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| author | ziejd2 | 2017-09-14 15:39:41 -0500 |
|---|---|---|
| committer | ziejd2 | 2017-09-14 15:57:50 -0500 |
| commit | c4f926438dcb8abe805e910399940f79ff643c4b (patch) | |
| tree | 3146d05ada5cf4b48d9bdd16c1baa498e8df7192 /sourcecodes/data | |
| parent | 57ebf49403b75dcf8482d174b59f7fd2a961d98e (diff) | |
| download | BNW-c4f926438dcb8abe805e910399940f79ff643c4b.tar.gz | |
Add files via upload
Diffstat (limited to 'sourcecodes/data')
235 files changed, 17123 insertions, 0 deletions
diff --git a/sourcecodes/data/Backupfiles/evidencemodified b/sourcecodes/data/Backupfiles/evidencemodified new file mode 100644 index 00000000..9b3f7563 --- /dev/null +++ b/sourcecodes/data/Backupfiles/evidencemodified Binary files differdiff --git a/sourcecodes/data/Backupfiles/initialstructure b/sourcecodes/data/Backupfiles/initialstructure new file mode 100644 index 00000000..9ecf1bc7 --- /dev/null +++ b/sourcecodes/data/Backupfiles/initialstructure Binary files differdiff --git a/sourcecodes/data/Backupfiles/newintervention b/sourcecodes/data/Backupfiles/newintervention new file mode 100644 index 00000000..d818a943 --- /dev/null +++ b/sourcecodes/data/Backupfiles/newintervention Binary files differdiff --git a/sourcecodes/data/Backupfiles/temp_evidence_file b/sourcecodes/data/Backupfiles/temp_evidence_file new file mode 100644 index 00000000..b687ceaf --- /dev/null +++ b/sourcecodes/data/Backupfiles/temp_evidence_file @@ -0,0 +1,36 @@ +#!/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 \ No newline at end of file diff --git a/sourcecodes/data/Backupfiles/temp_intervention_file b/sourcecodes/data/Backupfiles/temp_intervention_file new file mode 100644 index 00000000..cdf5ce0f --- /dev/null +++ b/sourcecodes/data/Backupfiles/temp_intervention_file @@ -0,0 +1,36 @@ +#!/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}"/newintervention \ No newline at end of file diff --git a/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure b/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure new file mode 100644 index 00000000..5d1c323d --- /dev/null +++ b/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure @@ -0,0 +1,36 @@ +#!/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 \ No newline at end of file diff --git a/sourcecodes/data/evidencemodified b/sourcecodes/data/evidencemodified new file mode 100644 index 00000000..9b3f7563 --- /dev/null +++ b/sourcecodes/data/evidencemodified Binary files differdiff --git a/sourcecodes/data/example1/Bqxban.txt b/sourcecodes/data/example1/Bqxban.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example1/Bqxban.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example1/Bqxcontinuous_input.txt b/sourcecodes/data/example1/Bqxcontinuous_input.txt new file mode 100644 index 00000000..5e296c45 --- /dev/null +++ b/sourcecodes/data/example1/Bqxcontinuous_input.txt @@ -0,0 +1,203 @@ +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 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b/sourcecodes/data/example1/Bqxgraphviz.txt @@ -0,0 +1,12 @@ +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 new file mode 100644 index 00000000..d00491fd --- /dev/null +++ b/sourcecodes/data/example1/Bqxk.txt @@ -0,0 +1 @@ +1 diff --git a/sourcecodes/data/example1/Bqxmap.txt b/sourcecodes/data/example1/Bqxmap.txt new file mode 100644 index 00000000..032b8928 --- /dev/null +++ b/sourcecodes/data/example1/Bqxmap.txt @@ -0,0 +1,8 @@ +Geno1 1 0.473175 1.335000 +Geno2 2 0.496318 1.570000 +Trait1 1 0.668009 -0.023903 +Trait2 1 0.796873 0.038552 +Trait3 2 1.036694 0.068708 +Trait4 1 0.984008 -0.010125 +Trait5 1 0.316471 0.008911 +Trait6 1 0.904542 -0.114267 diff --git a/sourcecodes/data/example1/Bqxmapdata.txt b/sourcecodes/data/example1/Bqxmapdata.txt new file mode 100644 index 00000000..42b2fd9c --- /dev/null +++ b/sourcecodes/data/example1/Bqxmapdata.txt @@ -0,0 +1 @@ +Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 diff --git a/sourcecodes/data/example1/Bqxname.txt b/sourcecodes/data/example1/Bqxname.txt new file mode 100644 index 00000000..8f42b468 --- /dev/null +++ b/sourcecodes/data/example1/Bqxname.txt @@ -0,0 +1 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 diff --git a/sourcecodes/data/example1/Bqxnet_figure.txt b/sourcecodes/data/example1/Bqxnet_figure.txt new file mode 100644 index 00000000..11113895 --- /dev/null +++ b/sourcecodes/data/example1/Bqxnet_figure.txt @@ -0,0 +1,652 @@ +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 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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 new file mode 100644 index 00000000..32457058 --- /dev/null +++ b/sourcecodes/data/example1/Bqxnlevels.txt @@ -0,0 +1,4 @@ +Geno1 1 2 +Geno2 1 2 + + diff --git a/sourcecodes/data/example1/Bqxnnode.txt b/sourcecodes/data/example1/Bqxnnode.txt new file mode 100644 index 00000000..45a4fb75 --- /dev/null +++ b/sourcecodes/data/example1/Bqxnnode.txt @@ -0,0 +1 @@ +8 diff --git a/sourcecodes/data/example1/Bqxnrows.txt b/sourcecodes/data/example1/Bqxnrows.txt new file mode 100644 index 00000000..3bc92d44 --- /dev/null +++ b/sourcecodes/data/example1/Bqxnrows.txt @@ -0,0 +1 @@ +201 diff --git a/sourcecodes/data/example1/Bqxparent.txt b/sourcecodes/data/example1/Bqxparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example1/Bqxparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example1/Bqxrun_initialstructure.sh b/sourcecodes/data/example1/Bqxrun_initialstructure.sh new file mode 100644 index 00000000..a8a8ebe0 --- /dev/null +++ b/sourcecodes/data/example1/Bqxrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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/Bqxstructure_input.txt b/sourcecodes/data/example1/Bqxstructure_input.txt new file mode 100644 index 00000000..09955440 --- /dev/null +++ b/sourcecodes/data/example1/Bqxstructure_input.txt @@ -0,0 +1,9 @@ +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 1 0 0 0 diff --git a/sourcecodes/data/example1/Bqxstructure_input_temp.txt b/sourcecodes/data/example1/Bqxstructure_input_temp.txt new file mode 100644 index 00000000..fc815603 --- /dev/null +++ b/sourcecodes/data/example1/Bqxstructure_input_temp.txt @@ -0,0 +1,9 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 diff --git a/sourcecodes/data/example1/Bqxstructure_old.txt b/sourcecodes/data/example1/Bqxstructure_old.txt new file mode 100644 index 00000000..7749d17e --- /dev/null +++ b/sourcecodes/data/example1/Bqxstructure_old.txt @@ -0,0 +1,7 @@ +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 new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/example1/Bqxthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example1/Bqxtier.txt b/sourcecodes/data/example1/Bqxtier.txt new file mode 100644 index 00000000..bc94239b --- /dev/null +++ b/sourcecodes/data/example1/Bqxtier.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..285a68af --- /dev/null +++ b/sourcecodes/data/example1/Bqxtype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example1/Bqxwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example1/standardized_data.txt b/sourcecodes/data/example1/standardized_data.txt new file mode 100644 index 00000000..743e8b02 --- /dev/null +++ b/sourcecodes/data/example1/standardized_data.txt @@ -0,0 +1,201 @@ +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 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b/sourcecodes/data/example2/hQGgraphviz.txt @@ -0,0 +1,11 @@ +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 new file mode 100644 index 00000000..29d6383b --- /dev/null +++ b/sourcecodes/data/example2/hQGk.txt @@ -0,0 +1 @@ +100 diff --git a/sourcecodes/data/example2/hQGmap.txt b/sourcecodes/data/example2/hQGmap.txt new file mode 100644 index 00000000..032b8928 --- /dev/null +++ b/sourcecodes/data/example2/hQGmap.txt @@ -0,0 +1,8 @@ +Geno1 1 0.473175 1.335000 +Geno2 2 0.496318 1.570000 +Trait1 1 0.668009 -0.023903 +Trait2 1 0.796873 0.038552 +Trait3 2 1.036694 0.068708 +Trait4 1 0.984008 -0.010125 +Trait5 1 0.316471 0.008911 +Trait6 1 0.904542 -0.114267 diff --git a/sourcecodes/data/example2/hQGmapdata.txt b/sourcecodes/data/example2/hQGmapdata.txt new file mode 100644 index 00000000..42b2fd9c --- /dev/null +++ b/sourcecodes/data/example2/hQGmapdata.txt @@ -0,0 +1 @@ +Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 diff --git a/sourcecodes/data/example2/hQGname.txt b/sourcecodes/data/example2/hQGname.txt new file mode 100644 index 00000000..8f42b468 --- /dev/null +++ b/sourcecodes/data/example2/hQGname.txt @@ -0,0 +1 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 diff --git a/sourcecodes/data/example2/hQGnet_figure.txt b/sourcecodes/data/example2/hQGnet_figure.txt new file mode 100644 index 00000000..893f9f14 --- /dev/null +++ b/sourcecodes/data/example2/hQGnet_figure.txt @@ -0,0 +1,652 @@ +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 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a/sourcecodes/data/example2/hQGnrows.txt b/sourcecodes/data/example2/hQGnrows.txt new file mode 100644 index 00000000..3bc92d44 --- /dev/null +++ b/sourcecodes/data/example2/hQGnrows.txt @@ -0,0 +1 @@ +201 diff --git a/sourcecodes/data/example2/hQGparent.txt b/sourcecodes/data/example2/hQGparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example2/hQGparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example2/hQGrun_initialstructure.sh b/sourcecodes/data/example2/hQGrun_initialstructure.sh new file mode 100644 index 00000000..7d4cbfea --- /dev/null +++ b/sourcecodes/data/example2/hQGrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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/hQGstructure_input.txt b/sourcecodes/data/example2/hQGstructure_input.txt new file mode 100644 index 00000000..410c0fa4 --- /dev/null +++ b/sourcecodes/data/example2/hQGstructure_input.txt @@ -0,0 +1,9 @@ +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/hQGstructure_input_temp.txt b/sourcecodes/data/example2/hQGstructure_input_temp.txt new file mode 100644 index 00000000..63380a62 --- /dev/null +++ b/sourcecodes/data/example2/hQGstructure_input_temp.txt @@ -0,0 +1,9 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +0.000000 0.000000 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 0.000000 0.108604 0.000000 1.000000 0.010570 0.000000 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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 new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/example2/hQGthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example2/hQGtier.txt b/sourcecodes/data/example2/hQGtier.txt new file mode 100644 index 00000000..bc94239b --- /dev/null +++ b/sourcecodes/data/example2/hQGtier.