[]){ - int N, K; - - if (argc != 3) { - fprintf(stderr, "Usage: reg N K\n"); - exit(2); - } - - N = atoi(argv[1]); - K = atoi(argv[2]); - - if (K<=0){ - fprintf(stderr, "K has to be a positive integer.\n"); - exit(2); - } - - if (N<0){ - fprintf(stderr, "N has to be a non-negative integer.\n"); - exit(2); - } - - - printf("%f\n", reg(N,K)); - - return 0; - } - -#endif diff --git a/sourcecodes/k-best/src/reg.h b/sourcecodes/k-best/src/reg.h deleted file mode 100644 index 2422f2e5..00000000 --- a/sourcecodes/k-best/src/reg.h +++ /dev/null @@ -1,7 +0,0 @@ -#ifndef __REG_H__ -#define __REG_H__ -#include "cfg.h" - -extern score_t reg(int N, int K); - -#endif diff --git a/sourcecodes/k-best/src/score_net.c b/sourcecodes/k-best/src/score_net.c deleted file mode 100644 index fccec93f..00000000 --- a/sourcecodes/k-best/src/score_net.c +++ /dev/null @@ -1,39 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" -#include "varpar.h" - -score_t score_net(char* netfile, char* dirprefix){ - score_t score = 0.0; - - int v; - varset_t varset; - FILE* netf = strcmp(netfile,"-") ? fopen(netfile, "rt") : stdin; - for(v=0; 1 == fscanf(netf, "%u", &varset); ++v){ - score_t vscore; - FILE* fin = open_file(dirprefix, v, "", "rb"); - fseek(fin, varset2parset(v, varset)*sizeof(score_t), SEEK_SET); - fread(&vscore, sizeof(score_t), 1, fin); - fclose(fin); - score += vscore; - } - fclose(netf); - return score; -} - -int main(int argc, char* argv[]) -{ - - if (argc!=3) { - fprintf(stderr, "Usage: score_net netfile dirname\n"); - return 1; - } - - printf("%.3f\n", score_net(argv[1], argv[2])); - - return 0; -} diff --git a/sourcecodes/k-best/src/score_nets.c b/sourcecodes/k-best/src/score_nets.c deleted file mode 100644 index 44ab3a27..00000000 --- a/sourcecodes/k-best/src/score_nets.c +++ /dev/null @@ -1,54 +0,0 @@ -#include "cfg.h" - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> - -#include "files.h" -#include "varpar.h" - -score_t score_net(char* netfile, char* dirprefix, int nof_vars, FILE** fins){ - score_t score = 0.0; - - int v; - varset_t varset; - FILE* netf = strcmp(netfile,"-") ? fopen(netfile, "r") : stdin; - for(v=0; 1 == fscanf(netf, "%u", &varset); ++v){ - score_t vscore; - fseek(fins[v], varset2parset(v, varset)*sizeof(score_t), SEEK_SET); - fread(&vscore, sizeof(score_t), 1, fins[v]); - rewind(fins[v]); - score += vscore; - } - fclose(netf); - return score; -} - -void score_nets(char* netfiles, char* dirprefix){ - char netfile[1024]; - FILE* netfs = strcmp(netfiles,"-") ? fopen(netfiles, "r") : stdin; - int nof_vars = 0; - FILE** fins = NULL; - while(EOF != fscanf(netfs, "%s", netfile)){ - if (0 == nof_vars){ - nof_vars = nof_lines(netfile); - fins = open_files(nof_vars, dirprefix,"","r"); - } - printf("%.3f\n", score_net(netfile, dirprefix, nof_vars, fins)); - } - free_files(nof_vars,fins); - fclose(netfs); -} - -int main(int argc, char* argv[]) -{ - - if (argc!=3) { - fprintf(stderr, "Usage: score_nets netfiles dirname\n"); - return 1; - } - - score_nets(argv[1], argv[2]); - - return 0; -} diff --git a/sourcecodes/k-best/src/varpar.c b/sourcecodes/k-best/src/varpar.c deleted file mode 100644 index 584799c6..00000000 --- a/sourcecodes/k-best/src/varpar.c +++ /dev/null @@ -1,19 +0,0 @@ -#include "varpar.h" - -varset_t parset2varset(int v, varset_t set){ - varset_t sinkleton = 1U<<v; - varset_t mask = sinkleton - 1; - varset_t low = set & mask; - varset_t high = set & ~mask; - return (high<<1) | low; -} - -varset_t varset2parset(int v, varset_t set){ - /* assumes v not set */ - varset_t sinkleton = 1U<<v; - varset_t mask = sinkleton - 1; - varset_t low = set & mask; - varset_t high = set & ~mask; - return (high>>1) | low; -} - diff --git a/sourcecodes/k-best/src/varpar.h b/sourcecodes/k-best/src/varpar.h deleted file mode 100644 index 3f28b64b..00000000 --- a/sourcecodes/k-best/src/varpar.h +++ /dev/null @@ -1,9 +0,0 @@ -#ifndef __VARPAR_H__ -#define __VARPAR_H__ - -#include "cfg.h" - -varset_t parset2varset(int v, varset_t set); -varset_t varset2parset(int v, varset_t set); - -#endif diff --git a/sourcecodes/k-best/src/xtab.h b/sourcecodes/k-best/src/xtab.h deleted file mode 100644 index 51d424c1..00000000 --- a/sourcecodes/k-best/src/xtab.h +++ /dev/null @@ -1,80 +0,0 @@ -#ifndef _XTAB_H_ -#define _XTAB_H_ - -#include <string.h> - -typedef struct xentry xentry; -typedef unsigned char uchar; -typedef unsigned int uint; - - -//Each xentry is one node in the linked list -struct xentry { - uchar* key; //Key value as a string - int* val; //value as int array - xentry* next; //pointer to the next xentry i.e. the next node in this linked list - uint h; /* h denotes hash key i.e to which row in the hash table it belongs to*/ -}; - -typedef struct xtab xtab; - -struct xtab { - int range; /* range of hash keys, for example 1024 */ //i.e. number of rows in hash table - xentry** ix; /* hashkey to xentry pointer mapping */ //pointer pointing to start of each row in the hash table - xentry* free; /* pointer to unused xentries */ - xentry* xentries; //Each entry in hash table -}; - -//Number of entries in the hash table are counted by (free-xentries) -#define xcount(t) ((t)->free - (t)->xentries) - -/*Reset memory to 0's from ix to the end of last xentry*/ - -# define xreset(t) \ -{\ - memset((t)->ix, 0, (t)->range * sizeof(xentry*));\ - memset((t)->xentries, 0, xcount(t) * sizeof(xentry));\ - (t)->free = (t)->xentries;\ -} - -xentry* xadd(xtab* t, uint h, uchar* key, int klen, int* new) { - - /* starting from ix[h], go through x:s and try to find key */ - - //Search in the linked list for that particular hash value and see if such a linked list has the particular key already - xentry* x = t->ix[h]; - xentry** p = t->ix + h; /* prev-pointer to chain the possibly new xentry */ - - //Compares the entry to be added with old entries. If the same key value does not already exist in the linked list, then just go to the next xentry and compare - //memcmp returns 0 if the strings are identical - for(; x && memcmp(x->key, key, klen); x = x->next) - p = &(x->next); - - //If the key value is not already present in the linked list for that hash value - *new = !x; - - if(*new){ - x = (t->free)++; //Free memory starts one block later because new element is inserted - x->h = h; //Set hash value - *p = x; /* link the new x */ - } - - return x; -} - -xtab* xcreate(int range, int nof_xentries){ - xtab* t = calloc(1,sizeof(xtab)); - t->range = range; - t->ix = calloc(range, sizeof(xentry*)); - t->xentries = calloc(nof_xentries, sizeof(xentry)); - t->free = t->xentries; - return t; -} - -void xdestroy(xtab* t) { - free(t->ix); - free(t->xentries); - free(t); -} - -#endif diff --git a/sourcecodes/layout_cyto.php b/sourcecodes/layout_cyto.php index b939f79a..0e512345 100644 --- a/sourcecodes/layout_cyto.php +++ b/sourcecodes/layout_cyto.php @@ -104,8 +104,8 @@ var default_layout = { name: 'dagre', spacingFactor: 1.25 } - $.getJSON("<?php print($input_json);?