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| author | ziejd2 | 2021-02-24 15:19:03 -0600 |
|---|---|---|
| committer | ziejd2 | 2021-02-24 15:19:03 -0600 |
| commit | 1427e9bf4f85823164b4573a3bcf1ba3ba6b04d0 (patch) | |
| tree | d4356879a9b0a3d44063a6b292ef0197173697af /sourcecodes | |
| parent | a2b306b10fb07f07c63235861ccfe460153e8609 (diff) | |
| download | BNW-1427e9bf4f85823164b4573a3bcf1ba3ba6b04d0.tar.gz | |
Moving final GENENET8 version to master
Diffstat (limited to 'sourcecodes')
172 files changed, 1900 insertions, 7880 deletions
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+ mso-tstyle-rowband-size:0; + mso-tstyle-colband-size:0; + mso-style-noshow:yes; + mso-style-priority:99; + mso-style-qformat:yes; + mso-style-parent:""; + mso-padding-alt:0in 5.4pt 0in 5.4pt; + mso-para-margin:0in; + mso-para-margin-bottom:.0001pt; + mso-pagination:widow-orphan; + font-size:10.0pt; + font-family:"Calibri","sans-serif"; + mso-ascii-font-family:Calibri; + mso-ascii-theme-font:minor-latin; + mso-hansi-font-family:Calibri; + mso-hansi-theme-font:minor-latin;} +</style> +<![endif]--><!--[if gte mso 9]><xml> + <o:shapedefaults v:ext="edit" spidmax="4098"/> +</xml><![endif]--><!--[if gte mso 9]><xml> + <o:shapelayout v:ext="edit"> + <o:idmap v:ext="edit" data="1"/> + </o:shapelayout></xml><![endif]--> +</head> + +<body lang=EN-US style='tab-interval:.5in'> + +<div class=WordSection1> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>This workflow will provide +an overview of how to use BNW to:<o:p></o:p></span></p> + +<p class=MsoListParagraphCxSpFirst style='margin-right:307.5pt;mso-add-space: +auto;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>1)<span +style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'>Select +a structure learning method and upload data into BNW<o:p></o:p></span></p> + +<p class=MsoListParagraphCxSpMiddle style='margin-right:307.5pt;mso-add-space: +auto;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2)<span +style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'>Use +the BNW structural restraint interface<o:p></o:p></span></p> + +<p class=MsoListParagraphCxSpLast style='margin-right:307.5pt;mso-add-space: +auto;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3)<span +style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'>Make +predictions with the network structure<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: +normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>1. +Select structure learning method and uploading data into BNW<o:p></o:p></span></b></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>For this workflow, we are +creating a network using a biological data set containing both continuous and +discrete variables. The variables are a genotype (the discrete variable), three +gene expression traits (Gene1, Gene2, Gene3), and a phenotype.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>We do not know the network +structure for this dataset, so we will first use BNW to learn the structure. Selecting +<u>Learn a network model from data</u> on the BNW home page presents a list of the +three structure learning methods that are currently implemented in BNW. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype + id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t" + path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f"> + <v:stroke joinstyle="miter"/> + <v:formulas> + <v:f eqn="if lineDrawn pixelLineWidth 0"/> + <v:f eqn="sum @0 1 0"/> + <v:f eqn="sum 0 0 @1"/> + <v:f eqn="prod @2 1 2"/> + <v:f eqn="prod @3 21600 pixelWidth"/> + <v:f eqn="prod @3 21600 pixelHeight"/> + <v:f eqn="sum @0 0 1"/> + <v:f eqn="prod @6 1 2"/> + <v:f eqn="prod @7 21600 pixelWidth"/> + <v:f eqn="sum @8 21600 0"/> + <v:f eqn="prod @7 21600 pixelHeight"/> + <v:f eqn="sum @10 21600 0"/> + </v:formulas> + <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> + <o:lock v:ext="edit" aspectratio="t"/> +</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1037" type="#_x0000_t75" + style='width:300pt;height:117pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image003.jpg" o:title="" croptop="19333f" + cropbottom="34461f" cropleft="11633f" cropright="33260f"/> +</v:shape><![endif]--><![if !vml]><img width=450 height=156 +src="BNW_workflow_test_files/image003.jpg" v:shapes="Picture_x0020_2"><![endif]></span><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>Because the network contains +only 5 variables, we can use any of these structure learning methods. If more +than 6 variables are present, using the global optimal search method would likely be necessary. +We will use the exhaustive search with model averaging method in this workflow. +More information about the structure learning methods can be found on the BNW +help page.