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..285a68af --- /dev/null +++ b/sourcecodes/data/example2/hQGtype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example2/hQGwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example2/standardized_data.txt b/sourcecodes/data/example2/standardized_data.txt new file mode 100644 index 00000000..743e8b02 --- /dev/null +++ b/sourcecodes/data/example2/standardized_data.txt @@ -0,0 +1,201 @@ +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 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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/example_chl/bWRcontinuous_input.txt b/sourcecodes/data/example_chl/bWRcontinuous_input.txt new file mode 100644 index 00000000..cf674ffd --- /dev/null +++ b/sourcecodes/data/example_chl/bWRcontinuous_input.txt @@ -0,0 +1,44 @@ +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 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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/bWRgraphviz.txt b/sourcecodes/data/example_chl/bWRgraphviz.txt new file mode 100644 index 00000000..2cd4e8cd --- /dev/null +++ b/sourcecodes/data/example_chl/bWRgraphviz.txt @@ -0,0 +1,11 @@ +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/bWRmap.txt b/sourcecodes/data/example_chl/bWRmap.txt new file mode 100644 index 00000000..b872d2f0 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRmap.txt @@ -0,0 +1,5 @@ +Ctrq3 2 0.487652 1.365854 +MAS 1 0.355012 0.479560 +Neutrophil 1 10.929756 15.048780 +Load 1 0.825354 4.077143 +Weight 1 0.088036 0.877077 diff --git a/sourcecodes/data/example_chl/bWRmapdata.txt b/sourcecodes/data/example_chl/bWRmapdata.txt new file mode 100644 index 00000000..ce5416ce --- /dev/null +++ b/sourcecodes/data/example_chl/bWRmapdata.txt @@ -0,0 +1 @@ +Ctrq3 MAS Load Neutrophil Weight diff --git a/sourcecodes/data/example_chl/bWRname.txt b/sourcecodes/data/example_chl/bWRname.txt new file mode 100644 index 00000000..48018335 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRname.txt @@ -0,0 +1 @@ +Ctrq3 MAS Neutrophil Load Weight diff --git a/sourcecodes/data/example_chl/bWRnet_figure.txt b/sourcecodes/data/example_chl/bWRnet_figure.txt new file mode 100644 index 00000000..1798da4f --- /dev/null +++ b/sourcecodes/data/example_chl/bWRnet_figure.txt @@ -0,0 +1,433 @@ +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 +-2.2595 0.0292 +-2.2129 0.0326 +-2.1662 0.0362 +-2.1196 0.0401 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+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/bWRnlevels.txt b/sourcecodes/data/example_chl/bWRnlevels.txt new file mode 100644 index 00000000..9f618060 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRnlevels.txt @@ -0,0 +1,2 @@ +Ctrq3 1 2 + diff --git a/sourcecodes/data/example_chl/bWRnnode.txt b/sourcecodes/data/example_chl/bWRnnode.txt new file mode 100644 index 00000000..7ed6ff82 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRnnode.txt @@ -0,0 +1 @@ +5 diff --git a/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh b/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh new file mode 100644 index 00000000..763a268b --- /dev/null +++ b/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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/bWRrun_initialstructure.sh b/sourcecodes/data/example_chl/bWRrun_initialstructure.sh new file mode 100644 index 00000000..3725f758 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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/bWRstructure_input.txt b/sourcecodes/data/example_chl/bWRstructure_input.txt new file mode 100644 index 00000000..efa98e06 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRstructure_input.txt @@ -0,0 +1,7 @@ +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/bWRstructure_old.txt b/sourcecodes/data/example_chl/bWRstructure_old.txt new file mode 100644 index 00000000..a6aed858 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRstructure_old.txt @@ -0,0 +1,5 @@ +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 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a/sourcecodes/data/example_chl/bWRtype.txt b/sourcecodes/data/example_chl/bWRtype.txt new file mode 100644 index 00000000..03b402ee --- /dev/null +++ b/sourcecodes/data/example_chl/bWRtype.txt @@ -0,0 +1,2 @@ +Ctrq3 MAS Neutrophil Load Weight +2 1 1 1 1 diff --git a/sourcecodes/data/example_chl/bWRvar.txt b/sourcecodes/data/example_chl/bWRvar.txt new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_chl/bWRvar.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_chl/bWRvardata.txt b/sourcecodes/data/example_chl/bWRvardata.txt new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_chl/bWRvardata.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_chl/bWRvarname.txt b/sourcecodes/data/example_chl/bWRvarname.txt new file mode 100644 index 00000000..6ef2df09 --- /dev/null +++ b/sourcecodes/data/example_chl/bWRvarname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..fdd12dda --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLban.txt @@ -0,0 +1,51 @@ +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 new file mode 100644 index 00000000..ca8ea1e5 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt @@ -0,0 +1,76 @@ +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 new file mode 100644 index 00000000..824e26d5 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt @@ -0,0 +1,32 @@ +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 new file mode 100644 index 00000000..29d6383b --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLk.txt @@ -0,0 +1 @@ +100 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmap.txt b/sourcecodes/data/example_chr2_spleen/cuLmap.txt new file mode 100644 index 00000000..325f9a8d --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLmap.txt @@ -0,0 +1,14 @@ +rs3664317 2 0.501140 1.452055 +Oas1a 1 0.347301 8.281466 +Parp9 1 0.216211 9.804164 +Dhx58 1 0.302026 8.891247 +Cd1d1 1 0.268738 9.643644 +Irf7 1 0.548579 10.009315 +Oas3 1 0.548788 8.957397 +Pml 1 0.190985 11.075425 +Mx1 1 0.336795 7.483137 +Ifit1 1 0.569192 8.828521 +Trim25 1 0.176657 10.255192 +Oas1g 1 0.458134 8.632151 +Pglyrp3 1 0.123345 6.070877 +Ifih1 1 0.387383 9.298137 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt b/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt new file mode 100644 index 00000000..64d3fc62 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..1cc6fe19 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..79f052a0 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt @@ -0,0 +1,1387 @@ +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 +-3.1997 0.0023 +-3.1378 0.0028 +-3.0758 0.0034 +-3.0138 0.0041 +-2.9518 0.0050 +-2.8899 0.0060 +-2.8279 0.0071 +-2.7659 0.0085 +-2.7039 0.0101 +-2.6420 0.0119 +-2.5800 0.0140 +-2.5180 0.0164 +-2.4560 0.0192 +-2.3941 0.0223 +-2.3321 0.0259 +-2.2701 0.0299 +-2.2081 0.0343 +-2.1462 0.0393 +-2.0842 0.0449 +-2.0222 0.0510 +-1.9602 0.0578 +-1.8983 0.0652 +-1.8363 0.0733 +-1.7743 0.0820 +-1.7124 0.0914 +-1.6504 0.1015 +-1.5884 0.1124 +-1.5264 0.1238 +-1.4645 0.1359 +-1.4025 0.1487 +-1.3405 0.1620 +-1.2785 0.1758 +-1.2166 0.1900 +-1.1546 0.2046 +-1.0926 0.2195 +-1.0306 0.2345 +-0.9687 0.2496 +-0.9067 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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 new file mode 100644 index 00000000..605579c3 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt @@ -0,0 +1,2 @@ +rs3664317 1 2 + diff --git a/sourcecodes/data/example_chr2_spleen/cuLnnode.txt b/sourcecodes/data/example_chr2_spleen/cuLnnode.txt new file mode 100644 index 00000000..8351c193 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnnode.txt @@ -0,0 +1 @@ +14 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnrows.txt b/sourcecodes/data/example_chr2_spleen/cuLnrows.txt new file mode 100644 index 00000000..fff0a247 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnrows.txt @@ -0,0 +1 @@ +74 diff --git a/sourcecodes/data/example_chr2_spleen/cuLparent.txt b/sourcecodes/data/example_chr2_spleen/cuLparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh new file mode 100644 index 00000000..5a228612 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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/cuLrun_initialstructure.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh new file mode 100644 index 00000000..1d0835a4 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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_chr2_spleen/cuLstructure_input.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_input.txt new file mode 100644 index 00000000..48837c69 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_input.txt @@ -0,0 +1,15 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +0 0 0 1 1 0 0 0 0 1 0 1 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 1 0 0 1 1 1 1 0 0 +0 0 0 0 0 0 1 0 0 0 1 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 1 0 +0 0 0 0 0 0 1 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 1 0 0 1 0 0 0 0 0 +0 0 1 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 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 1 1 0 1 0 0 1 1 0 0 0 diff --git a/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt new file mode 100644 index 00000000..f3589770 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt @@ -0,0 +1,15 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +0.000000 0.808614 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.250558 1.000000 0.000000 0.960922 0.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.596398 0.000000 0.786929 0.055837 0.000000 0.000000 0.590731 0.000000 0.000000 +0.000000 0.942409 0.000000 0.000000 0.000000 0.018121 0.000000 0.000000 0.000000 0.409269 0.000000 0.401871 0.000000 0.000000 +0.000000 0.590731 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.018396 0.000000 +0.000000 0.038935 0.000000 0.500000 0.000000 0.036744 1.000000 0.000000 0.000000 0.000000 1.000000 0.039078 1.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.786929 0.164752 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.056298 0.000000 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a/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt new file mode 100644 index 00000000..f0815c7a --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt @@ -0,0 +1,14 @@ +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 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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 new file mode 100644 index 00000000..b63ba696 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLthr.txt @@ -0,0 +1 @@ +0.9 diff --git a/sourcecodes/data/example_chr2_spleen/cuLtier.txt b/sourcecodes/data/example_chr2_spleen/cuLtier.txt new file mode 100644 index 00000000..e71cfdda --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLtier.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..1b707710 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLtype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt b/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt new file mode 100644 index 00000000..b31e4c3c --- /dev/null +++ b/sourcecodes/data/example_sci/LluOyOgrviz_name_file.txt @@ -0,0 +1,6 @@ +Genotype +Gene3 +Gene2 +Phenotype +Gene1 + diff --git a/sourcecodes/data/example_sci/Lluban.txt b/sourcecodes/data/example_sci/Lluban.txt new file mode 100644 index 00000000..38108f00 --- /dev/null +++ b/sourcecodes/data/example_sci/Lluban.txt @@ -0,0 +1,15 @@ +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 new file mode 100644 index 00000000..79295d7e --- /dev/null +++ b/sourcecodes/data/example_sci/Llucontinuous_input.txt @@ -0,0 +1,503 @@ +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 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/dev/null +++ b/sourcecodes/data/example_sci/Lluk.txt @@ -0,0 +1 @@ +1000 diff --git a/sourcecodes/data/example_sci/Llumap.txt b/sourcecodes/data/example_sci/Llumap.txt new file mode 100644 index 00000000..958281d5 --- /dev/null +++ b/sourcecodes/data/example_sci/Llumap.txt @@ -0,0 +1,5 @@ +Genotype 2 0.500305 1.514000 +Gene3 1 1.027261 -0.015284 +Gene2 1 1.160583 0.138097 +Phenotype 1 1.554104 0.069005 +Gene1 1 1.515414 0.174451 diff --git a/sourcecodes/data/example_sci/Llumapdata.txt b/sourcecodes/data/example_sci/Llumapdata.txt new file mode 100644 index 00000000..d684ea06 --- /dev/null +++ b/sourcecodes/data/example_sci/Llumapdata.txt @@ -0,0 +1 @@ +Genotype Gene1 Gene2 Gene3 Phenotype diff --git a/sourcecodes/data/example_sci/Lluname.txt b/sourcecodes/data/example_sci/Lluname.txt new file mode 100644 index 00000000..f3a1f5bf --- /dev/null +++ b/sourcecodes/data/example_sci/Lluname.txt @@ -0,0 +1 @@ +Genotype Gene3 Gene2 Phenotype Gene1 diff --git a/sourcecodes/data/example_sci/Llunet_figure.txt b/sourcecodes/data/example_sci/Llunet_figure.txt new file mode 100644 index 00000000..bdc07cbd --- /dev/null +++ b/sourcecodes/data/example_sci/Llunet_figure.txt @@ -0,0 +1,433 @@ +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 +-3.5013 0.0009 +-3.4313 0.0012 +-3.3613 0.0015 +-3.2912 0.0019 +-3.2212 0.0024 +-3.1512 0.0030 +-3.0811 0.0037 +-3.0111 0.0046 +-2.9411 0.0056 +-2.8710 0.0069 +-2.8010 0.0083 +-2.7310 0.0101 +-2.6609 0.0121 +-2.5909 0.0145 +-2.5209 0.0174 +-2.4508 0.0206 +-2.3808 0.0243 +-2.3108 0.0286 +-2.2407 0.0335 +-2.1707 0.0389 +-2.1007 0.0451 +-2.0306 0.0520 +-1.9606 0.0597 +-1.8906 0.0682 +-1.8205 0.0775 +-1.7505 0.0876 +-1.6805 0.0986 +-1.6104 0.1105 +-1.5404 0.1231 +-1.4704 0.1366 +-1.4003 0.1508 +-1.3303 0.1657 +-1.2603 0.1811 +-1.1902 0.1971 +-1.1202 0.2134 +-1.0502 0.2300 +-0.9801 0.2467 +-0.9101 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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 new file mode 100644 index 00000000..714e56bd --- /dev/null +++ b/sourcecodes/data/example_sci/Llunlevels.txt @@ -0,0 +1,2 @@ +Genotype 1 2 + diff --git a/sourcecodes/data/example_sci/Llunnode.txt b/sourcecodes/data/example_sci/Llunnode.txt new file mode 100644 index 00000000..7ed6ff82 --- /dev/null +++ b/sourcecodes/data/example_sci/Llunnode.txt @@ -0,0 +1 @@ +5 diff --git a/sourcecodes/data/example_sci/Llunrows.txt b/sourcecodes/data/example_sci/Llunrows.txt new file mode 100644 index 00000000..c15fb720 --- /dev/null +++ b/sourcecodes/data/example_sci/Llunrows.txt @@ -0,0 +1 @@ +501 diff --git a/sourcecodes/data/example_sci/Lluparent.txt b/sourcecodes/data/example_sci/Lluparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example_sci/Lluparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example_sci/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci/Llurun_evidencemodified.sh new file mode 100644 index 00000000..ee0dde13 --- /dev/null +++ b/sourcecodes/data/example_sci/Llurun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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/Llurun_initialstructure.sh b/sourcecodes/data/example_sci/Llurun_initialstructure.sh new file mode 100644 index 00000000..adde14dd --- /dev/null +++ b/sourcecodes/data/example_sci/Llurun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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_sci/Llustructure_input.txt b/sourcecodes/data/example_sci/Llustructure_input.txt new file mode 100644 index 00000000..bcf72d97 --- /dev/null +++ b/sourcecodes/data/example_sci/Llustructure_input.txt @@ -0,0 +1,6 @@ +Genotype Gene3 Gene2 Phenotype Gene1 +0 1 0 0 1 +0 0 0 1 0 +0 1 0 1 0 +0 0 0 0 0 +0 0 1 0 0 diff --git a/sourcecodes/data/example_sci/Llustructure_input_temp.txt b/sourcecodes/data/example_sci/Llustructure_input_temp.txt new file mode 100644 index 00000000..95aa7a5d --- /dev/null +++ b/sourcecodes/data/example_sci/Llustructure_input_temp.txt @@ -0,0 +1,6 @@ +Genotype Gene3 Gene2 Phenotype Gene1 +0.000000 0.999929 0.183248 0.000431 1.000000 +0.000000 0.000000 0.000000 1.000000 0.000000 +0.000000 0.935752 0.000000 1.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.053385 0.881001 0.156255 0.000000 diff --git a/sourcecodes/data/example_sci/Llustructure_old.txt b/sourcecodes/data/example_sci/Llustructure_old.txt new file mode 100644 index 00000000..5b464577 --- /dev/null +++ b/sourcecodes/data/example_sci/Llustructure_old.txt @@ -0,0 +1,5 @@ +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 new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/example_sci/Lluthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example_sci/Llutier.txt b/sourcecodes/data/example_sci/Llutier.txt new file mode 100644 index 00000000..da7084fb --- /dev/null +++ b/sourcecodes/data/example_sci/Llutier.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..9ea66ce4 --- /dev/null +++ b/sourcecodes/data/example_sci/Llutype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_sci/Lluvar.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluvardata.txt b/sourcecodes/data/example_sci/Lluvardata.txt new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_sci/Lluvardata.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluvarname.txt b/sourcecodes/data/example_sci/Lluvarname.txt new file mode 100644 index 00000000..3fe283bd --- /dev/null +++ b/sourcecodes/data/example_sci/Lluvarname.txt @@ -0,0 +1 @@ +Genotype \ No newline at end of file diff --git a/sourcecodes/data/example_sci/Lluwhite.txt b/sourcecodes/data/example_sci/Lluwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example_sci/Lluwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example_sci_bk/Lluban.txt b/sourcecodes/data/example_sci_bk/Lluban.txt new file mode 100644 index 00000000..38108f00 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluban.txt @@ -0,0 +1,15 @@ +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_bk/Llucontinuous_input.txt b/sourcecodes/data/example_sci_bk/Llucontinuous_input.txt new file mode 100644 index 00000000..79295d7e --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llucontinuous_input.txt @@ -0,0 +1,503 @@ +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 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a/sourcecodes/data/example_sci_bk/Lluk.txt b/sourcecodes/data/example_sci_bk/Lluk.txt new file mode 100644 index 00000000..83b33d23 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluk.txt @@ -0,0 +1 @@ +1000 diff --git a/sourcecodes/data/example_sci_bk/Llumap.txt b/sourcecodes/data/example_sci_bk/Llumap.txt new file mode 100644 index 00000000..958281d5 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llumap.txt @@ -0,0 +1,5 @@ +Genotype 2 0.500305 1.514000 +Gene3 1 1.027261 -0.015284 +Gene2 1 1.160583 0.138097 +Phenotype 1 1.554104 0.069005 +Gene1 1 1.515414 0.174451 diff --git a/sourcecodes/data/example_sci_bk/Llumapdata.txt b/sourcecodes/data/example_sci_bk/Llumapdata.txt new file mode 100644 index 00000000..d684ea06 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llumapdata.txt @@ -0,0 +1 @@ +Genotype Gene1 Gene2 Gene3 Phenotype diff --git a/sourcecodes/data/example_sci_bk/Lluname.txt b/sourcecodes/data/example_sci_bk/Lluname.txt new file mode 100644 index 00000000..f3a1f5bf --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluname.txt @@ -0,0 +1 @@ +Genotype Gene3 Gene2 Phenotype Gene1 diff --git a/sourcecodes/data/example_sci_bk/Llunet_figure.txt b/sourcecodes/data/example_sci_bk/Llunet_figure.txt new file mode 100644 index 00000000..bdc07cbd --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llunet_figure.txt @@ -0,0 +1,433 @@ +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 +-3.5013 0.0009 +-3.4313 0.0012 +-3.3613 0.0015 +-3.2912 0.0019 +-3.2212 0.0024 +-3.1512 0.0030 +-3.0811 0.0037 +-3.0111 0.0046 +-2.9411 0.0056 +-2.8710 0.0069 +-2.8010 0.0083 +-2.7310 0.0101 +-2.6609 0.0121 +-2.5909 0.0145 +-2.5209 0.0174 +-2.4508 0.0206 +-2.3808 0.0243 +-2.3108 0.0286 +-2.2407 0.0335 +-2.1707 0.0389 +-2.1007 0.0451 +-2.0306 0.0520 +-1.9606 0.0597 +-1.8906 0.0682 +-1.8205 0.0775 +-1.7505 0.0876 +-1.6805 0.0986 +-1.6104 0.1105 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b/sourcecodes/data/example_sci_bk/Llunet_figure_new.txt new file mode 100644 index 00000000..7e6f0d97 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llunet_figure_new.txt @@ -0,0 +1,433 @@ +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 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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_bk/Llunlevels.txt b/sourcecodes/data/example_sci_bk/Llunlevels.txt new file mode 100644 index 00000000..714e56bd --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llunlevels.txt @@ -0,0 +1,2 @@ +Genotype 1 2 + diff --git a/sourcecodes/data/example_sci_bk/Llunnode.txt b/sourcecodes/data/example_sci_bk/Llunnode.txt new file mode 100644 index 00000000..7ed6ff82 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llunnode.txt @@ -0,0 +1 @@ +5 diff --git a/sourcecodes/data/example_sci_bk/Llunrows.txt b/sourcecodes/data/example_sci_bk/Llunrows.txt new file mode 100644 index 00000000..c15fb720 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llunrows.txt @@ -0,0 +1 @@ +501 diff --git a/sourcecodes/data/example_sci_bk/Lluparent.txt b/sourcecodes/data/example_sci_bk/Lluparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh new file mode 100644 index 00000000..ee0dde13 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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_bk/Llurun_initialstructure.sh b/sourcecodes/data/example_sci_bk/Llurun_initialstructure.sh new file mode 100644 index 00000000..adde14dd --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llurun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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_sci_bk/Llustructure_input.txt b/sourcecodes/data/example_sci_bk/Llustructure_input.txt new file mode 100644 index 00000000..bcf72d97 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llustructure_input.txt @@ -0,0 +1,6 @@ +Genotype Gene3 Gene2 Phenotype Gene1 +0 1 0 0 1 +0 0 0 1 0 +0 1 0 1 0 +0 0 0 0 0 +0 0 1 0 0 diff --git a/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt b/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt new file mode 100644 index 00000000..95aa7a5d --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt @@ -0,0 +1,6 @@ +Genotype Gene3 Gene2 Phenotype Gene1 +0.000000 0.999929 0.183248 0.000431 1.000000 +0.000000 0.000000 0.000000 1.000000 0.000000 +0.000000 0.935752 0.000000 1.