>",function (data) { - //$.getJSON("./data/cwHnetwork.json",function (data) { + //$.getJSON("<?php print($input_json);?>",function (data) { + $.getJSON("./data/sample_network.json",function (dumm) { // console.log(data); // document.addEventListener('DOMContentLoaded', function(){ var cy = window.cy = cytoscape({ diff --git a/sourcecodes/layout_svg_no.php b/sourcecodes/layout_svg_no.php index f7268788..89f6ffbb 100644 --- a/sourcecodes/layout_svg_no.php +++ b/sourcecodes/layout_svg_no.php @@ -112,10 +112,21 @@ if(file_exists($filename1)) //onload = "makeDraggable(evt)"; +<<<<<<< HEAD d3.xml("<?php print($svg_file);?>", function(error, documentFragment){ if (error) {console.log(error); return;} +======= +<?php +$svg_xml = json_encode(file("file://".$dir.$svg_file)); +?> +d3.xml("", function(dumm){ + var data1 = <?php echo $svg_xml;?>; + var data2 = data1.join(""); + parser = new DOMParser(); + documentFragment = parser.parseFromString(data2,"text/xml"); +>>>>>>> genenet8_initial_1.3 var svgNode = documentFragment .getElementsByTagName("svg")[0]; diff --git a/sourcecodes/localscore/index.html b/sourcecodes/localscore/index.html deleted file mode 100644 index 429668c7..00000000 --- a/sourcecodes/localscore/index.html +++ /dev/null @@ -1,6 +0,0 @@ -<html> -<head> -<title>Bayesian Network Web Server</title> -<meta HTTP-EQUIV="REFRESH" content="0; url=http://compbio.uthsc.edu/BNW/sourcecodes/home.php"> -</head> -</html> diff --git a/sourcecodes/network_score b/sourcecodes/network_score deleted file mode 100644 index 2fc22d5a..00000000 --- a/sourcecodes/network_score +++ /dev/null Binary files differdiff --git a/sourcecodes/parameter_learning/prepareInput.m b/sourcecodes/parameter_learning/prepareInput.m index 39368582..638dfece 100644 --- a/sourcecodes/parameter_learning/prepareInput.m +++ b/sourcecodes/parameter_learning/prepareInput.m @@ -92,9 +92,26 @@ end % Remove all rows that have missing data from data file +% Missing data could be NA or empty lines in the input file. remove_count = sum(any(strcmp(data,"NA"),2)); data(any(strcmp(data,"NA"),2),:)=[]; ncases = ncases - remove_count; +remove_count_total = remove_count; + +remove_count = 0; +ii = ncases; +for i=1:ii + for j=1:nnodes + if isempty(data{i,j}) + data(i,:) = []; + remove_count = remove_count + 1 + i = i - 1 + ii = ii -1 + end + end +end +ncases = ncases - remove_count; +remove_count_total=remove_count_total+remove_count; % Determine whether or not the nodes are continuous or discrete. @@ -293,7 +310,7 @@ if size(remove,1) > 0 fprintf(dout,['\n']); end fprintf(dout,'There are %i variables and %i cases(rows).\n',size(labels,2),ncases); -fprintf(dout,'%i cases(rows) have been removed because they contained NA (missing data).\n',remove_count); +fprintf(dout,'%i cases(rows) have been removed because they contained NA (missing data).\n',remove_count_total); fprintf(dout_table,'Variable\tType\tStates/Mean (St Dev)\tReason for classification\n'); fprintf(dout,'The variable names are:\n'); fprintf(dout,'%s\t',labels{1:end-1}); @@ -316,7 +333,7 @@ for i=1:nnodes fprintf(dout_table,'%s\tDiscrete\t%i\t%s\n',labels{i},levels{i},reason{i}); end end -fprintf(dout_table,'There are %i variables and %i cases; %i variables and %i rows were removed.\n',size(labels,2),ncases,size(remove,1),remove_count); +fprintf(dout_table,'There are %i variables and %i cases; %i variables and %i rows were removed.\n',size(labels,2),ncases,size(remove,1),remove_count_total); fclose(dout); fclose(dout_table); @@ -350,4 +367,4 @@ fclose(fout); end -% end of prepareInput.m \ No newline at end of file +% end of prepareInput.m diff --git a/sourcecodes/scripts/accordion.js~ b/sourcecodes/scripts/accordion.js~ deleted file mode 100644 index 51949b96..00000000 --- a/sourcecodes/scripts/accordion.js~ +++ /dev/null @@ -1,31 +0,0 @@ -$(function() { -var acc = document.getElementsByClassName("accordion"); -var panel = document.getElementsByClassName("panel"); -var icons = document.getElementsByClassName("i"); -var i; - -for (var i = 0; i < acc.length; i++) { - acc[i].onclick = function() { - var setClasses = !this.classList.contains('active'); - setClass(acc, 'active', 'remove'); - setClass(panel, 'show', 'remove'); - if (setClasses) { - this.classList.toggle("active"); - this.nextElementSibling.classList.toggle("show"); - } - } -} - -function setClass(els, className, fnName) { - for (var i = 0; i < els.length; i++) { - els[i].classList[fnName](className); - } -} - -$('button').click(function() { - $('i').not($(this).find('i')).removeClass('fa-minus') - $('i').not($(this).find('i')).addClass('fa-plus') - $(this).find('i').toggleClass('fa-plus fa-minus') - }); - } - ) \ No newline at end of file diff --git a/sourcecodes/scripts/create_table.js~ b/sourcecodes/scripts/create_table.js~ deleted file mode 100644 index 85df8edb..00000000 --- a/sourcecodes/scripts/create_table.js~ +++ /dev/null @@ -1,82 +0,0 @@ -function tabulate_caption(container,data,caption_text) { - var table = d3.select(container).append('table'); - var caption = table.append("caption").text(caption_text); - //var titles = d3.keys(data[0]); - var titles = data.columns; - var headers = table.append('thead').append('tr') - .selectAll('th') - .data(titles).enter() - .append('th') - .text(function (d) { - return d; - }); - - var rows = table.append('tbody').selectAll('tr') - .data(data).enter() - .append('tr'); - rows.selectAll('td') - .data(function (d) { - return titles.map(function (k) { - return { 'value': d[k], 'name': k}; - }); - }).enter() - .append('td') - .attr('data-th', function (d) { - return d.name; - }) - .text(function (d) { - return d.value; - }); - return table; -} - -function tabulate_header_row(container,data,caption_text) { - var table = d3.select(container).append('table'); - var caption = table.append("caption").text(caption_text); - var titles = d3.keys(data[0]); - for (var i=0; i<data.length ;i++) { - delete data[i][""]; - data[i]["From\\To"] = titles[i]; - } - var titles = d3.keys(data[0]); - titles.pop(); - titles.unshift("From\\To"); - var headers = table.append('thead').append('tr') - .selectAll('th') - .data(titles).enter() - .append('th') - .attr("class", function(d) { - if (d == "From\\To") { - return "corner-header" - } - }) - .text(function (d) { - return d; - }); - - var rows = table.append('tbody').selectAll('tr') - .data(data).enter() - .append('tr'); - rows.selectAll('td') - .data(function (d) { - return titles.map(function (k) { - return { 'value': d[k], 'name': k}; - }); - }).enter() - .append('td') - .attr('data-th', function (d) { - return d.name; - }) - .attr("class", function(d) { - if (d.name == "From\\To") { - return "horizontal-header" - } - }) - .text(function (d) { - return d.value; - }); - - - - return table; -} diff --git a/sourcecodes/scripts/font-awesome.css~ b/sourcecodes/scripts/font-awesome.css~ deleted file mode 100644 index 46ca5253..00000000 --- a/sourcecodes/scripts/font-awesome.css~ +++ /dev/null @@ -1,821 +0,0 @@ -/*! - * Font Awesome 4.0.3 by @davegandy - http://fontawesome.io - @fontawesome - * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) - */ -/* FONT PATH - * -------------------------- */ -@font-face { - font-family: 'FontAwesome'; - src: url('../fonts/fontawesome-webfont.eot?v=4.0.3'); - src: url('../fonts/fontawesome-webfont.eot?#iefix&v=4.0.3') format('embedded-opentype'), url('../fonts/fontawesome-webfont.woff?v=4.0.3') format('woff'), url('../fonts/fontawesome-webfont.ttf?v=4.0.3') format('truetype'), url('../fonts/fontawesome-webfont.svg?v=4.0.3#fontawesomeregular') format('svg'); - font-weight: normal; - font-style: normal; -} -.fa { - display: inline-block; - font-family: FontAwesome; - font-style: normal; - font-weight: normal; - line-height: 1; - -webkit-font-smoothing: antialiased; - -moz-osx-font-smoothing: grayscale; -} -/* makes the font 33% larger relative to the icon container */ -.fa-lg { - font-size: 1.3333333333333333em; - line-height: 0.75em; - vertical-align: -15%; -} -.fa-2x { - font-size: 2em; -} -.fa-3x { - font-size: 3em; -} -.fa-4x { - font-size: 4em; -} -.fa-5x { - font-size: 5em; -} -.fa-fw { - width: 1.2857142857142858em; - text-align: center; -} -.fa-ul { - padding-left: 0; - margin-left: 2.142857142857143em; - list-style-type: none; -} -.fa-ul > li { - position: relative; -} -.fa-li { - position: absolute; - left: -2.142857142857143em; - width: 2.142857142857143em; - top: 0.14285714285714285em; - text-align: center; -} -.fa-li.fa-lg { - left: -1.8571428571428572em; -} -.fa-border { - padding: .2em .25em .15em; - border: solid 0.08em #eeeeee; - border-radius: .1em; -} -.pull-right { - float: right; -} -.pull-left { - float: left; -} -.fa.pull-left { - margin-right: .3em; -} -.fa.pull-right { - margin-left: .3em; -} -.fa-spin { - -webkit-animation: spin 2s infinite linear; - -moz-animation: spin 2s infinite linear; - -o-animation: spin 2s infinite linear; - animation: spin 2s infinite linear; -} -@-moz-keyframes spin { - 0% { - -moz-transform: rotate(0deg); - } - 100% { - -moz-transform: rotate(359deg); - } -} -@-webkit-keyframes spin { - 0% { - -webkit-transform: rotate(0deg); - } - 100% { - -webkit-transform: rotate(359deg); - } -} -@-o-keyframes spin { - 0% { - -o-transform: rotate(0deg); - } - 100% { - -o-transform: rotate(359deg); - } -} -@-ms-keyframes spin { - 0% { - -ms-transform: rotate(0deg); - } - 100% { - -ms-transform: rotate(359deg); - } -} -@keyframes spin { - 0% { - transform: rotate(0deg); - } - 100% { - transform: rotate(359deg); - } -} -.fa-rotate-90 { - filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=1); - -webkit-transform: rotate(90deg); - -moz-transform: rotate(90deg); - -ms-transform: rotate(90deg); - -o-transform: rotate(90deg); - transform: rotate(90deg); -} -.fa-rotate-180 { - filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2); - -webkit-transform: rotate(180deg); - -moz-transform: rotate(180deg); - -ms-transform: rotate(180deg); - -o-transform: rotate(180deg); - transform: rotate(180deg); -} -.fa-rotate-270 { - filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=3); - -webkit-transform: rotate(270deg); - -moz-transform: rotate(270deg); - -ms-transform: rotate(270deg); - -o-transform: rotate(270deg); - transform: rotate(270deg); -} -.fa-flip-horizontal { - filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1); - -webkit-transform: scale(-1, 1); - -moz-transform: scale(-1, 1); - -ms-transform: scale(-1, 1); - -o-transform: scale(-1, 1); - transform: scale(-1, 1); -} -.fa-flip-vertical { - filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1); - -webkit-transform: scale(1, -1); - -moz-transform: scale(1, -1); - -ms-transform: scale(1, -1); - -o-transform: scale(1, -1); - transform: scale(1, -1); -} -.fa-stack { - position: relative; - display: inline-block; - width: 2em; - height: 2em; - line-height: 2em; - vertical-align: middle; -} -.fa-stack-1x, -.fa-stack-2x { - position: absolute; - left: 0; - width: 100%; - text-align: center; -} -.fa-stack-1x { - line-height: inherit; -} -.fa-stack-2x { - font-size: 2em; -} -.fa-inverse { - color: #ffffff; -} -/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen - readers do not read off random characters that represent icons */ -.fa-glass:before { - content: "\f000"; -} -.fa-music:before { - content: "\f001"; -} -.fa-search:before { - content: "\f002"; -} -.fa-envelope-o:before { - content: "\f003"; -} -.fa-heart:before { - content: "\f004"; -} -.fa-star:before { - content: "\f005"; -} -.fa-star-o:before { - content: "\f006"; -} -.fa-user:before { - content: "\f007"; -} -.fa-film:before { - content: "\f008"; -} -.fa-th-large:before { - content: "\f009"; -} -.fa-th:before { - content: "\f00a"; -} -.fa-th-list:before { - content: "\f00b"; -} -.fa-check:before { - content: "\f00c"; -} -.fa-times:before { - content: "\f00d"; -} -.fa-search-plus:before { - content: "\f00e"; -} -.fa-search-minus:before { - content: "\f010"; -} -.fa-power-off:before { - content: "\f011"; -} -.fa-signal:before { - content: "\f012"; -} -.fa-gear:before, -.fa-cog:before { - content: "\f013"; -} -.fa-trash-o:before { - content: "\f014"; -} -.fa-home:before { - content: "\f015"; -} -.fa-file-o:before { - content: "\f016"; -} -.fa-clock-o:before { - content: "\f017"; -} -.fa-road:before { - content: "\f018"; -} -.fa-download:before { - content: "\f019"; -} -.fa-arrow-circle-o-down:before { - content: "\f01a"; -} -.fa-arrow-circle-o-up:before { - content: "\f01b"; -} -.fa-inbox:before { - content: "\f01c"; -} -.fa-play-circle-o:before { - content: "\f01d"; -} -.fa-rotate-right:before, -.fa-repeat:before { - content: "\f01e"; -} -.fa-refresh:before { - content: "\f021"; -} -.fa-list-alt:before { - content: "\f022"; -} -.fa-lock:before { - content: "\f023"; -} -.fa-flag:before { - content: "\f024"; -} -.fa-headphones:before { - content: "\f025"; -} -.fa-volume-off:before { - content: "\f026"; -} -.fa-volume-down:before { - content: "\f027"; -} -.fa-volume-up:before { - content: "\f028"; -} -.fa-qrcode:before { - content: "\f029"; -} -.fa-barcode:before { - content: "\f02a"; -} -.fa-tag:before { - content: "\f02b"; -} -.fa-tags:before { - content: "\f02c"; -} -.fa-book:before { - content: "\f02d"; -} -.fa-bookmark:before { - content: "\f02e"; -} -.fa-print:before { - content: "\f02f"; -} -.fa-camera:before { - content: "\f030"; -} -.fa-font:before { - content: "\f031"; -} -.fa-bold:before { - content: "\f032"; -} -.fa-italic:before { - content: "\f033"; -} -.fa-text-height:before { - content: "\f034"; -} -.fa-text-width:before { - content: "\f035"; -} -.fa-align-left:before { - content: "\f036"; -} -.fa-align-center:before { - content: "\f037"; -} -.fa-align-right:before { - content: "\f038"; -} -.fa-align-justify:before { - content: "\f039"; -} -.fa-list:before { - content: "\f03a"; -} -.fa-dedent:before, -.fa-outdent:before { - content: "\f03b"; -} -.fa-indent:before { - content: "\f03c"; -} -.fa-video-camera:before { - content: "\f03d"; -} -.fa-picture-o:before { - content: "\f03e"; -} -.fa-pencil:before { - content: "\f040"; -} -.fa-map-marker:before { - content: "\f041"; -} -.fa-adjust:before { - content: "\f042"; -} -.fa-tint:before { - content: "\f043"; -} -.fa-edit:before, -.fa-pencil-square-o:before { - content: "\f044"; -} -.fa-share-square-o:before { - content: "\f045"; -} -.fa-check-square-o:before { - content: "\f046"; -} -.fa-arrows:before { - content: "\f047"; -} -.fa-step-backward:before { - content: "\f048"; -} -.fa-fast-backward:before { - content: "\f049"; -} -.fa-backward:before { - content: "\f04a"; -} -.fa-play:before { - content: "\f04b"; -} -.fa-pause:before { - content: "\f04c"; -} -.fa-stop:before { - content: "\f04d"; -} -.fa-forward:before { - content: "\f04e"; -} -.fa-fast-forward:before { - content: "\f050"; -} -.fa-step-forward:before { - content: "\f051"; -} -.fa-eject:before { - content: "\f052"; -} -.fa-chevron-left:before { - content: "\f053"; -} -.fa-chevron-right:before { - content: "\f054"; -} -.fa-plus-circle:before { - content: "\f055"; -} -.fa-minus-circle:before { - content: "\f056"; -} -.fa-times-circle:before { - content: "\f057"; -} -.fa-check-circle:before { - content: "\f058"; -} -.fa-question-circle:before { - content: "\f059"; -} -.fa-info-circle:before { - content: "\f05a"; -} -.fa-crosshairs:before { - content: "\f05b"; -} -.fa-times-circle-o:before { - content: "\f05c"; -} -.fa-check-circle-o:before { - content: "\f05d"; -} -.fa-ban:before { - content: "\f05e"; -} -.fa-arrow-left:before { - content: "\f060"; -} -.fa-arrow-right:before { - content: "\f061"; -} -.fa-arrow-up:before { - content: "\f062"; -} -.fa-arrow-down:before { - content: "\f063"; -} -.fa-mail-forward:before, -.fa-share:before { - content: "\f064"; -} -.fa-expand:before { - content: "\f065"; -} -.fa-compress:before { - content: "\f066"; -} -.fa-plus:before { - content: "\f067"; -} -.fa-minus:before { - content: "\f068"; -} -.fa-asterisk:before { - content: "\f069"; -} -.fa-exclamation-circle:before { - content: "\f06a"; -} -.fa-gift:before { - cont content: "\f06d"; -} -.fa-eye:before { - content: "\f06e"; -} -.fa-eye-sla content: "\f07c"; -} -.fa-arrows-v:before { - content: "\f07d"; -} -.fa-arrows-h:before { - content: "\f07e"; -} -.fa-bar-chart-o:before { - content: "\f080"; -} -.fa-twitter-square:before { - content: "\f081"; -} -.fa-facebook-square:before { - content: "\f082"; -} -.fa-c content: "\f084"; -} -.fa-gears:before, -.fa-cogs:before { - content: content: "\f091"; -} -.fa-github-square:before { - conte} -.fa-credit-card:before { - content: "\f09d"; -} -.fa-rss:before { - content: "\f09e"; -} -.fa-hdd-o:before { - content: "\f} -.fa-certificate.fa-wrench:before { - content: "\f0ad"; -} -.fa-tasks:before { - content: "\f0ae"; -} -.fa-filter:before { - content: "\f0b0"; -} -.fa-briefcase:before { - content: "\f0b1"; -} -.fa-arrows-alt:before { - content: "\f0b2"; -} -.fa-group:before, -.fa-users:before { - content: "\f0c0"; -} -.fa-chai.fa-cut:before, -.fa-scissors:before { - content: .fa-files-o:before { - content: "\f0c5"; -} -.fa-paperclip:before { - content: "\f0c6"; -} -.fa-save:before, -.fa-floppy-o:before { - content: "\f0c7"; -} -.fa-square:before { - content: "\f0c8"; -} -.fa-bars:before { - content: "\f0c9"; -} -.fa-list-ul:before { - content: "\f0ca"; -} -.fa-list-ol:before { - content: "\f0cb"; -} -.fa-strikethrough:before { - content: "\f0cc"; -} -.fa-underline:before { - content: "\f0cd"; -} -.fa-table:before { - content: "\f0ce"; -} -.fa-magic:before { - content: "\f0d0"; -} -.fa-truck:before { - content: "\f0d1"; -} -.fa-pinterest:before { - content: "\f0d2"; -} -.fa-pinterest-square:before { - content: "\f0d3"; -} -.fa-google-plus-square:before { - content: "\f0d4"; -} -.fa-google-plus:before { - content: "\f0d5"; -} -.fa-money:before { - content: "\f0d6"; -} -.fa-caret-down:before { - content: "\f0d7"; -} -.fa-caret-up:before { - content: "\f0d8"; -} -.fa-caret-left:before { - content: } -.fa-ambulance:before { - content: "\f0f9"; -} -.