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>After selecting the +Exhaustive Search button, we are prompted to upload a file containing the data. +<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<img width=700 height=225 +src="BNW_workflow_test_files/image006.jpg" v:shapes="Picture_x0020_5"><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><br>The figure +below shows BNW after we have uploaded the data file. The first line of the +data contains the names of the variables included in the network, while the +remaining lines are the variable values for individual samples. A description +of how to format data files for use in BNW can be found on the BNW help page and can be accessed by the the <u>Data formatting guidelines</u> option in the left menu. Additionally, two additional options, <u>Select additional constraints</u> or <u>Perform Bayesian network modeling with no restraints</u>, appear in the left menu after loading the data file.<o:p></o:p></span></p><br> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=675 height=225 +src="BNW_workflow_test_files/image008.jpg" v:shapes="Picture_x0020_8"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: +normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>2. +Use the structural constraint interface<o:p></o:p></span></b></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>Here, we will use the +structural constraint interface to help identify biologically meaningful +network structures. Specifically, we want to investigate how the genotype +impacts gene expression which then impacts the phenotype.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>The first +section of the structural constraint interface allows users to assign the variables +(nodes) in the network to tiers. By default, three tiers are shown, but this +can be changed by selecting a different number in the drop-down menu. The +leftmost box of this section contains draggable boxes with the names of the +variables in the network. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=750 height=300 +src="BNW_workflow_test_files/image010.jpg" v:shapes="Picture_x0020_14"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>For this +network, we want to assign Genotype to Tier1, the gene expression traits to +Tier2, and the Phenotype to Tier3.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=750 height=300 +src="BNW_workflow_test_files/image012.jpg" v:shapes="Picture_x0020_17"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>The second +section in the structural constraint interface allows users to specify the +types of interactions that are allowed both between and within tiers. In this +case, we will keep the default settings, which will allow there to be edges +between nodes within a tier, prevent nodes in Tier1 from being the child of +Tier2 and Tier3 nodes, and prevent nodes in Tier2 from being the child of Tier2 +nodes. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><![if !vml]><img width=475 height=200 +src="BNW_workflow_test_files/image014.jpg" v:shapes="Picture_x0020_20"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>The final +section of the structural constraint interface would allow for the +specification of particular edges that should be banned from the network or +required to be in the network. Users can identify these edges by dragging the +nodes to appropriate boxes. In this case, we do not want to ban or require any +specific edges. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=430 height=227 +src="BNW_workflow_test_files/image016.jpg" v:shapes="Picture_x0020_23"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>After +entering the structural constraints, BNW will perform structure learning from +the data after clicking <u>Perform Bayesin network modeling</u> on the left menu and +present the structure of the network as shown below. Genotype, the discrete +node, is shown as a bar chart with the bars showing the fraction of samples +with each genotype in the data, while the other nodes are shown as lines with +the Gaussian distributions that best fit the data.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_26" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:367.5pt; + height:400.5pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image017.png" o:title="" croptop="11774f" + cropbottom="5139f" cropleft="15267f" cropright="16897f"/> +</v:shape><![endif]--><![if !vml]><img width=490 height=534 +src="BNW_workflow_test_files/image018.jpg" v:shapes="Picture_x0020_26"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>To further +investigate the structure of the network, users can select <u>Display Structure +Matrix</u> in the left menu. This will bring up a popup windoe containing a table +showing the confidence of each directed edge in the network after model +averaging. For this network, all of the nodes included in the network were +present in almost all high scoring networks, as the values of the edges are all +near 1. BNW displays all edges with a confidence greater than 0.5 in the +network structure. A second table in the window shows the structure matrix with +a 1 for edges included in the structure and 0 for edges that are not included. These +tables can be downloaded by clicking the download link.