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.053385 0.881001 0.156255 0.000000 diff --git a/sourcecodes/data/example_sci_bk/Llustructure_old.txt b/sourcecodes/data/example_sci_bk/Llustructure_old.txt new file mode 100644 index 00000000..5b464577 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llustructure_old.txt @@ -0,0 +1,5 @@ +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_bk/Lluthr.txt b/sourcecodes/data/example_sci_bk/Lluthr.txt new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example_sci_bk/Llutier.txt b/sourcecodes/data/example_sci_bk/Llutier.txt new file mode 100644 index 00000000..da7084fb --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llutier.txt @@ -0,0 +1 @@ +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_bk/Llutype.txt b/sourcecodes/data/example_sci_bk/Llutype.txt new file mode 100644 index 00000000..9ea66ce4 --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Llutype.txt @@ -0,0 +1,2 @@ +Genotype Gene3 Gene2 Phenotype Gene1 +2 1 1 1 1 diff --git a/sourcecodes/data/example_sci_bk/Lluvar.txt b/sourcecodes/data/example_sci_bk/Lluvar.txt new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluvar.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluvardata.txt b/sourcecodes/data/example_sci_bk/Lluvardata.txt new file mode 100644 index 00000000..56a6051c --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluvardata.txt @@ -0,0 +1 @@ +1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluvarname.txt b/sourcecodes/data/example_sci_bk/Lluvarname.txt new file mode 100644 index 00000000..3fe283bd --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluvarname.txt @@ -0,0 +1 @@ +Genotype \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluwhite.txt b/sourcecodes/data/example_sci_bk/Lluwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example_sci_bk/Lluwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example_time_series/TEbban.txt b/sourcecodes/data/example_time_series/TEbban.txt new file mode 100644 index 00000000..7b0aa551 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbban.txt @@ -0,0 +1,73 @@ +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 new file mode 100644 index 00000000..34b3b957 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbcontinuous_input.txt @@ -0,0 +1,503 @@ +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 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100644 index 00000000..d8bbfe4b --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbgraphviz.txt @@ -0,0 +1,11 @@ +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 new file mode 100644 index 00000000..29d6383b --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbk.txt @@ -0,0 +1 @@ +100 diff --git a/sourcecodes/data/example_time_series/TEbmap.txt b/sourcecodes/data/example_time_series/TEbmap.txt new file mode 100644 index 00000000..a9e0ef24 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbmap.txt @@ -0,0 +1,10 @@ +Genotype 1 0.499053 1.462000 +TraitA_T1 1 1.306059 0.037189 +TraitA_T2 1 1.304164 -0.061147 +TraitA_T3 1 1.174305 -0.083449 +TraitB_T1 2 0.929161 -0.056347 +TraitB_T2 1 1.021691 -0.045299 +TraitB_T3 1 0.940946 0.012204 +TraitC_T1 1 0.907725 -0.001607 +TraitC_T2 1 0.923711 0.091657 +TraitC_T3 1 1.015189 0.017718 diff --git a/sourcecodes/data/example_time_series/TEbmapdata.txt b/sourcecodes/data/example_time_series/TEbmapdata.txt new file mode 100644 index 00000000..7e9af6ce --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbmapdata.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..69919d0f --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..7b46ba95 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbnet_figure.txt @@ -0,0 +1,963 @@ +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 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--git a/sourcecodes/data/example_time_series/TEbparent.txt b/sourcecodes/data/example_time_series/TEbparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh b/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh new file mode 100644 index 00000000..ff2eafcd --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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/TEbrun_initialstructure.sh b/sourcecodes/data/example_time_series/TEbrun_initialstructure.sh new file mode 100644 index 00000000..3417deda --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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/example_time_series/TEbstructure_input.txt b/sourcecodes/data/example_time_series/TEbstructure_input.txt new file mode 100644 index 00000000..0770c53d --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbstructure_input.txt @@ -0,0 +1,11 @@ +Genotype TraitA_T1 TraitA_T2 TraitA_T3 TraitB_T1 TraitB_T2 TraitB_T3 TraitC_T1 TraitC_T2 TraitC_T3 +0 1 1 1 0 1 0 0 0 0 +0 0 0 0 0 1 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 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 diff --git a/sourcecodes/data/example_time_series/TEbstructure_input_temp.txt b/sourcecodes/data/example_time_series/TEbstructure_input_temp.txt new file mode 100644 index 00000000..975379b8 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbstructure_input_temp.txt @@ -0,0 +1,11 @@ +Genotype TraitA_T1 TraitA_T2 TraitA_T3 TraitB_T1 TraitB_T2 TraitB_T3 TraitC_T1 TraitC_T2 TraitC_T3 +0.000000 1.000000 1.000000 1.000000 0.048181 1.000000 0.000000 0.008486 0.000000 0.000000 +0.000000 0.000000 0.125496 0.031272 0.018658 1.000000 0.010369 0.010548 0.064699 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.010256 0.000000 0.018179 0.038732 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.010700 0.000000 0.000000 0.000000 +0.000000 0.000000 0.041559 0.000000 0.000000 0.000000 0.011348 0.000000 0.009653 0.027519 +0.000000 0.000000 0.000000 0.012552 0.000000 0.000000 0.010464 0.000000 0.017873 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.023996 +0.000000 0.000000 0.000000 0.000000 0.010647 0.000000 0.032409 0.000000 0.435382 0.032829 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.011094 0.000000 0.000000 0.047523 +0.000000 0.000000 0.000000 0.236851 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 diff --git a/sourcecodes/data/example_time_series/TEbstructure_old.txt b/sourcecodes/data/example_time_series/TEbstructure_old.txt new file mode 100644 index 00000000..2d164e66 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbstructure_old.txt @@ -0,0 +1,6 @@ +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 new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example_time_series/TEbtier.txt b/sourcecodes/data/example_time_series/TEbtier.txt new file mode 100644 index 00000000..29aafcbe --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbtier.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..e4d7d174 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbtype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..301160a9 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbvar.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..f36841a7 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbvardata.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..aa23daa0 --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbvarname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example_time_series/TEbwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/examplecar/OVIban.txt b/sourcecodes/data/examplecar/OVIban.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/examplecar/OVIban.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/examplecar/OVIcontinuous_input.txt b/sourcecodes/data/examplecar/OVIcontinuous_input.txt new file mode 100644 index 00000000..3a2846cf --- /dev/null +++ b/sourcecodes/data/examplecar/OVIcontinuous_input.txt @@ -0,0 +1,1004 @@ +Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter +2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 +2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 +1 1 1 1 1 1 1 1.09219 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 8.35719 1 3 3 1 2 1 1 1 2 1 1 +2 1 1 1 1 2 1 4.87697 1 1 1 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 3.40886 2 3 3 1 2 1 1 1 2 1 1 +1 1 1 1 1 1 1 0.823531 1 1 1 1 1 1 1 1 2 1 1 +1 1 1 1 1 1 1 1.29151 1 1 1 1 1 1 1 1 1 1 1 +2 1 1 1 1 1 1 3.2245 1 1 1 1 2 1 1 1 2 1 1 +2 2 2 1 1 2 1 3.32396 1 3 1 2 2 2 1 2 1 1 1 +2 1 2 1 1 2 1 4.81455 2 3 3 1 2 3 1 1 1 1 1 +2 1 2 1 1 1 1 1.8855 2 2 2 2 1 1 2 2 1 1 1 +2 1 2 1 1 2 1 3.16074 2 3 3 1 2 1 1 1 1 1 1 +2 1 1 1 1 1 1 1.32025 1 1 1 2 1 1 1 2 1 1 1 +2 1 1 1 1 1 1 0.725881 1 1 1 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 9.15429 2 3 3 1 2 1 1 2 2 1 2 +2 1 2 1 1 1 1 1.29503 2 3 2 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.55555 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 0.899695 2 1 1 1 1 1 2 2 1 1 1 +2 1 2 1 1 2 1 0.972723 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 3.62187 2 3 3 2 2 3 1 1 1 1 1 +1 1 2 1 1 1 1 7.11136 1 1 1 1 1 2 1 1 1 1 1 +1 1 1 1 1 1 1 1.10928 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 2.61643 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 6.2605 1 2 2 1 2 1 1 2 1 1 1 +2 1 2 1 1 2 1 8.55173 1 1 1 1 2 3 1 1 1 1 1 +1 1 1 1 1 1 1 1.86787 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 1.23631 1 3 1 1 2 3 1 1 1 1 1 +2 1 2 1 1 1 1 0.728145 1 1 1 1 2 3 1 1 1 1 1 +2 1 2 1 1 2 1 4.66434 2 3 3 1 2 3 2 2 1 1 1 +2 1 2 1 1 1 1 3.56254 2 3 3 1 1 2 1 1 2 2 1 +2 1 2 1 1 2 1 2.63999 2 3 3 1 2 3 1 2 2 2 1 +2 1 2 1 1 2 