} -.fa-h-square:before { - content: "\f0fd"; -} -.fa-plus-square:before { - content: "\f0fe"; -} -.} -.fa-angle-left:before { - content: "\f104"; -} -.fa-angle-right:before { - content: "\f105"; -} -.fa-angle-up:before { - content: "\f106"; -} -.fa-angle-down:before { - content: "\f107"; -} -.fa-desktop:before { - content: "\f108"; -} -.fa-laptop:before { - content: "\f109"; -} -.fa-tablet:before { - content: .fa-frown-o:before { - content: "\f119"; -} -.fa-meh-.fa-star-half-o:before { - content: "\f123"; -} -.fa-location-arrow:before { - content: "} -.fa-puzzle-piece:before { - content: "\f12e"; -} -.fa-microphone:before { - content: "\f130"; -} -.fa-microphone-slash:before { - content: "\f131"; -} -.fa-shield:before { - content: "\f132"; -} -.fa-calendar-o:before { - content: "\f133"; -} -.fa-fire-extinguisher:before { - content: "\f134"; -} -.fa-rocket:before { - content: "\f135"; -} -.fa-maxcdn:before { - content: "\f136"; -} -.fa} -.fa-html5:before { - content: "\f13b"; -} -.fa-css3:before { - content: "\f1.fa-minus-square-o:before { - content: "\f147"; -} -.fa-level-up:before { - content: "\f148"; -} -.fa-level-down:before { - content: "\f149"; -} -.fa-check-square:before { - content: "\f14a"; -} -.fa-pencil-square:before { - content: "\f14b"; -} -.fa-external-link-square:before { - content: "\f14c"; -} -.fa-share-square:before { - content: "\f14d"; -} -.fa-compass:before { - content: "\f14e"; -} -.fa-toggle-down:before, -.fa-caret-square-o-down:before { - content: "\f150"; -} -.fa-toggle-up:before, -.fa-caret-square-o-up:before { - content: "\f151"; -} -.fa-toggle-right:before, -.fa-caret-square-o-right:before { - content: "\f152"; -} -.fa-euro:before, -.fa-eur:before { - content: "\f153"; -} -.fa-gbp:before { - content: "\f154"; -} -.fa-dollar:before, -.fa-usd:before { - content: "\f155"; -} -.fa-rupee:before, -.fa-inr:before { - content: "\f156"; -} -.fa-cny:before, -.fa-rmb:before, -.fa-yen:before, -.fa-jpy:before { - content: "\f157"; -} -.fa-ruble:before, -.fa-rouble:before, -.fa-rub:before { - content: "\f158"; -} -.fa-won:before, -.fa-krw:before { - content: "\f159"; -} -.fa-bitcoin:before, -.fa-btc:befo} -.fa-thumbs-up:before { - content: "\f164";.fa-thumbs-down:before { - content: "\f165"; -} -.fa-youtube-square:before { - content: "\f166"; -} -.fa-youtube:before { - content: "\f167"; -} -.fa-xing:before { - content: "\f168"; -} -.fa-xing-square:before { content: "\f177"; -} -.fa-long-arr content: "\f185"; -} -.fa-moon-o:before { - content: "\f186"; -} -.fa-archive:before { - content: "\f187"; -} -.fa-bug:before { - content: "\f188"; -} -.fa-vk:before { - content: "\f189"; -} -.fa-weibo:before { - content: "\f18a"; -} -.fa-renren:before { - content: "\f18b"; -} -.fa-pagelines:before { - content: "\f18c"; -} -.fa-stack-exchange:before { - content: "\f18d"; -} -.fa-arrow-circle-o-right:before { - content: "\f18e"; -} -.fa-arrow-circle-o-left:before { - content: "\f190"; -} -.fa-toggle-left:before, -.fa-caret-square-o-left:before { - content: "\f191"; -} -.fa-dot-circle-o:before { - content: "\f192"; -} -.fa-wheelchair:before { - content: "\f193"; -} -.fa-vimeo-square:before { - content: "\f194"; -} -.fa-turkish-lira:before, -.fa-try:before { - content: "\f195"; -} -.fa-plus-square-o:before { - content: "\f196"; -} diff --git a/sourcecodes/scripts/table.css~ b/sourcecodes/scripts/table.css~ deleted file mode 100644 index 576f690f..00000000 --- a/sourcecodes/scripts/table.css~ +++ /dev/null @@ -1,42 +0,0 @@ - * { -margin: 0; -padding: 0; -} -d3_table { -width: 100%; - border-collapse: collapse; - margin: 8; -} -d3_caption { - font-size: 16pt; - text-align: left; -} -/* Zebra striping */ -d3_tr:nth-of-type(even) { -background: LightGrey; -} -d3_th { -background: #3071a9; -color: white; -font-size: 12pt; -font-weight: normal; -} - -d3_td, d3_th { -padding: 6px; -border: 1px solid #ccc; - text-align: center; -} -.horizontal-header { -background: #3071a9; -color: white; - font-size: 12pt; -} -.corner-header { -background: LightGrey; -color: black; - font-size: 12pt; -} - - - diff --git a/sourcecodes/structure b/sourcecodes/structure deleted file mode 100644 index e9856f6d..00000000 --- a/sourcecodes/structure +++ /dev/null Binary files differdiff --git a/sourcecodes/build.sh b/var_lib_genenet_bnw/build.sh index a5958fd7..7f63840d 100644 --- a/sourcecodes/build.sh +++ b/var_lib_genenet_bnw/build.sh @@ -3,7 +3,7 @@ gcc ./localscore/network_score.c ./localscore/libRmath.so -lm -o network_score gcc ./print_structure/structure.c -lm -o structure cd ./k-best/src/ -./buildk_poster.sh +sh buildk_poster.sh diff --git a/sourcecodes/k-best/src/Arguments.h b/var_lib_genenet_bnw/k-best/src/Arguments.h index 574b2bf7..574b2bf7 100644 --- a/sourcecodes/k-best/src/Arguments.h +++ b/var_lib_genenet_bnw/k-best/src/Arguments.h diff --git a/sourcecodes/k-best/src/Engine.h b/var_lib_genenet_bnw/k-best/src/Engine.h index 2e16a701..2e16a701 100644 --- a/sourcecodes/k-best/src/Engine.h +++ b/var_lib_genenet_bnw/k-best/src/Engine.h diff --git a/var_lib_genenet_bnw/k-best/src/buildk_poster.sh b/var_lib_genenet_bnw/k-best/src/buildk_poster.sh new file mode 100644 index 00000000..a7c11183 --- /dev/null +++ b/var_lib_genenet_bnw/k-best/src/buildk_poster.