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:358.5pt; + height:158.25pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image033.png" o:title="" croptop="19224f" + cropbottom="21354f" cropleft="10363f" cropright="12698f"/> +</v:shape><![endif]--><![if !vml]><img width=478 height=211 +src="BNW_workflow_test_files/image020.jpg" v:shapes="Picture_x0020_41"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: +normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-no-proof:yes'>3) </span></b><b style='mso-bidi-font-weight:normal'><span +style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>Make +predictions with the network structure<o:p></o:p></span></b></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>BNW can be used to both +predict the values of variables in a network given known evidence and to +investigate how the network might change in response to interventions. Users +can switch between evidence and intervention modes by selecting the proper +button on the top of the page containing the network structure.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>For example, +suppose we want to use the model to make predictions for a new sample that was +not in the original dataset. We know that this sample was from an individual +with Genotype=2 and want to predict the values of the genes and phenotype for +the individual. To enter this evidence in the network, we simply click on the +Genotype node in the network and enter 2 in the popup window. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>The figure below shows the +changes in the network after entering this evidence.The node for which evidence was entered now contains a red outline and all of the nodes in the network now contain both blue and red lines. The blue lines show the original values of the distributions, while the red lines shown the predicted values given the +evidence. In this case, knowing that the individual had Genotype=2 would cause +us to predict that the expression of Gene1 and the value of the phenotype would +be above average, while the expression of Gene2 and Gene3 would be decreases. +The specific changes in the predicted values can be investigated by hovering +over the nodes and observing the values at the peaks of the distribution.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_29" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:352.5pt; + height:464.25pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image019.png" o:title="" croptop="5662f" + cropbottom="3557f" cropleft="15900f" cropright="17569f"/> +</v:shape><![endif]--><![if !vml]><img width=470 height=619 +src="BNW_workflow_test_files/image022.jpg" v:shapes="Picture_x0020_29"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>Evidence +can be entered in more than one node in the network. For example, the figure +below shows predicted values for the network after entering evidence for both +Genotype and Gene1.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_32" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:291.75pt; + height:414pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image021.png" o:title="" croptop="9437f" + cropbottom="5850f" cropleft="16919f" cropright="22117f"/> +</v:shape><![endif]--><![if !vml]><img width=389 height=552 +src="BNW_workflow_test_files/image024.jpg" v:shapes="Picture_x0020_32"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>To use the +network to predict the results of intervention, select the proper button on the +top of the window to enter intervention mode. While evidence simply changes the +predicted values of the other nodes in the network, intervention has a larger +effect, as it removes the dependence of the intervened network on its parents +and changes the network structure. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_35" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:295.5pt; + height:417.75pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image023.png" o:title="" croptop="9437f" + cropbottom="5375f" cropleft="16718f" cropright="21976f"/> +</v:shape><![endif]--><![if !vml]><img width=394 height=557 +src="BNW_workflow_test_files/image026.jpg" v:shapes="Picture_x0020_35"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>The figure +below shows the changes in the network in BNW after intervention on Gene1 that +results Gene1 having a low value. The predictions of the network after this +intervention could be compared with experiments that prevent Gene1 from being +expressed. Intervention that decreases Gene1 is predicted to result in an increase +in Gene2 and a decrease in the phenotype. Note that Genotype and Gene3, which +are not descendents of Gene1, are not affected by the intervention.