1 0.715897 2 3 3 1 2 2 1 1 1 1 1 +2 1 2 1 1 2 1 1.85198 2 3 3 1 2 2 1 1 2 2 1 +2 1 1 1 1 1 1 3.63826 1 1 1 1 1 1 2 2 2 1 1 +2 1 2 1 1 1 1 7.73862 2 3 3 1 1 3 1 1 2 2 1 +2 1 2 1 1 2 1 10.1699 2 3 3 1 2 1 1 1 1 1 1 +2 1 1 1 1 2 2 2.97722 1 1 1 1 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 4.50117 2 2 2 1 1 3 1 1 1 1 1 +2 1 2 1 1 1 1 0.640869 2 2 2 1 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 1.72775 1 3 1 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 5.46047 2 3 3 1 2 3 1 1 1 1 1 +2 1 2 1 1 1 1 2.21929 1 2 2 1 2 2 1 1 2 1 1 +1 1 1 1 1 1 1 0.438026 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 0.0684539 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 4.15012 2 3 3 1 2 2 1 1 1 1 1 +2 1 2 1 1 2 1 0.161533 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 1.11862 2 3 3 1 2 2 1 1 2 1 2 +2 1 1 1 1 1 1 0.410719 1 1 1 1 2 1 1 1 2 1 1 +2 1 2 1 1 2 1 0.0322208 2 3 3 1 2 1 1 1 2 2 1 +1 1 1 1 1 1 1 3.37212 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 2.78532 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.40432 1 1 1 1 1 1 2 1 1 1 1 +2 1 2 1 1 2 1 3.22403 2 3 3 1 1 3 1 1 2 1 1 +2 1 2 1 1 2 1 1.7234 2 3 3 1 2 1 1 2 1 1 1 +2 1 2 1 1 2 1 0.674939 2 3 3 1 2 1 1 1 1 1 1 +1 1 1 1 1 1 1 6.9812 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.82705 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 0.935587 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 0.992564 1 1 1 1 1 3 1 1 1 1 1 +2 1 2 1 1 2 1 3.47892 1 2 2 1 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 6.52634 1 2 2 1 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 3.68841 1 1 1 1 1 3 1 1 2 2 1 +1 1 2 1 1 1 1 0.50506 2 2 2 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 4.33453 1 2 2 1 2 3 1 1 2 1 1 +2 1 2 1 1 1 1 3.39695 2 2 2 2 2 1 1 1 1 1 1 +2 1 2 1 1 1 1 0.482289 1 2 1 1 2 2 1 1 1 1 1 +2 1 2 1 1 2 1 0.385094 2 3 3 1 2 1 1 1 1 1 1 +1 1 1 1 1 1 1 3.92753 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 9.63027 2 3 3 1 2 1 1 1 2 2 1 +1 1 1 1 1 1 1 1.77681 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 15.8749 2 2 2 1 1 1 2 2 1 1 1 +1 1 1 1 1 1 1 0.863939 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 3.5007 2 3 2 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.46447 1 1 1 2 1 1 2 2 1 1 1 +2 1 2 1 1 1 1 4.00622 2 2 2 1 1 3 1 1 2 1 1 +1 1 2 1 1 1 1 2.62894 1 1 1 1 1 2 1 1 1 1 1 +1 1 1 1 1 1 1 0.772251 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 0.254104 1 1 1 1 1 1 1 2 1 1 1 +2 1 2 1 1 1 1 1.35669 1 1 1 1 1 3 1 1 2 2 1 +1 1 1 1 1 1 1 0.408515 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 4.73523 2 3 3 1 2 3 1 1 1 1 1 +2 1 2 1 1 2 1 4.84404 2 3 3 1 2 1 1 1 1 1 1 +2 2 2 1 1 2 1 3.08909 2 3 3 2 2 1 1 1 2 2 1 +2 1 1 1 1 1 1 0.500373 1 1 1 2 1 1 1 2 1 1 1 +1 1 2 1 1 1 1 1.42352 1 1 1 1 1 3 2 1 1 1 1 +2 1 2 1 1 2 1 3.19283 2 2 2 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 2.65803 2 3 3 1 2 1 1 1 2 1 2 +1 1 1 1 1 1 1 4.35117 1 1 1 1 1 1 1 1 1 1 1 +2 1 1 1 1 1 1 0.448913 1 1 1 1 1 1 1 1 2 2 1 +2 1 2 1 1 2 1 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+2 1 2 1 1 2 1 0.0085396 2 3 3 1 2 1 1 1 2 2 1 +2 1 2 1 1 2 1 3.75628 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 4.46408 2 3 3 1 2 1 2 2 1 1 1 +1 1 2 1 1 1 1 4.407 1 2 2 1 1 1 2 1 1 1 1 +2 1 2 1 1 2 1 12.9879 2 3 3 1 2 1 1 1 2 1 1 +2 1 2 1 1 2 1 5.42745 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 2.27077 2 3 3 1 2 1 1 1 2 1 1 +1 1 1 1 1 1 1 4.19191 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.43925 1 1 1 1 1 1 1 2 1 1 1 +1 1 1 1 1 1 1 4.98537 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 1.71189 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 4.91003 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 2 2 1 0.809663 2 3 3 1 2 1 1 1 1 1 1 +2 1 2 1 1 2 1 3.78373 2 3 3 1 2 1 1 1 1 1 1 +2 1 1 1 1 1 1 1.64728 1 1 1 1 2 1 1 2 2 1 1 +2 1 2 1 1 2 1 0.977114 2 3 3 1 2 2 1 1 1 1 1 +2 1 2 1 1 2 1 4.78619 2 3 3 1 2 1 1 1 1 1 1 +2 1 1 1 1 2 1 4.88483 1 1 1 2 2 1 1 1 2 1 1 +1 1 1 1 1 1 1 0.0447191 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 2 1 6.22958 2 3 3 1 2 1 1 1 1 1 1 +1 1 1 1 1 1 1 4.02524 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 5.10729 1 3 2 1 1 1 1 1 2 2 1 +2 1 2 1 1 2 1 8.97099 2 3 3 1 2 3 1 1 1 1 1 +2 1 2 1 1 2 1 5.59486 2 3 3 1 2 1 1 1 1 1 1 +1 1 1 1 1 1 1 1.13786 1 1 1 1 1 1 1 1 1 1 1 +2 1 2 1 1 1 1 11.3795 1 2 2 1 1 1 1 1 1 1 1 + diff --git a/sourcecodes/data/examplecar/OVIgraphviz.txt b/sourcecodes/data/examplecar/OVIgraphviz.txt new file mode 100644 index 00000000..2aaaecb2 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIgraphviz.txt @@ -0,0 +1,70 @@ +digraph G { +size="10,10"; ratio = fill; +node [shape=square,width=1.5]; +Dist -> BatAge; +Dist -> Timing; +Dist -> Plugs; +Dist -> AirFilter; +Dist -> GasTank; +Dist -> GasFilter; +SpkQual -> Starts; +MFuse -> Starts; +MFuse -> Dist; +MFuse -> SpkQual; +MFuse -> Starter; +MFuse -> BatAge; +MFuse -> Charging; +MFuse -> Timing; +MFuse -> Cranks; +MFuse -> Plugs; +MFuse -> AirFilter; +MFuse -> Air; +MFuse -> Fuel; +MFuse -> GasTank; +MFuse -> GasFilter; +Alter -> Dist; +Alter -> MFuse; +Alter -> BatAge; +Alter -> Charging; +Alter -> Timing; +Alter -> Plugs; +Alter -> AirFilter; +Alter -> Air; +Alter -> GasTank; +Alter -> GasFilter; +Starter -> Cranks; +StMotor -> MFuse; +StMotor -> Alter; +StMotor -> Starter; +StMotor -> BatAge; +StMotor -> Timing; +StMotor -> Plugs; +StMotor -> AirFilter; +StMotor -> Air; +StMotor -> Fuel; +StMotor -> GasTank; +StMotor -> GasFilter; +PlugVolt -> Starts; +PlugVolt -> Dist; +PlugVolt -> SpkQual; +PlugVolt -> MFuse; +PlugVolt -> Alter; +PlugVolt -> Starter; +PlugVolt -> StMotor; +PlugVolt -> Charging; +PlugVolt -> Cranks; +BatVolt -> Starts; +BatVolt -> Dist; +BatVolt -> SpkQual; +BatVolt -> MFuse; +BatVolt -> Alter; +BatVolt -> Starter; +BatVolt -> StMotor; +BatVolt -> Charging; +BatVolt -> PlugVolt; +BatVolt -> Cranks; +Plugs -> SpkQual; +AirFilter -> Air; +GasTank -> Fuel; +GasFilter -> Fuel; +} \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIk.txt b/sourcecodes/data/examplecar/OVIk.txt new file mode 100644 index 00000000..d00491fd --- /dev/null +++ b/sourcecodes/data/examplecar/OVIk.txt @@ -0,0 +1 @@ +1 diff --git a/sourcecodes/data/examplecar/OVImap.txt b/sourcecodes/data/examplecar/OVImap.txt new file mode 100644 index 00000000..eda717d2 --- /dev/null +++ b/sourcecodes/data/examplecar/OVImap.txt @@ -0,0 +1,19 @@ +Starts 3 0.432505 1.751249 +Dist 3 0.094441 1.008991 +SpkQual 2 0.434234 1.748252 +MFuse 2 0.031607 1.000999 +Alter 2 0.054690 1.002997 +Starter 2 0.490666 1.402597 +StMotor 2 0.070534 1.004995 +BatAge 2 2.948418 3.295892 +Charging 2 0.500244 1.497502 +PlugVolt 2 0.908145 2.090909 +BatVolt 2 0.914876 1.999001 +Timing 2 0.293230 1.094905 +Cranks 2 0.500010 1.515485 +Plugs 2 0.819700 1.518482 +AirFilter 3 0.294607 1.095904 +Air 2 0.375671 1.169830 +Fuel 2 0.416982 1.223776 +GasTank 2 0.295974 1.096903 +GasFilter 1 0.164975 1.027972 diff --git a/sourcecodes/data/examplecar/OVImapdata.txt b/sourcecodes/data/examplecar/OVImapdata.txt new file mode 100644 index 00000000..d1eac895 --- /dev/null +++ b/sourcecodes/data/examplecar/OVImapdata.txt @@ -0,0 +1 @@ +BatVolt PlugVolt StMotor Alter MFuse Charging Starter Cranks Dist GasFilter GasTank Fuel AirFilter Air Plugs SpkQual Starts Timing BatAge diff --git a/sourcecodes/data/examplecar/OVIname.txt b/sourcecodes/data/examplecar/OVIname.txt new file mode 100644 index 00000000..e7901e87 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIname.txt @@ -0,0 +1 @@ +Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter diff --git a/sourcecodes/data/examplecar/OVInet_figure.txt b/sourcecodes/data/examplecar/OVInet_figure.txt new file mode 100644 index 00000000..ceed746e --- /dev/null +++ b/sourcecodes/data/examplecar/OVInet_figure.txt @@ -0,0 +1,237 @@ +19 +2100 1800 +BatVolt 788 0 +PlugVolt 998 180 +StMotor 788 360 +Alter 998 540 +MFuse 788 720 +Charging 472 900 +Starter 998 900 +Cranks 0 1080 +Dist 1523 900 +GasFilter 263 1080 +GasTank 525 1080 +Fuel 472 1260 +AirFilter 788 1080 +Air 998 1260 +Plugs 1050 1080 +SpkQual 1523 1260 +Starts 788 1440 +Timing 1313 1080 +BatAge 1575 1080 +BatVolt 3 +250 150 +0 +10 2 3 4 5 6 7 8 9 16 17 +1 0.4184 +2 0.1639 +3 0.4177 +PlugVolt 3 +250 150 +1 1 +9 3 4 5 6 7 8 9 16 17 +1 0.3706 +2 0.1678 +3 0.4616 +StMotor 2 +250 150 +2 1 2 +11 4 5 7 10 11 12 13 14 15 18 19 +1 0.9955 +2 0.0045 +Alter 2 +250 150 +3 1 2 3 +10 5 6 9 10 11 13 14 15 18 19 +1 0.9970 +2 0.0030 +MFuse 2 +250 150 +4 1 2 3 4 +14 6 7 8 9 10 11 12 13 14 15 16 17 18 19 +1 0.9990 +2 0.0010 +Charging 2 +250 150 +4 1 2 4 5 +0 +1 0.5024 +2 0.4976 +Starter 2 +250 150 +4 1 2 3 5 +1 8 +1 0.5977 +2 0.4023 +Cranks 2 +250 150 +4 1 2 5 7 +0 +1 0.4848 +2 0.5152 +Dist 2 +250 150 +4 1 2 4 5 +6 10 11 13 15 18 19 +1 0.9910 +2 0.0090 +GasFilter 2 +250 150 +4 3 4 5 9 +1 12 +1 0.9725 +2 0.0275 +GasTank 2 +250 150 +4 3 4 5 9 +1 12 +1 0.9031 +2 0.0969 +Fuel 2 +250 150 +4 3 5 10 11 +0 +1 0.7756 +2 0.2244 +AirFilter 2 +250 150 +4 3 4 5 9 +1 14 +1 0.9040 +2 0.0960 +Air 2 +250 150 +4 3 4 5 13 +0 +1 0.8301 +2 0.1699 +Plugs 3 +250 150 +4 3 4 5 9 +1 16 +1 0.6922 +2 0.0970 +3 0.2109 +SpkQual 2 +250 150 +4 1 2 5 15 +1 17 +1 0.2568 +2 0.7432 +Starts 2 +250 150 +4 1 2 5 16 +0 +1 0.2497 +2 0.7503 +Timing 2 +250 150 +4 3 4 5 9 +0 +1 0.9053 +2 0.0947 +BatAge 1 +250 150 +4 3 4 5 9 +0 +-2.1178 0.0437 +-2.0287 0.0524 +-1.9396 0.0623 +-1.8505 0.0736 +-1.7614 0.0862 +-1.6723 0.1001 +-1.5832 0.1155 +-1.4941 0.1321 +-1.4050 0.1499 +-1.3159 0.1689 +-1.2268 0.1888 +-1.1377 0.2093 +-1.0486 0.2303 +-0.9595 0.2515 +-0.8704 0.2725 +-0.7813 0.2929 +-0.6922 0.3124 +-0.6031 0.3306 +-0.5140 0.3471 +-0.4249 0.3617 +-0.3358 0.3740 +-0.2467 0.3836 +-0.1576 0.3905 +-0.0685 0.3944 +0.0206 0.3952 +0.1097 0.3930 +0.1988 0.3877 +0.2879 0.3795 +0.3770 0.3687 +0.4661 0.3553 +0.5552 0.3398 +0.6443 0.3225 +0.7334 0.3036 +0.8225 0.2837 +0.9116 0.2629 +1.0007 0.2419 +1.0898 0.2207 +1.1789 0.1999 +1.2680 0.1796 +1.3571 0.1601 +1.4462 0.1417 +1.5353 0.1243 +1.6244 0.1083 +1.7135 0.0936 +1.8026 0.0803 +1.8917 0.0683 +1.9808 0.0576 +2.0699 0.0483 +2.1590 0.0401 +2.2481 0.0331 +2.3372 0.0271 +2.4263 0.0220 +2.5154 0.0177 +2.6045 0.0142 +2.6936 0.0112 +2.7827 0.0088 +2.8718 0.0069 +2.9609 0.0054 +3.0500 0.0041 +3.1391 0.0031 +3.2282 0.0024 +3.3173 0.0018 +3.4064 0.0013 +3.4954 0.0010 +3.5845 0.0007 +3.6736 0.0005 +3.7627 0.0004 +3.8518 0.0003 +3.9409 0.0002 +4.0300 0.0001 +4.1191 0.0001 +4.2082 0.0001 +4.2973 0.0000 +4.3864 0.0000 +4.4755 0.0000 +4.5646 0.0000 +4.6537 0.0000 +4.7428 0.0000 +4.8319 0.0000 +4.9210 0.0000 +5.0101 0.0000 +5.0992 0.0000 +5.1883 0.0000 +5.2774 0.0000 +5.3665 0.0000 +5.4556 0.0000 +5.5447 0.0000 +5.6338 0.0000 +5.7229 0.0000 +5.8120 0.0000 +5.9011 0.0000 +5.9902 0.0000 +6.0793 0.0000 +6.1684 0.0000 +6.2575 0.0000 +6.3466 0.0000 +6.4357 0.0000 +6.5248 0.0000 +6.6139 0.0000 +6.7030 0.0000 +6.7921 0.0000 diff --git a/sourcecodes/data/examplecar/OVInet_figure_new.txt b/sourcecodes/data/examplecar/OVInet_figure_new.txt new file mode 100644 index 00000000..bd2ec975 --- /dev/null +++ b/sourcecodes/data/examplecar/OVInet_figure_new.txt @@ -0,0 +1,138 @@ +19 +19 +2100 1800 +BatVolt 788 0 +PlugVolt 998 180 +StMotor 788 360 +Alter 998 540 +MFuse 788 720 +Charging 472 900 +Starter 998 900 +Cranks 0 1080 +Dist 1523 900 +GasFilter 263 1080 +GasTank 525 1080 +Fuel 472 1260 +AirFilter 788 1080 +Air 998 1260 +Plugs 1050 1080 +SpkQual 1523 1260 +Starts 788 1440 +Timing 1313 1080 +BatAge 1575 1080 +BatVolt 3 +250 150 +0 +10 2 3 4 5 6 7 8 9 16 17 +1 0.4186 +2 0.1642 +3 0.4172 +PlugVolt 3 +250 150 +1 1 +9 3 4 5 6 7 8 9 16 17 +1 0.3716 +2 0.1684 +3 0.4600 +StMotor 2 +250 150 +2 1 2 +11 4 5 7 10 11 12 13 14 15 18 19 +1 0.9982 +2 0.0018 +Alter 2 +250 150 +3 1 2 3 +10 5 6 9 10 11 13 14 15 18 19 +1 0.9985 +2 0.0015 +MFuse 2 +250 150 +4 1 2 3 4 +14 6 7 8 9 10 11 12 13 14 15 16 17 18 19 +1 1.0000 +2 0.0000 +Charging 2 +250 150 +4 1 2 4 5 +0 +1 0.5027 +2 0.4973 +Starter 2 +250 150 +4 1 2 3 5 +1 8 +1 0.5996 +2 0.4004 +Cranks 2 +250 150 +4 1 2 5 7 +0 +1 0.4861 +2 0.5139 +Dist 2 +250 150 +4 1 2 4 5 +6 10 11 13 15 18 19 +1 0.9948 +2 0.0052 +GasFilter 2 +250 150 +4 3 4 5 9 +1 12 +1 0.9736 +2 0.0264 +GasTank 2 +250 150 +4 3 4 5 9 +1 12 +1 0.9048 +2 0.0952 +Fuel 2 +250 150 +4 3 5 10 11 +0 +1 0.7770 +2 0.2230 +AirFilter 2 +250 150 +4 3 4 5 9 +1 14 +1 0.9045 +2 0.0955 +Air 2 +250 150 +4 3 4 5 13 +0 +1 0.8304 +2 0.1696 +Plugs 3 +250 150 +4 3 4 5 9 +1 16 +1 0.6923 +2 0.0968 +3 0.2108 +SpkQual 2 +250 150 +4 1 2 5 15 +1 17 +1 0.2573 +2 0.7427 +Starts 2 +250 150 +4 1 2 5 16 +0 +1 0.2504 +2 0.7496 +Timing 2 +250 150 +4 3 4 5 9 +0 +1 0.9080 +2 0.0920 +BatAge 1 +250 150 +4 3 4 5 9 +0 +-1.3159 1.0000 diff --git a/sourcecodes/data/examplecar/OVInnode.txt b/sourcecodes/data/examplecar/OVInnode.txt new file mode 100644 index 00000000..d6b24041 --- /dev/null +++ b/sourcecodes/data/examplecar/OVInnode.txt @@ -0,0 +1 @@ +19 diff --git a/sourcecodes/data/examplecar/OVInrows.txt b/sourcecodes/data/examplecar/OVInrows.txt new file mode 100644 index 00000000..7d802a3e --- /dev/null +++ b/sourcecodes/data/examplecar/OVInrows.txt @@ -0,0 +1 @@ +1002 diff --git a/sourcecodes/data/examplecar/OVIparent.txt b/sourcecodes/data/examplecar/OVIparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/examplecar/OVIparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh b/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh new file mode 100644 index 00000000..dab5c39a --- /dev/null +++ b/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh @@ -0,0 +1,38 @@ +#!/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 OVI +fi +exit diff --git a/sourcecodes/data/examplecar/OVIrun_initialstructure.sh b/sourcecodes/data/examplecar/OVIrun_initialstructure.sh new file mode 100644 index 00000000..d47ae324 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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 OVI +fi +exit diff --git a/sourcecodes/data/examplecar/OVIstructure_input.txt b/sourcecodes/data/examplecar/OVIstructure_input.txt new file mode 100644 index 00000000..cad732f3 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIstructure_input.txt @@ -0,0 +1,20 @@ +Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter +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 1 0 1 1 0 0 1 1 +1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 1 1 0 0 1 0 1 1 0 0 1 1 1 1 1 1 1 1 +0 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 0 1 1 +0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 +0 0 0 1 1 1 0 1 0 0 0 1 0 1 1 1 1 1 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 +1 1 1 1 1 1 1 0 1 0 0 0 1 0 0 0 0 0 0 +1 1 1 1 1 1 1 0 1 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 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 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 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 0 0 0 1 0 0 diff --git a/sourcecodes/data/examplecar/OVIstructure_input_temp.txt b/sourcecodes/data/examplecar/OVIstructure_input_temp.txt new file mode 100644 index 00000000..09d40aa3 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIstructure_input_temp.txt @@ -0,0 +1,20 @@ +Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 +1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 +0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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a/sourcecodes/data/examplecar/OVIstructure_old.txt b/sourcecodes/data/examplecar/OVIstructure_old.txt new file mode 100644 index 00000000..22f14ba3 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIstructure_old.txt @@ -0,0 +1,19 @@ +Dist 0.9910 0.0090 +BatAge 0.0437 0.0524 0.0623 0.0736 0.0862 0.1001 0.1155 0.1321 0.1499 0.1689 0.1888 0.2093 0.2303 0.2515 0.2725 0.2929 0.3124 0.3306 0.3471 0.3617 0.3740 0.3836 0.3905 0.3944 0.3952 0.3930 0.3877 0.3795 0.3687 0.3553 0.3398 0.3225 0.3036 0.2837 0.2629 0.2419 0.2207 0.1999 0.1796 0.1601 0.1417 0.1243 0.1083 0.0936 0.0803 0.0683 0.0576 0.0483 0.0401 0.0331 0.0271 0.0220 0.0177 0.0142 0.0112 0.0088 0.0069 0.0054 0.0041 0.0031 0.0024 0.0018 0.0013 0.0010 0.0007 0.0005 0.0004 0.0003 0.0002 0.0001 0.0001 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 +Timing 0.9053 0.0947 +Plugs 0.6922 0.0970 0.2109 +AirFilter 0.9040 0.0960 +GasTank 0.9031 0.0969 +GasFilter 0.9725 0.0275 +SpkQual 0.2568 0.7432 +Starts 0.2497 0.7503 +MFuse 0.9990 0.0010 +Starter 0.5977 0.4023 +Charging 0.5024 0.4976 +Cranks 0.4848 0.5152 +Air 0.8301 0.1699 +Fuel 0.7756 0.2244 +Alter 0.9970 0.0030 +StMotor 0.9955 0.0045 +PlugVolt 0.3706 0.1678 0.4616 +BatVolt 0.4184 0.1639 0.4177 diff --git a/sourcecodes/data/examplecar/OVIthr.txt b/sourcecodes/data/examplecar/OVIthr.txt new file mode 100644 index 00000000..2eb3c4fe --- /dev/null +++ b/sourcecodes/data/examplecar/OVIthr.txt @@ -0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/examplecar/OVItype.txt b/sourcecodes/data/examplecar/OVItype.txt new file mode 100644 index 00000000..0b76081c --- /dev/null +++ b/sourcecodes/data/examplecar/OVItype.txt @@ -0,0 +1,2 @@ +Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter +2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 diff --git a/sourcecodes/data/examplecar/OVIvar.txt b/sourcecodes/data/examplecar/OVIvar.txt new file mode 100644 index 00000000..dec2bf5d --- /dev/null +++ b/sourcecodes/data/examplecar/OVIvar.txt @@ -0,0 +1 @@ +19 \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIvardata.txt b/sourcecodes/data/examplecar/OVIvardata.txt new file mode 100644 index 00000000..e595bf94 --- /dev/null +++ b/sourcecodes/data/examplecar/OVIvardata.txt @@ -0,0 +1 @@ +-1.3159 \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIvarname.txt b/sourcecodes/data/examplecar/OVIvarname.txt new file mode 100644 index 00000000..2453221d --- /dev/null +++ b/sourcecodes/data/examplecar/OVIvarname.txt @@ -0,0 +1 @@ +BatAge \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIwhite.txt b/sourcecodes/data/examplecar/OVIwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/examplecar/OVIwhite.txt @@ -0,0 +1 @@ +From To diff --git 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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 new file mode 100644 index 00000000..56dcd027 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXgraphviz.txt @@ -0,0 +1,20 @@ +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 new file mode 100644 index 00000000..af7330d6 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXmap.txt @@ -0,0 +1,15 @@ +Voltage_at_plug 2 0.827795 2.021000 +Car_cranks 2 0.500234 1.504000 +Spark_plugs 2 0.820310 2.042000 +Spark_quality 2 0.816376 2.014000 +Distributer 3 0.500241 1.497000 +Spark_timing 2 0.810222 2.014000 +Car_starts 2 0.500054 1.486000 +Headlights 3 0.810946 2.032000 +Alternator 3 0.500214 1.494000 +Charging_system 2 0.500234 1.496000 +Battery_voltage 3 0.806400 2.037000 +Battery_age 3 0.561294 1.708000 +Main_fuse 3 0.500150 1.490000 +Starter_system 3 0.499674 1.476000 +Starter_motor 2 0.500201 1.493000 diff --git a/sourcecodes/data/examplecar15node/MtXmapdata.txt b/sourcecodes/data/examplecar15node/MtXmapdata.txt new file mode 100644 index 00000000..67939bd1 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXmapdata.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..2957eff7 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..5a5a3bb9 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXnet_figure.txt @@ -0,0 +1,114 @@ +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 new file mode 100644 index 00000000..60d3b2f4 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXnnode.txt @@ -0,0 +1 @@ +15 diff --git a/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh b/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh new file mode 100644 index 00000000..8012f054 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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/examplecar15node/MtXstructure_input.txt b/sourcecodes/data/examplecar15node/MtXstructure_input.txt new file mode 100644 index 00000000..549070d3 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXstructure_input.txt @@ -0,0 +1,17 @@ +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 new file mode 100644 index 00000000..cad36b88 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXstructure_old.txt @@ -0,0 +1,15 @@ +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 new file mode 100644 index 00000000..75ee3397 --- /dev/null +++ b/sourcecodes/data/examplecar15node/MtXtype.txt @@ -0,0 +1,2 @@ +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 new file mode 100644 index 00000000..66dddb9f --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAcontinuous_input.txt @@ -0,0 +1,1003 @@ +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 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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 new file mode 100644 index 00000000..56dcd027 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAgraphviz.txt @@ -0,0 +1,20 @@ +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 new file mode 100644 index 00000000..e96a904a --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAmap.txt @@ -0,0 +1,15 @@ +Voltage_at_plug 2 0.908185 1.905000 +Car_cranks 2 0.500106 1.488000 +Spark_plugs 2 0.778947 2.543000 +Spark_quality 2 0.853627 1.757000 +Distributer 3 0.099549 1.990000 +Spark_timing 2 0.357390 2.880000 +Car_starts 2 0.469352 1.327000 +Headlights 3 0.917301 1.951000 +Alternator 3 0.044699 1.998000 +Charging_system 2 0.500246 1.502000 +Battery_voltage 3 0.915330 2.003000 +Battery_age 3 0.500554 1.236000 +Main_fuse 3 0.121613 1.985000 +Starter_system 3 0.494126 1.578000 +Starter_motor 2 0.063151 1.996000 diff --git a/sourcecodes/data/examplecar15node/eIAmapdata.txt b/sourcecodes/data/examplecar15node/eIAmapdata.txt new file mode 100644 index 00000000..67939bd1 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAmapdata.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..2957eff7 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAname.txt @@ -0,0 +1 @@ +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 new file mode 100644 index 00000000..29896806 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAnet_figure.txt @@ -0,0 +1,114 @@ +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 new file mode 100644 index 00000000..7ccbca8e --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAnlevels.txt @@ -0,0 +1,15 @@ +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 new file mode 100644 index 00000000..60d3b2f4 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAnnode.txt @@ -0,0 +1 @@ +15 diff --git a/sourcecodes/data/examplecar15node/eIAstructure_input.txt b/sourcecodes/data/examplecar15node/eIAstructure_input.txt new file mode 100644 index 00000000..6e7eaef0 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAstructure_input.txt @@ -0,0 +1,17 @@ +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/eIAstructure_old.txt b/sourcecodes/data/examplecar15node/eIAstructure_old.txt new file mode 100644 index 00000000..774a14fe --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAstructure_old.txt @@ -0,0 +1,15 @@ +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 new file mode 100644 index 00000000..75ee3397 --- /dev/null +++ b/sourcecodes/data/examplecar15node/eIAtype.txt @@ -0,0 +1,2 @@ +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/examplezoo/fSfban.txt b/sourcecodes/data/examplezoo/fSfban.txt new file mode 100644 index 00000000..9197eeec --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfban.txt @@ -0,0 +1,261 @@ +From To +aquatic airborne +aquatic venomous +aquatic predator +aquatic domestic +airborne aquatic +airborne venomous +airborne predator +airborne domestic +venomous aquatic +venomous airborne +venomous predator +venomous domestic +predator aquatic +predator airborne +predator venomous +predator domestic +domestic aquatic +domestic airborne +domestic venomous +domestic predator +eggs aquatic +eggs airborne +eggs venomous +eggs predator +eggs domestic +milk aquatic +milk airborne +milk venomous +milk predator +milk domestic +backbone aquatic +backbone airborne +backbone venomous +backbone predator +backbone domestic +breathes aquatic +breathes airborne +breathes venomous +breathes predator +breathes domestic +catsize aquatic +catsize airborne +catsize venomous +catsize predator +catsize domestic +tail aquatic +tail airborne +tail venomous +tail predator +tail domestic +toothed aquatic +toothed airborne +toothed venomous +toothed predator +toothed domestic +hair aquatic +hair airborne +hair venomous +hair predator +hair domestic +feathers aquatic +feathers airborne +feathers venomous +feathers predator +feathers domestic +fins aquatic +fins airborne +fins venomous +fins predator +fins domestic +legs aquatic +legs airborne +legs venomous +legs predator +legs domestic +type aquatic +type airborne +type venomous +type predator +type domestic +eggs aquatic +eggs airborne +eggs venomous +eggs predator +eggs domestic +milk aquatic +milk airborne +milk venomous +milk predator +milk domestic +backbone aquatic +backbone airborne +backbone venomous +backbone predator +backbone domestic +breathes aquatic +breathes airborne +breathes venomous +breathes predator +breathes domestic +catsize eggs +catsize milk +catsize backbone +catsize breathes +tail eggs +tail milk +tail backbone +tail breathes +toothed eggs +toothed milk +toothed backbone +toothed breathes +hair eggs +hair milk +hair backbone +hair breathes +feathers eggs +feathers milk +feathers backbone +feathers breathes +fins eggs +fins milk +fins backbone +fins breathes +legs eggs +legs milk +legs backbone +legs breathes +type eggs +type milk +type backbone +type breathes +catsize tail +catsize toothed +catsize hair +catsize feathers +catsize fins +catsize legs +tail catsize +tail toothed +tail hair +tail feathers +tail fins +tail legs +toothed catsize +toothed tail +toothed hair +toothed feathers +toothed fins +toothed legs +hair catsize +hair tail +hair toothed +hair feathers +hair fins +hair legs +feathers catsize +feathers tail +feathers toothed +feathers hair +feathers fins +feathers legs +fins catsize +fins tail +fins toothed +fins hair +fins feathers +fins legs +legs catsize +legs tail +legs toothed +legs hair +legs feathers +legs fins +catsize aquatic +catsize airborne +catsize venomous +catsize predator +catsize domestic +tail aquatic +tail airborne +tail venomous +tail predator +tail domestic +toothed aquatic +toothed airborne +toothed venomous +toothed predator +toothed domestic +hair aquatic +hair airborne +hair venomous +hair predator +hair domestic +feathers aquatic +feathers airborne +feathers venomous +feathers predator +feathers domestic +fins aquatic +fins airborne +fins venomous +fins predator +fins domestic +legs aquatic +legs airborne +legs venomous +legs predator +legs domestic +catsize eggs +catsize milk +catsize backbone +catsize breathes +tail eggs +tail milk +tail backbone +tail breathes +toothed eggs +toothed milk +toothed backbone +toothed breathes +hair eggs +hair milk +hair backbone +hair breathes +feathers eggs +feathers milk +feathers backbone +feathers breathes +fins eggs +fins milk +fins backbone +fins breathes +legs eggs +legs milk +legs backbone +legs breathes +type catsize +type tail +type toothed +type hair +type feathers +type fins +type legs +type aquatic +type airborne +type venomous +type predator +type domestic +type eggs +type milk +type backbone +type breathes +type catsize +type tail +type toothed +type hair +type feathers +type fins +type legs diff --git a/sourcecodes/data/examplezoo/fSfcontinuous_input.txt b/sourcecodes/data/examplezoo/fSfcontinuous_input.txt new file mode 100644 index 00000000..340ad4f6 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfcontinuous_input.txt @@ -0,0 +1,104 @@ +hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type +2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 2 1 2 2 1 1 2 1 2 2 1 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 7 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 +1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1 +1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 1 2 2 2 2 2 1 1 2 1 1 3 +1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1 +1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 +2 1 1 2 1 2 2 2 2 2 1 2 1 1 1 2 1 +1 1 1 1 1 2 2 2 2 1 2 1 1 2 1 1 3 +1 1 2 1 1 2 2 1 1 1 2 1 1 1 1 1 7 +1 1 2 1 1 1 2 2 2 2 1 1 1 2 1 1 3 +1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7 +1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 +1 1 2 1 1 2 2 2 2 1 2 2 1 2 1 2 4 +1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 +1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 +1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 +1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 2 2 +2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1 +2 1 1 2 1 1 2 2 2 2 1 1 2 1 2 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 2 1 1 2 1 +1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 1 1 1 1 2 2 1 1 2 2 1 2 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 +1 2 2 1 1 2 2 1 2 2 1 1 2 2 1 2 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 2 2 +2 1 1 2 1 2 2 2 2 2 1 2 2 2 1 2 1 +1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 +2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 1 1 +1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 2 2 +2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1 +1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 2 2 +2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 2 1 +1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 +2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 1 2 1 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +1 1 2 1 1 2 2 1 1 1 1 1 3 1 1 1 7 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +1 1 2 1 1 2 2 2 2 2 1 1 3 1 1 1 5 +1 1 2 1 1 2 2 2 2 2 2 1 3 1 1 1 5 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 1 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 2 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +1 1 2 1 1 2 2 2 2 2 1 1 3 2 1 1 5 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 +2 1 2 2 1 2 2 1 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 2 2 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 +1 1 2 1 1 2 1 2 2 2 1 1 3 1 1 1 5 +1 1 2 1 1 1 1 1 2 2 1 1 3 2 1 2 3 +1 1 2 1 1 1 2 2 2 2 1 1 3 2 1 1 3 +2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1 +2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 +1 1 2 1 1 2 2 1 1 1 1 1 4 1 1 1 7 +1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7 +1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6 +1 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 +2 1 2 1 2 1 1 1 1 2 2 1 5 1 2 1 6 +2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 +1 1 2 1 2 1 2 1 1 2 1 1 5 1 1 1 6 +1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7 +2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 +1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6 +2 1 2 1 2 1 1 1 1 2 2 1 5 1 1 1 6 +1 1 2 1 1 2 2 1 1 1 1 1 6 1 1 2 7 +1 1 1 1 1 1 2 1 1 2 2 1 6 2 1 1 7 + diff --git a/sourcecodes/data/examplezoo/fSfgraphviz.txt b/sourcecodes/data/examplezoo/fSfgraphviz.txt new file mode 100644 index 00000000..701801c6 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfgraphviz.txt @@ -0,0 +1,61 @@ +digraph G { +size="10,10"; ratio = fill; +node [shape=square,width=1.5]; +feathers -> type; +eggs -> hair; +eggs -> feathers; +eggs -> toothed; +eggs -> backbone; +eggs -> breathes; +eggs -> legs; +eggs -> tail; +eggs -> catsize; +milk -> hair; +milk -> feathers; +milk -> toothed; +milk -> backbone; +milk -> breathes; +milk -> legs; +milk -> tail; +milk -> catsize; +milk -> type; +airborne -> eggs; +airborne -> milk; +airborne -> backbone; +airborne -> breathes; +airborne -> catsize; +aquatic -> eggs; +aquatic -> milk; +aquatic -> breathes; +aquatic -> fins; +backbone -> hair; +backbone -> feathers; +backbone -> toothed; +backbone -> fins; +backbone -> legs; +backbone -> tail; +backbone -> type; +breathes -> hair; +breathes -> toothed; +breathes -> backbone; +breathes -> fins; +breathes -> legs; +breathes -> catsize; +breathes -> type; +venomous -> hair; +venomous -> feathers; +venomous -> eggs; +venomous -> milk; +venomous -> toothed; +venomous -> backbone; +venomous -> breathes; +venomous -> fins; +venomous -> legs; +venomous -> tail; +venomous -> catsize; +legs -> type; +domestic -> eggs; +domestic -> milk; +domestic -> fins; +domestic -> tail; +} \ No newline at end of file diff --git a/sourcecodes/data/examplezoo/fSfk.txt b/sourcecodes/data/examplezoo/fSfk.txt new file mode 100644 index 00000000..f599e28b --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfk.txt @@ -0,0 +1 @@ +10 diff --git a/sourcecodes/data/examplezoo/fSfmap.txt b/sourcecodes/data/examplezoo/fSfmap.txt new file mode 100644 index 00000000..4a123441 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfmap.txt @@ -0,0 +1,17 @@ +hair 2 0.496921 1.425743 +feathers 2 0.400495 1.198020 +eggs 2 0.495325 1.584158 +milk 2 0.493522 1.405941 +airborne 2 0.427750 1.237624 +aquatic 2 0.481335 1.356436 +predator 2 0.499505 1.554455 +toothed 2 0.491512 1.603960 +backbone 2 0.384605 1.821782 +breathes 2 0.407844 1.792079 +venomous 2 0.271410 1.079208 +fins 6 0.376013 1.168317 +legs 2 1.253194 2.544554 +tail 2 0.439397 1.742574 +domestic 2 0.336552 1.128713 +catsize 7 0.498314 1.435644 +type 2 2.102709 2.831683 diff --git a/sourcecodes/data/examplezoo/fSfmapdata.txt b/sourcecodes/data/examplezoo/fSfmapdata.txt new file mode 100644 index 00000000..19d91997 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfmapdata.txt @@ -0,0 +1 @@ +domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair diff --git a/sourcecodes/data/examplezoo/fSfname.txt b/sourcecodes/data/examplezoo/fSfname.txt new file mode 100644 index 00000000..c68267c4 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfname.txt @@ -0,0 +1 @@ +hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type diff --git a/sourcecodes/data/examplezoo/fSfnet_figure.txt b/sourcecodes/data/examplezoo/fSfnet_figure.txt new file mode 100644 index 00000000..0c8f9428 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfnet_figure.txt @@ -0,0 +1,130 @@ +17 +1800 1200 +domestic 43 0 +venomous 343 0 +predator 643 0 +aquatic 943 0 +airborne 1243 0 +milk 523 171 +eggs 1123 171 +breathes 643 343 +catsize 523 514 +backbone 1123 514 +tail 0 686 +legs 257 686 +fins 514 686 +toothed 771 686 +feathers 1029 686 +type 823 857 +hair 1286 686 +domestic 2 +250 150 +0 +4 6 7 11 13 +1 0.8672 +2 0.1328 +venomous 2 +250 150 +0 +11 6 7 8 9 10 11 12 13 14 15 17 +1 0.8860 +2 0.1140 +predator 2 +250 150 +0 +0 +1 0.4455 +2 0.5545 +aquatic 2 +250 150 +0 +4 6 7 8 13 +1 0.6726 +2 0.3274 +airborne 2 +250 150 +0 +5 6 7 8 9 10 +1 0.8149 +2 0.1851 +milk 2 +250 150 +4 1 2 4 5 +9 8 9 10 11 12 14 15 16 17 +1 0.4703 +2 0.5297 +eggs 2 +250 150 +4 1 2 4 5 +8 8 9 10 11 12 14 15 17 +1 0.4962 +2 0.5038 +breathes 2 +250 150 +5 2 4 5 6 7 +7 9 10 12 13 14 16 17 +1 0.1666 +2 0.8334 +catsize 2 +250 150 +5 2 5 6 7 8 +0 +1 0.4789 +2 0.5211 +backbone 2 +250 150 +5 2 5 6 7 8 +7 11 12 13 14 15 16 17 +1 0.1743 +2 0.8257 +tail 2 +250 150 +5 1 2 6 7 10 +0 +1 0.2426 +2 0.7574 +legs 6 +250 150 +5 2 6 7 8 10 +1 16 +1 0.1827 +2 0.2108 +3 0.4747 +4 0.0111 +5 0.0799 +6 0.0409 +fins 2 +250 150 +5 1 2 4 8 10 +0 +1 0.8751 +2 0.1249 +toothed 2 +250 150 +5 2 6 7 8 10 +0 +1 0.3799 +2 0.6201 +feathers 2 +250 150 +4 2 6 7 10 +1 16 +1 0.8693 +2 0.1307 +type 7 +250 150 +5 6 8 10 12 15 +0 +1 0.5297 +2 0.1307 +3 0.0476 +4 0.0854 +5 0.0323 +6 0.0578 +7 0.1165 +hair 2 +250 150 +5 2 6 7 8 10 +0 +1 0.4597 +2 0.5403 diff --git a/sourcecodes/data/examplezoo/fSfnnode.txt b/sourcecodes/data/examplezoo/fSfnnode.txt new file mode 100644 index 00000000..98d9bcb7 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfnnode.txt @@ -0,0 +1 @@ +17 diff --git a/sourcecodes/data/examplezoo/fSfnrows.txt b/sourcecodes/data/examplezoo/fSfnrows.txt new file mode 100644 index 00000000..257e5632 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfnrows.txt @@ -0,0 +1 @@ +102 diff --git a/sourcecodes/data/examplezoo/fSfparent.txt b/sourcecodes/data/examplezoo/fSfparent.txt new file mode 100644 index 00000000..7ed6ff82 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfparent.txt @@ -0,0 +1 @@ +5 diff --git a/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh b/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh new file mode 100644 index 00000000..f20a9a29 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/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 fSf +fi +exit diff --git a/sourcecodes/data/examplezoo/fSfstructure_input.txt b/sourcecodes/data/examplezoo/fSfstructure_input.txt new file mode 100644 index 00000000..c49d600b --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfstructure_input.txt @@ -0,0 +1,18 @@ +hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type +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 +1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 0 +1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 1 +0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 1 0 +0 0 1 1 0 0 0 0 0 1 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 +1 1 0 0 0 0 0 1 0 0 0 1 1 1 0 0 1 +1 0 0 0 0 0 0 1 1 0 0 1 1 0 0 1 1 +1 1 1 1 0 0 0 1 1 1 0 1 1 1 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 1 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 1 1 0 0 0 0 0 0 0 1 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 diff --git a/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt b/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt new file mode 100644 index 00000000..8910aaee --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt @@ -0,0 +1,18 @@ +hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 +1.000000 0.800011 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 0.000000 +1.000000 1.000000 0.500003 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 +0.000000 0.400004 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 +0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 +0.800018 0.799985 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 +1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.199982 0.000000 0.900015 0.900010 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 diff --git a/sourcecodes/data/examplezoo/fSfstructure_old.txt b/sourcecodes/data/examplezoo/fSfstructure_old.txt new file mode 100644 index 00000000..bf00f5d5 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfstructure_old.txt @@ -0,0 +1,16 @@ +feathers 0.8693 0.1307 +type 0.5297 0.1307 0.0476 0.0854 0.0323 0.0578 0.1165 +eggs 0.4962 0.5038 +hair 0.4597 0.5403 +toothed 0.3799 0.6201 +backbone 0.1743 0.8257 +breathes 0.1666 0.8334 +legs 0.1827 0.2108 0.4747 0.0111 0.0799 0.0409 +tail 0.2426 0.7574 +catsize 0.4789 0.5211 +milk 0.4703 0.5297 +airborne 0.8149 0.1851 +aquatic 0.6726 0.3274 +fins 0.8751 0.1249 +venomous 0.8860 0.1140 +domestic 0.8672 0.1328 diff --git a/sourcecodes/data/examplezoo/fSfthr.txt b/sourcecodes/data/examplezoo/fSfthr.txt new file mode 100644 index 00000000..aec258df --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfthr.txt @@ -0,0 +1 @@ +0.8 diff --git a/sourcecodes/data/examplezoo/fSftier.txt b/sourcecodes/data/examplezoo/fSftier.txt new file mode 100644 index 00000000..ca417b31 --- /dev/null +++ b/sourcecodes/data/examplezoo/fSftier.txt @@ -0,0 +1 @@ +4,Tier1,5,aquatic,airborne,venomous,predator,domestic,Tier2,4,eggs,milk,backbone,breathes,Tier3,7,catsize,tail,toothed,hair,feathers,fins,legs,Tier4,1,type, \ No newline at end of file diff --git a/sourcecodes/data/examplezoo/fSftype.txt b/sourcecodes/data/examplezoo/fSftype.txt new file mode 100644 index 00000000..41c0f73e --- /dev/null +++ b/sourcecodes/data/examplezoo/fSftype.txt @@ -0,0 +1,2 @@ +hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type +2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7 diff --git a/sourcecodes/data/examplezoo/fSfwhite.txt b/sourcecodes/data/examplezoo/fSfwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/examplezoo/fSfwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/examplezoo/standardized_data.txt b/sourcecodes/data/examplezoo/standardized_data.txt new file mode 100644 index 00000000..0975061e --- /dev/null +++ b/sourcecodes/data/examplezoo/standardized_data.txt @@ -0,0 +1,102 @@ +domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair +1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +2 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 7 1 +1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1 +1 1 2 2 1 2 1 2 2 2 2 1 2 2 1 1 1 +1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 2 2 1 1 1 2 2 1 2 2 1 1 2 1 3 1 +1 1 2 2 1 2 1 2 2 2 2 1 2 2 1 1 1 +1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 1 2 2 1 2 1 2 2 2 1 1 2 2 1 1 2 +1 2 2 2 1 1 1 1 1 2 2 1 1 2 1 3 1 +1 2 2 2 1 1 2 1 1 1 1 1 1 1 1 7 1 +1 1 2 1 1 1 2 2 1 2 2 1 1 2 1 3 1 +1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 7 1 +1 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1 +1 2 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1 +1 1 2 2 1 1 2 1 2 2 2 1 2 2 1 4 1 +1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 7 1 +2 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+2.0866 1 -0.19274 0.066839 2 -0.30442 -0.70635 0.8594 +-1.3268 1 -1.2952 0.023312 1 1.4432 0.036383 0.89534 +-1.4174 1 -0.43139 -0.97617 1 1.9378 0.79311 -0.17685 +-0.30469 1 0.072833 -0.069195 1 1.2683 -0.62404 0.25508 diff --git a/sourcecodes/data/temp_evidence_file b/sourcecodes/data/temp_evidence_file new file mode 100644 index 00000000..b687ceaf --- /dev/null +++ b/sourcecodes/data/temp_evidence_file @@ -0,0 +1,36 @@ +#!/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 \ No newline at end of file diff --git a/sourcecodes/data/temp_intervention_file b/sourcecodes/data/temp_intervention_file new file mode 100644 index 00000000..cdf5ce0f --- /dev/null +++ b/sourcecodes/data/temp_intervention_file @@ -0,0 +1,36 @@ +#!/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}"/newintervention \ No newline at end of file diff --git a/sourcecodes/data/temp_shell_file_initial_structure b/sourcecodes/data/temp_shell_file_initial_structure new file mode 100644 index 00000000..5d1c323d --- /dev/null +++ b/sourcecodes/data/temp_shell_file_initial_structure @@ -0,0 +1,36 @@ +#!/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 \ No newline at end of file |