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +D=g++ + +$D -o get_kbest_parents get_kbest_parents.cc +$D -o get_kbest_nets get_kbest_nets.cc + diff --git a/sourcecodes/k-best/src/cfg.h b/var_lib_genenet_bnw/k-best/src/cfg.h index 15e3fe89..15e3fe89 100644 --- a/sourcecodes/k-best/src/cfg.h +++ b/var_lib_genenet_bnw/k-best/src/cfg.h diff --git a/sourcecodes/k-best/src/data2netk_poster.sh b/var_lib_genenet_bnw/k-best/src/data2netk_poster.sh index 6b3a34ca..19d8f7cd 100644 --- a/sourcecodes/k-best/src/data2netk_poster.sh +++ b/var_lib_genenet_bnw/k-best/src/data2netk_poster.sh @@ -14,7 +14,7 @@ k=$1;shift n=$1;shift nof_vars=`head -1 $datafile|wc -w` -echo "The number of variables is $nof_vars." +#echo "The number of variables is $nof_vars." #HR: if [ "$n" -eq 0 ] @@ -25,13 +25,13 @@ else fi #maxindegree=`expr $nof_vars - 1` -echo "maxindegree is $maxindegree." +#echo "maxindegree is $maxindegree." #HR: nof_instances=`cat $datafile | wc -l` #delete the header and type nof_instances=`expr $nof_instances - 2` -echo "The number of instances is $nof_instances." +#echo "The number of instances is $nof_instances." START=$(date +%s%N) @@ -40,8 +40,8 @@ $binpath/get_kbest_parents $nof_vars ${rdir} $k END=$(date +%s%N) #DIFF=$(( $END - $START )) DIFF2=$(( $END - $START )) -echo "get_kbest_parents is done." -echo "get_kbest_parents took $DIFF2 n-seconds." +#echo "get_kbest_parents is done." +#echo "get_kbest_parents took $DIFF2 n-seconds." START=$(date +%s%N) $binpath/get_kbest_nets $nof_vars ${rdir} $k @@ -49,8 +49,8 @@ $binpath/get_kbest_nets $nof_vars ${rdir} $k END=$(date +%s%N) #DIFF=$(( $END - $START )) DIFF3=$(( $END - $START )) -echo "get_kbest_nets is done." -echo "get_kbest_nets took $DIFF3 n-seconds." +#echo "get_kbest_nets is done." +#echo "get_kbest_nets took $DIFF3 n-seconds." DIFF=`expr $DIFF1 + $DIFF2 + $DIFF3` -echo "The total process took $DIFF n-seconds." +#echo "The total process took $DIFF n-seconds." diff --git a/sourcecodes/k-best/src/files.h b/var_lib_genenet_bnw/k-best/src/files.h index f11dd09e..f11dd09e 100644 --- a/sourcecodes/k-best/src/files.h +++ b/var_lib_genenet_bnw/k-best/src/files.h diff --git a/sourcecodes/k-best/src/files.o b/var_lib_genenet_bnw/k-best/src/files.o index 33f376d3..33f376d3 100644 --- a/sourcecodes/k-best/src/files.o +++ b/var_lib_genenet_bnw/k-best/src/files.o Binary files differdiff --git a/sourcecodes/k-best/src/get_kbest_nets b/var_lib_genenet_bnw/k-best/src/get_kbest_nets index 032b1a33..1c4a6041 100644 --- a/sourcecodes/k-best/src/get_kbest_nets +++ b/var_lib_genenet_bnw/k-best/src/get_kbest_nets Binary files differdiff --git a/sourcecodes/k-best/src/get_kbest_nets.cc b/var_lib_genenet_bnw/k-best/src/get_kbest_nets.cc index 9aafe83c..2ee35265 100644 --- a/sourcecodes/k-best/src/get_kbest_nets.cc +++ b/var_lib_genenet_bnw/k-best/src/get_kbest_nets.cc @@ -1503,10 +1503,10 @@ void get_kbest_nets(int nof_vars, FILE** fp,int k, char* dirname){ //comp_post(&kbnetscore[nof_combs-1],k,dirname); //new function: compute the posterior prob. comp_post_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars); - cout << "comp_post_compl(&kbnetscore[nof_combs-1],k,dirname) is done." << endl; + //cout << "comp_post_compl(&kbnetscore[nof_combs-1],k,dirname) is done." << endl; //comp_postExact_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars); - cout << "comp_postExact_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars) is not done. we will change it if requires" << endl; + //cout << "comp_postExact_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars) is not done. we will change it if requires" << endl; //HR: // print_scores(kbnetscore,dirname,k,nof_vars); diff --git a/var_lib_genenet_bnw/k-best/src/get_kbest_parents b/var_lib_genenet_bnw/k-best/src/get_kbest_parents new file mode 100644 index 00000000..c31a73ee --- /dev/null +++ b/var_lib_genenet_bnw/k-best/src/get_kbest_parents Binary files differdiff --git a/sourcecodes/k-best/src/get_kbest_parents.cc b/var_lib_genenet_bnw/k-best/src/get_kbest_parents.cc index 9377d11e..9377d11e 100644 --- a/sourcecodes/k-best/src/get_kbest_parents.cc +++ b/var_lib_genenet_bnw/k-best/src/get_kbest_parents.cc diff --git a/sourcecodes/k-best/src/varpar.o b/var_lib_genenet_bnw/k-best/src/varpar.o index 4fa1b165..4fa1b165 100644 --- a/sourcecodes/k-best/src/varpar.o +++ b/var_lib_genenet_bnw/k-best/src/varpar.o Binary files differdiff --git a/sourcecodes/localscore/Applic.h b/var_lib_genenet_bnw/localscore/Applic.h index 0ae5e981..0ae5e981 100644 --- a/sourcecodes/localscore/Applic.h +++ b/var_lib_genenet_bnw/localscore/Applic.h diff --git a/sourcecodes/localscore/Arith.h b/var_lib_genenet_bnw/localscore/Arith.h index 4a0030f1..4a0030f1 100644 --- a/sourcecodes/localscore/Arith.h +++ b/var_lib_genenet_bnw/localscore/Arith.h diff --git a/sourcecodes/localscore/BLAS.h b/var_lib_genenet_bnw/localscore/BLAS.h index 98c192e9..98c192e9 100644 --- a/sourcecodes/localscore/BLAS.h +++ b/var_lib_genenet_bnw/localscore/BLAS.h diff --git a/sourcecodes/localscore/Boolean.h b/var_lib_genenet_bnw/localscore/Boolean.h index ea855a29..ea855a29 100644 --- a/sourcecodes/localscore/Boolean.h +++ b/var_lib_genenet_bnw/localscore/Boolean.h diff --git a/sourcecodes/localscore/Callbacks.h b/var_lib_genenet_bnw/localscore/Callbacks.h index cb1d64ca..cb1d64ca 100644 --- a/sourcecodes/localscore/Callbacks.h +++ b/var_lib_genenet_bnw/localscore/Callbacks.h diff --git a/sourcecodes/localscore/Complex.h b/var_lib_genenet_bnw/localscore/Complex.h index 06417a71..06417a71 100644 --- a/sourcecodes/localscore/Complex.h +++ b/var_lib_genenet_bnw/localscore/Complex.h diff --git a/sourcecodes/localscore/Constants.h b/var_lib_genenet_bnw/localscore/Constants.h index 08e3d158..08e3d158 100644 --- a/sourcecodes/localscore/Constants.h +++ b/var_lib_genenet_bnw/localscore/Constants.h diff --git a/sourcecodes/localscore/Error.h b/var_lib_genenet_bnw/localscore/Error.h index 1a8905c6..1a8905c6 100644 --- a/sourcecodes/localscore/Error.h +++ b/var_lib_genenet_bnw/localscore/Error.h diff --git a/sourcecodes/localscore/GetX11Image.h b/var_lib_genenet_bnw/localscore/GetX11Image.h index a7181fa3..a7181fa3 100644 --- a/sourcecodes/localscore/GetX11Image.h +++ b/var_lib_genenet_bnw/localscore/GetX11Image.h diff --git a/sourcecodes/localscore/GraphicsDevice.h b/var_lib_genenet_bnw/localscore/GraphicsDevice.h index 10851b26..10851b26 100644 --- a/sourcecodes/localscore/GraphicsDevice.h +++ b/var_lib_genenet_bnw/localscore/GraphicsDevice.h diff --git a/sourcecodes/localscore/GraphicsEngine.h b/var_lib_genenet_bnw/localscore/GraphicsEngine.h index 8d4a8748..8d4a8748 100644 --- a/sourcecodes/localscore/GraphicsEngine.h +++ b/var_lib_genenet_bnw/localscore/GraphicsEngine.h diff --git a/sourcecodes/localscore/Lapack.h b/var_lib_genenet_bnw/localscore/Lapack.h index ad044ef7..ad044ef7 100644 --- a/sourcecodes/localscore/Lapack.h +++ b/var_lib_genenet_bnw/localscore/Lapack.h diff --git a/sourcecodes/localscore/Linpack.h b/var_lib_genenet_bnw/localscore/Linpack.h index 95cb753e..95cb753e 100644 --- a/sourcecodes/localscore/Linpack.h +++ b/var_lib_genenet_bnw/localscore/Linpack.h diff --git a/sourcecodes/localscore/MathThreads.h b/var_lib_genenet_bnw/localscore/MathThreads.h index 41234442..41234442 100644 --- a/sourcecodes/localscore/MathThreads.h +++ b/var_lib_genenet_bnw/localscore/MathThreads.h diff --git a/sourcecodes/localscore/Memory.h b/var_lib_genenet_bnw/localscore/Memory.h index 306c9835..306c9835 100644 --- a/sourcecodes/localscore/Memory.h +++ b/var_lib_genenet_bnw/localscore/Memory.h diff --git a/sourcecodes/localscore/Parse.h b/var_lib_genenet_bnw/localscore/Parse.h index a1d8cc87..a1d8cc87 100644 --- a/sourcecodes/localscore/Parse.h +++ b/var_lib_genenet_bnw/localscore/Parse.h diff --git a/sourcecodes/localscore/Print.h b/var_lib_genenet_bnw/localscore/Print.h index 7beeaf17..7beeaf17 100644 --- a/sourcecodes/localscore/Print.h +++ b/var_lib_genenet_bnw/localscore/Print.h diff --git a/sourcecodes/localscore/PrtUtil.h b/var_lib_genenet_bnw/localscore/PrtUtil.h index 1ef06d9a..1ef06d9a 100644 --- a/sourcecodes/localscore/PrtUtil.h +++ b/var_lib_genenet_bnw/localscore/PrtUtil.h diff --git a/sourcecodes/localscore/QuartzDevice.h b/var_lib_genenet_bnw/localscore/QuartzDevice.h index ceb513e2..ceb513e2 100644 --- a/sourcecodes/localscore/QuartzDevice.h +++ b/var_lib_genenet_bnw/localscore/QuartzDevice.h diff --git a/sourcecodes/localscore/R-ftp-http.h b/var_lib_genenet_bnw/localscore/R-ftp-http.h index 665bfb87..665bfb87 100644 --- a/sourcecodes/localscore/R-ftp-http.h +++ b/var_lib_genenet_bnw/localscore/R-ftp-http.h diff --git a/sourcecodes/localscore/R.h b/var_lib_genenet_bnw/localscore/R.h index 5c5696b3..5c5696b3 100644 --- a/sourcecodes/localscore/R.h +++ b/var_lib_genenet_bnw/localscore/R.h diff --git a/sourcecodes/localscore/RConverters.h b/var_lib_genenet_bnw/localscore/RConverters.h index 9ac0da33..9ac0da33 100644 --- a/sourcecodes/localscore/RConverters.h +++ b/var_lib_genenet_bnw/localscore/RConverters.h diff --git a/sourcecodes/localscore/RS.h b/var_lib_genenet_bnw/localscore/RS.h index e8ce2ef2..e8ce2ef2 100644 --- a/sourcecodes/localscore/RS.h +++ b/var_lib_genenet_bnw/localscore/RS.h diff --git a/sourcecodes/localscore/RStartup.h b/var_lib_genenet_bnw/localscore/RStartup.h index 5b89e7fe..5b89e7fe 100644 --- a/sourcecodes/localscore/RStartup.h +++ b/var_lib_genenet_bnw/localscore/RStartup.h diff --git a/sourcecodes/localscore/Random.h b/var_lib_genenet_bnw/localscore/Random.h index 1615778d..1615778d 100644 --- a/sourcecodes/localscore/Random.h +++ b/var_lib_genenet_bnw/localscore/Random.h diff --git a/sourcecodes/localscore/Rconfig.h b/var_lib_genenet_bnw/localscore/Rconfig.h index 2541c8a9..2541c8a9 100644 --- a/sourcecodes/localscore/Rconfig.h +++ b/var_lib_genenet_bnw/localscore/Rconfig.h diff --git a/sourcecodes/localscore/Rdynload.h b/var_lib_genenet_bnw/localscore/Rdynload.h index 982b571a..982b571a 100644 --- a/sourcecodes/localscore/Rdynload.h +++ b/var_lib_genenet_bnw/localscore/Rdynload.h diff --git a/sourcecodes/localscore/Riconv.h b/var_lib_genenet_bnw/localscore/Riconv.h index 13864ee6..13864ee6 100644 --- a/sourcecodes/localscore/Riconv.h +++ b/var_lib_genenet_bnw/localscore/Riconv.h diff --git a/sourcecodes/localscore/Rmath.h b/var_lib_genenet_bnw/localscore/Rmath.h index 1acd1dbb..1acd1dbb 100644 --- a/sourcecodes/localscore/Rmath.h +++ b/var_lib_genenet_bnw/localscore/Rmath.h diff --git a/sourcecodes/localscore/Utils.h b/var_lib_genenet_bnw/localscore/Utils.h index 61efaaaa..61efaaaa 100644 --- a/sourcecodes/localscore/Utils.h +++ b/var_lib_genenet_bnw/localscore/Utils.h diff --git a/sourcecodes/localscore/Visibility.h b/var_lib_genenet_bnw/localscore/Visibility.h index aa35e342..aa35e342 100644 --- a/sourcecodes/localscore/Visibility.h +++ b/var_lib_genenet_bnw/localscore/Visibility.h diff --git a/sourcecodes/localscore/eventloop.h b/var_lib_genenet_bnw/localscore/eventloop.h index 842cf9bb..842cf9bb 100644 --- a/sourcecodes/localscore/eventloop.h +++ b/var_lib_genenet_bnw/localscore/eventloop.h diff --git a/sourcecodes/localscore/libRmath.so b/var_lib_genenet_bnw/localscore/libRmath.so index 8c56eb4f..8c56eb4f 100644 --- a/sourcecodes/localscore/libRmath.so +++ b/var_lib_genenet_bnw/localscore/libRmath.so Binary files differdiff --git a/sourcecodes/localscore/libextern.h b/var_lib_genenet_bnw/localscore/libextern.h index 3f61fb1e..3f61fb1e 100644 --- a/sourcecodes/localscore/libextern.h +++ b/var_lib_genenet_bnw/localscore/libextern.h diff --git a/sourcecodes/localscore/matrix.h b/var_lib_genenet_bnw/localscore/matrix.h index b37772b4..b37772b4 100644 --- a/sourcecodes/localscore/matrix.h +++ b/var_lib_genenet_bnw/localscore/matrix.h diff --git a/sourcecodes/localscore/modified_matrix.c b/var_lib_genenet_bnw/localscore/modified_matrix.c index 8737b51b..8737b51b 100644 --- a/sourcecodes/localscore/modified_matrix.c +++ b/var_lib_genenet_bnw/localscore/modified_matrix.c diff --git a/sourcecodes/localscore/modified_postc.c b/var_lib_genenet_bnw/localscore/modified_postc.c index f223fdb8..f223fdb8 100644 --- a/sourcecodes/localscore/modified_postc.c +++ b/var_lib_genenet_bnw/localscore/modified_postc.c diff --git a/sourcecodes/localscore/network_score_old.c b/var_lib_genenet_bnw/localscore/network_score.c index b1ca59a9..56388236 100644 --- a/sourcecodes/localscore/network_score_old.c +++ b/var_lib_genenet_bnw/localscore/network_score.c @@ -191,7 +191,7 @@ main(int argc, char *argv[]) network.node[i].prob=(double *)malloc(sizeof(double)*2); //probability array of size 2 for continuous node network.node[i].prob[0]=0.0; //initialization network.node[i].prob[1]=0.0; - network.node[i].cdata=(double *)malloc(sizeof(double)*row); //data matrix for continuous node + network.node[i].cdata=(double *)malloc(sizeof(double)*(row+1)); //data matrix for continuous node } else { @@ -199,7 +199,7 @@ main(int argc, char *argv[]) network.node[i].post_alpha=(double *)calloc(network.node[i].type,sizeof(double)); //prepare total count of each discrete data lebel initialize with zero by calloc which is used in learnnode id++; network.node[i].prob=(double *)malloc(sizeof(double)*c); //probability array of size equals to number of levels for discrete node - network.node[i].ddata=(char **)malloc(sizeof(char *)*row); //data matrix for continuous node + network.node[i].ddata=(char **)malloc(sizeof(char *)*(row+1)); //data matrix for continuous node network.node[i].label=(char **)malloc(sizeof(char *)*c); //label array for(j=0;j<c;j++) network.node[i].prob[j]=1.0/c; @@ -336,9 +336,6 @@ main(int argc, char *argv[]) whitef=fopen (argv[3],"r"); //white list file name //read banlist -// fgets (line,2500,banf); //header - - strcpy(nf,""); strcpy(nt,""); @@ -371,6 +368,7 @@ while (fgets (line,2500,banf)!