<o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><!--[if gte vml 1]><v:shape + id="Picture_x0020_38" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:297.75pt; + height:406.5pt;visibility:visible;mso-wrap-style:square'> + <v:imagedata src="BNW_workflow_test_files/image025.png" o:title="" croptop="9382f" + cropbottom="6755f" cropleft="16815f" cropright="21642f"/> +</v:shape><![endif]--><![if !vml]><img width=397 height=542 +src="BNW_workflow_test_files/image039.jpg" v:shapes="Picture_x0020_38"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span 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+<body lang=EN-US style='tab-interval:.5in'> + +<div class=WordSection1> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>This workflow contains examples of using the BNW structural constraint interface to help identify biologically meaningful genetic network models for two cases:<o:p></o:p></span></p> + +<p class=MsoListParagraphCxSpFirst style='margin-right:307.5pt;mso-add-space: +auto;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>1)<span +style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'>A genetic network linking genotype and phenotype<o:p></o:p></span></p> + +<p class=MsoListParagraphCxSpMiddle style='margin-right:307.5pt;mso-add-space: +auto;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"; +mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2)<span +style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'>A genetic network with multiple genotypes and cis- and trans-regulated genes<o:p></o:p></span></p> + + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: +normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>1. +A genetic network linking genotype and phenotype<o:p></o:p></span></b></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>In this example, we will use the structural constraint interface to create a genetic network linking a genotype with intermediated phenotypes (i.e., gene expression or other cellular level traits) and a higher-order phenotype. The figure below shows a screenshot of BNW after loading the data file and selecting <u>Go to structure learning settings and the BNW structural constraint interface</u>. There are 5 nodes in the network, Genotype, Int1, Int2, Int3, and a Phenotype.<br><br><o:p></o:p></span></p> +<![if !vml]><img width=520 height=205 +src="BNW_workflow_test_files/image2_1.jpg" v:shapes="Picture_x0020_2"><![endif]></span><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'><o:p></o:p></span></p> +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'> We want to assign the nodes to three tiers in this example, so we will keep the number of tiers at the default setting, and drag the nodes to the proper tiers.<br><br><o:p></o:p></span></p> +<![if !vml]><img width=520 height=205 +src="BNW_workflow_test_files/image2_2.jpg" v:shapes="Picture_x0020_2"><![endif]></span><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif"'>In this example, we do not want the genotype to be the direct parent of the phenotype, so we made some changes to the <u>Define interactions allowed between tiers</u> section of the structural constraint interface. Specifically, we have unchecked two boxes that are different from the default settings: (1) we have unchecked the box that allows the node(s) in Tier1 from being the parents of the node(s) in Tier3 and (2) we have unchecked the box that allows the node(s) in Tier3 from being the children of the node(s) in Tier1. Actually, unchecking either of these boxes would have been sufficient in preventing direct interactions between Genotype and Phenotype, but, there is no harm in unchecking both boxes. There are no additional specific edges that we want to ban or require in the network, so we do not have to add any edges to the <u>Specify additional constraint</u> section and we can proceed with structure learning.<br><br><o:p></o:p></span></p> +<![if !vml]><img width=650 height=200 +src="BNW_workflow_test_files/image2_3.jpg" v:shapes="Picture_x0020_2"><![endif]></span><span +style='font-size:12.0pt;line-height:115%;font-family:"Arial","sans-serif"'><o:p></o:p></span></p> + + +<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: +normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>2. +A genetic network with multiple genotypes and cis- and trans-regulated genes.<o:p></o:p></span></b></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> In this example, we will add restrictions to a network containing 8 nodes: 2 genotype nodes (Geno1 and Geno2), 3 cis-regulated gene expression traits (cisGene1, cisGene2, and cisGene3), 2 trans-regulated gene expression traits (transGene1 and transGene2), and a phenotype (Pheno). We have four tiers of nodes (genotypes, cis-regulated genes, trans-regulated genes, and phenotype), so we have selected 4 from the dropdown menu at the top of the page and assigned the nodes to the correct tiers. We could make a more complex system of tiers that would allow us to specify which genes are regulated by which genotypes (for example, Geno1 regulates cisGene1 and transGene1, while Geno2 regulates cisGene2, cisGene3, and transGene2), but, for this example, we will use a simpler system of 4 tiers.<br><br><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=537 height=258 +src="BNW_workflow_test_files/image2_4.jpg" v:shapes="Picture_x0020_14"><![endif]><o:p></o:p></span></p> + + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> We have made one change to the default setting in the <u>Define interactions allowed between tiers</u> section. For Tier1, which contains the genotypes, we have selected "No" for the "Are within tier interactions allowed?", as it does not make biological sense for one genotype variation to cause the variation in another genotype in this examples.<br><br><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=536 height=133 +src="BNW_workflow_test_files/image2_5.jpg" v:shapes="Picture_x0020_14"><![endif]><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: +0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'>Assume that a known regulatory relationship between cisGene1 and transGene1 has been established from previous experiments. We can require that this relationship is included in the network by adding the edge list of required edges in the <u>Specify additional constraints</u> section.<br><br><o:p></o:p></span></p> + +<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; +line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> +<![if !vml]><img width=750 height=300 +src="BNW_workflow_test_files/image2_6.jpg" v:shapes="Picture_x0020_17"><![endif]><o:p></o:p></span></p> +</div> + +</body> + +</html> diff --git a/sourcecodes/BNW_workflow_test_files/image2_4.jpg b/sourcecodes/BNW_workflow_test_files/image2_4.jpg deleted file mode 100644 index 1f9070f1..00000000 --- a/sourcecodes/BNW_workflow_test_files/image2_4.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/image2_5.jpg b/sourcecodes/BNW_workflow_test_files/image2_5.jpg deleted file mode 100644 index 41051f92..00000000 --- a/sourcecodes/BNW_workflow_test_files/image2_5.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/sci_5node_network1.jpg b/sourcecodes/BNW_workflow_test_files/sci_5node_network1.jpg deleted file mode 100644 index ed710d68..00000000 --- a/sourcecodes/BNW_workflow_test_files/sci_5node_network1.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/sci_5node_part1.jpg b/sourcecodes/BNW_workflow_test_files/sci_5node_part1.jpg deleted file mode 100644 index 21cca66d..00000000 --- a/sourcecodes/BNW_workflow_test_files/sci_5node_part1.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/sci_5node_part2.jpg b/sourcecodes/BNW_workflow_test_files/sci_5node_part2.jpg deleted file mode 100644 index d1803d1b..00000000 --- a/sourcecodes/BNW_workflow_test_files/sci_5node_part2.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/sci_5node_part3.jpg b/sourcecodes/BNW_workflow_test_files/sci_5node_part3.jpg deleted file mode 100644 index 0644daf9..00000000 --- a/sourcecodes/BNW_workflow_test_files/sci_5node_part3.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/BNW_workflow_test_files/sci_5node_upload.jpg b/sourcecodes/BNW_workflow_test_files/sci_5node_upload.jpg deleted file mode 100644 index caa75e13..00000000 --- a/sourcecodes/BNW_workflow_test_files/sci_5node_upload.jpg +++ /dev/null Binary files differdiff --git a/sourcecodes/add_evd.php b/sourcecodes/add_evd.php index 50740d02..008844b8 100644 --- a/sourcecodes/add_evd.php +++ b/sourcecodes/add_evd.php @@ -40,8 +40,7 @@ function mapid($name,$keyval) { //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $nm=$dir.$keyval."mapdata.txt"; $namelist=file_get_contents("$nm"); @@ -68,8 +67,7 @@ return $val; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $lfile=$dir.$keyval."nlevels.txt"; $dmapdata=file_get_contents($lfile); diff --git a/sourcecodes/add_inv.php b/sourcecodes/add_inv.php index 013ba61e..26d089ed 100644 --- a/sourcecodes/add_inv.php +++ b/sourcecodes/add_inv.php @@ -35,8 +35,7 @@ function mapid($name,$keyval) { //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $nm=$dir."$keyval"."mapdata.txt"; $namelist=file_get_contents("$nm"); @@ -64,8 +63,7 @@ return $val; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $lfile=$dir.