=NULL){ j++; network.node[i].blist.n=j; } + } } @@ -382,8 +380,6 @@ while (fgets (line,2500,banf)!=NULL){ //read whitelist -//fgets (line,2500,whitef); //header - strcpy(nf,""); strcpy(nt,""); @@ -401,7 +397,7 @@ for(i=0;i<network.num;i++) { if(strcmp(name[l],nf)==0) { - white_flag=0; + white_flag=0; for(k=0;k<network.node[i].wlist.n;k++) { if(network.node[i].wlist.list[k]==l) @@ -417,6 +413,7 @@ for(i=0;i<network.num;i++) j++; network.node[i].wlist.n=j; } + } } @@ -452,8 +449,8 @@ for(i=0;i<network.num;i++) for(j=0;j<m;j++) { - ban_flag=0; - + + bit= (j+1 >> i) & 1; if(bit!=1) //check if the child itself is present in parent list @@ -474,10 +471,11 @@ for(i=0;i<network.num;i++) } - if(network.node[i].type>1) //if discrete node checck if any continuous node is included in the parent list - { + if(network.node[i].type>1) //if discrete node checck if any continuous node is included in the parent list + { flag=0; - ban_flag=0; + ban_flag=0; + for(l=0;l<network.num;l++) { bit= (j+1 >> l) & 1; @@ -734,14 +732,12 @@ for(i=0;i<network.num;i++) min_score*=10; inputFiles= (FILE **) malloc(network.num * sizeof(FILE*)); -printf("%s\n",argv[5]); for(i=0;i<network.num;i++) { strcpy(line,argv[5]); - sprintf(line+10,"/%d",i); //sprintf(line+52,"%d",i); - - // strcat(line,".txt"); + k=strlen(line); + sprintf(line+k,"/%d",i); inputFiles[i] = fopen(line, "wb"); diff --git a/sourcecodes/localscore/postc0.c b/var_lib_genenet_bnw/localscore/postc0.c index 16e9ccec..16e9ccec 100644 --- a/sourcecodes/localscore/postc0.c +++ b/var_lib_genenet_bnw/localscore/postc0.c diff --git a/sourcecodes/localscore/rlocale.h b/var_lib_genenet_bnw/localscore/rlocale.h index ac08f341..ac08f341 100644 --- a/sourcecodes/localscore/rlocale.h +++ b/var_lib_genenet_bnw/localscore/rlocale.h diff --git a/sourcecodes/localscore/stats_package.h b/var_lib_genenet_bnw/localscore/stats_package.h index 3717c482..3717c482 100644 --- a/sourcecodes/localscore/stats_package.h +++ b/var_lib_genenet_bnw/localscore/stats_package.h diff --git a/sourcecodes/localscore/stats_stubs.h b/var_lib_genenet_bnw/localscore/stats_stubs.h index bc46821e..bc46821e 100644 --- a/sourcecodes/localscore/stats_stubs.h +++ b/var_lib_genenet_bnw/localscore/stats_stubs.h diff --git a/var_lib_genenet_bnw/print_structure/structure.c b/var_lib_genenet_bnw/print_structure/structure.c new file mode 100644 index 00000000..0b490324 --- /dev/null +++ b/var_lib_genenet_bnw/print_structure/structure.c @@ -0,0 +1,86 @@ +#include<stdio.h> +#include<stdlib.h> +#include<string.h> +#include<math.h> + +struct st{ +char *name; +double *data; +}*st_tab; + +main(int argc,char *argv[]) +{ +FILE *fp1,*fp2,*fp3; +char line[2500]; +int i,j,rd; +double d,row; +double thr=atof(argv[5]); + +fp1=fopen(argv[2],"r"); +fp2=fopen(argv[3],"w"); + +fp3=fopen(argv[4],"w"); + + +row=0.0; +while(fgets(line,2500,fp1)!=NULL) + row++; + +rd=(int)sqrt(row); + +printf("%d\n",rd); + +fclose(fp1); +fp1=fopen(argv[1],"r"); + +st_tab=(struct st *)malloc(sizeof(struct st)*rd); + +for(i=0;i<rd;i++) +{ + fscanf(fp1,"%s",line); + st_tab[i].name=(char *)malloc(sizeof(char)*(sizeof(line)+1)); + strcpy(st_tab[i].name,line); + st_tab[i].data=(double *)calloc(rd,sizeof(double)); +} + +fclose(fp1); +fp1=fopen(argv[2],"r"); + +for(i=0;i<rd;i++) +{ + for(j=0;j<rd;j++) + { + fscanf(fp1,"%s",line); + fscanf(fp1,"%s",line); + fscanf(fp1,"%s",line); + fscanf(fp1,"%lf",&d); + st_tab[i].data[j]=d; + + } +} + + + +for(i=0;i<rd;i++) +{ + fprintf(fp2,"%s\t",st_tab[i].name); + fprintf(fp3,"%s\t",st_tab[i].name); +} +fprintf(fp2,"\n"); +fprintf(fp3,"\n"); + +for(i=0;i<rd;i++) +{ + for(j=0;j<rd;j++) + { + fprintf(fp2,"%lf\t",st_tab[j].data[i]); + if(st_tab[j].data[i]>thr) + fprintf(fp3,"1\t"); + else + fprintf(fp3,"0\t"); + } + fprintf(fp2,"\n"); + fprintf(fp3,"\n"); +} + +} diff --git a/var_lib_genenet_bnw/run.sh b/var_lib_genenet_bnw/run.sh new file mode 100644 index 00000000..d7389dad --- /dev/null +++ b/var_lib_genenet_bnw/run.sh @@ -0,0 +1,58 @@ +#!/bin/bash +d=`dirname $0` +#Name of the data directory +data=$1 + +DIR="$d/$data/tmp" +DIR_1="$d/$data/tmp/" + +mkdir -p $DIR +#Arguments. User can modify these arguments. + +#Input data file name. +input="$d/$data/input.txt" + +#Input banlist file +ban="$d/$data/banlist.txt" + +#Input whitelist file +white="$d/$data/whitelist.txt" + +#Max parents. We set the number of maximum parents to 4 +maxparent=4 + +#k is the numbeer of structure considered in each step of k-best structure learning algorithm. We set the value of k=100 +k=100 + +#Model averaging threshold. We set the model averaging threshold to 0.5 +THR=0.5 + + +echo "Dataset with number of variables:" +head -1 $input|wc -w +echo "Dataset with number of samples:" +wc -l $input|cut -d' ' -f1 +echo "Parameters are: max parent = $maxparent, k= $k and model averaging threshold = $THR" + +start_time1=`date +%s` +#execute local score +./network_score $input $ban $white $maxparent $DIR +end_time=`date +%s` +echo "Local score execution time was `expr $end_time - $start_time1` s." + +start_time=`date +%s` +#execute k-best structure learning +sh $d/k-best/src/data2netk_poster.sh $input $DIR $k $maxparent + +end_time=`date +%s` +echo "k-best parent total execution time was `expr $end_time - $start_time` s." + +start_time=`date +%s` +#execute print structure +./structure $input $DIR/postProbEachEdge.txt $d/$data/model_averaging_probabilities.txt $d/$data/model_structure.txt $THR + +end_time1=`date +%s` +echo "Preparing structure output file from model averaging matrix. Execution time was `expr $end_time1 - $start_time` s." +echo "Total execution time was `expr $end_time1 - $start_time1` s." +rm -r $DIR_1* +rmdir $DIR |