$keyval."nlevels.txt"; $dmapdata=file_get_contents($lfile); diff --git a/sourcecodes/bn_after_upload_gom.php b/sourcecodes/bn_after_upload_gom.php index 11a92650..f9427435 100644 --- a/sourcecodes/bn_after_upload_gom.php +++ b/sourcecodes/bn_after_upload_gom.php @@ -18,7 +18,7 @@ include("input_validate.php"); //$searchID=""; $searchID="YES"; $UploadValue="NO"; -$TextFile=$_FILES["MyFile"]["name"]; +$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; /////////////Generate a random key///////////////////// @@ -45,9 +45,9 @@ $TextFile=$_FILES["MyFile"]["name"]; //$TextinFile=$dir.$sid."_orig.txt"; -if(isset($_POST["searchkey"])) +if(isset($HTTP_POST_VARS["searchkey"])) { - $searchID=$_POST["searchkey"]; + $searchID=$HTTP_POST_VARS["searchkey"]; } @@ -67,15 +67,15 @@ if($searchID=="") } -if(isset($_POST["MyUpload"])) +if(isset($HTTP_POST_VARS["MyUpload"])) { - $UploadValue=$_POST["MyUpload"]; + $UploadValue=$HTTP_POST_VARS["MyUpload"]; if ($UploadValue=="YES") { if($TextFile!="") { // $TextFile = valid_input($TextFile); - $sta=move_uploaded_file($_FILES['MyFile']['tmp_name'],$TextinFile); + $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); if(!$sta) { echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; @@ -135,7 +135,7 @@ if($searchID!="") //$keyval = valid_keyval($keyval); //shell_exec('./run_scripts/run_prep_input '.$keyval); $keyval=valid_keyval($_GET["My_key"]); - $input_table_file="/var/lib/genenet/bnw/".$keyval."input_table.txt"; + $input_table_file="./data/".$keyval."input_table.txt"; $parent_number=4; $k_number=1; $runtime=exe_time($keyval,$parent_number,$k_number); @@ -156,16 +156,11 @@ if($searchID!="") <br> <p><h3>The uploaded data file has the following properties: <br></h3> -<?php -$table_text = json_encode(file("file://".$input_table_file)); -?> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error, raw_temp){ - var dsv = d3.dsvFormat("\t"); - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data = dsv.parse(data2); + d3.text("<?php print($input_table_file);?>", function(error, raw){ + var dsv = d3.dsvFormat("\t") + var data = dsv.parse(raw) var caption_text = data.pop(); if (error) throw error; tabulate_caption("#table_div1",data,caption_text.Variable); diff --git a/sourcecodes/bn_file_load_gom.php b/sourcecodes/bn_file_load_gom.php index d2480cd4..6509cdeb 100644 --- a/sourcecodes/bn_file_load_gom.php +++ b/sourcecodes/bn_file_load_gom.php @@ -13,7 +13,7 @@ include("runtime_check.php"); include("input_validate.php"); $searchID=""; $UploadValue="NO"; -$TextFile=$_FILES["MyFile"]["name"]; +$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; /////////////Generate a random key///////////////////// @@ -34,17 +34,15 @@ if($_POST["My_key"]!="") $sid=$keyval."continuous_input"; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; -//$input_table_file="./data/".$keyval."input_table.txt"; -$input_table_file=$dir.$keyval."input_table.txt"; +$dir="/tmp/bnw/"; +$input_table_file="./data/".$keyval."input_table.txt"; $TextinFile=$dir.$sid."_orig.txt"; -if(isset($_POST["searchkey"])) +if(isset($HTTP_POST_VARS["searchkey"])) { - $searchID=$_POST["searchkey"]; + $searchID=$HTTP_POST_VARS["searchkey"]; } @@ -64,15 +62,15 @@ if($searchID=="") } -if(isset($_POST["MyUpload"])) +if(isset($HTTP_POST_VARS["MyUpload"])) { - $UploadValue=$_POST["MyUpload"]; + $UploadValue=$HTTP_POST_VARS["MyUpload"]; if ($UploadValue=="YES") { if($TextFile!="") { // $TextFile = valid_input($TextFile); - $sta=move_uploaded_file($_FILES['MyFile']['tmp_name'],$TextinFile); + $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); if(!$sta) { echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; @@ -167,17 +165,12 @@ if($searchID!="") <br> <p><h3>The uploaded data file has the following properties: <br></h3> -<?php -$table_text = json_encode(file("file://".$input_table_file)); -?> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error, raw_temp){ + d3.text("<?php print($input_table_file);?>", function(error, raw){ var dsv = d3.dsvFormat("\t") - var data1 = <?php echo $table_text?> - var data2 = data1.join("") - var data = dsv.parse(data2) - var caption_text = data.pop() + var data = dsv.parse(raw) + var caption_text = data.pop(); if (error) throw error; tabulate_caption("#table_div1",data,caption_text.Variable); }); diff --git a/sourcecodes/create_tiers_gom_part1.php b/sourcecodes/create_tiers_gom_part1.php index f2125367..891d0170 100644 --- a/sourcecodes/create_tiers_gom_part1.php +++ b/sourcecodes/create_tiers_gom_part1.php @@ -8,8 +8,7 @@ include("input_validate.php"); $keyval=$_GET["My_key"]; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $type_n=array(); @@ -193,4 +192,4 @@ print("Estimated run time for the current parameters: $runtime seconds"); </p> <br> <a class=button3 href="create_tiers_gom_part2.php?My_key=<?php print($keyval);?>">Continue to assign variables to tiers</a> -<br> +<br> \ No newline at end of file diff --git a/sourcecodes/create_tiers_gom_part2.php b/sourcecodes/create_tiers_gom_part2.php index 9bec2c88..62422781 100644 --- a/sourcecodes/create_tiers_gom_part2.php +++ b/sourcecodes/create_tiers_gom_part2.php @@ -8,8 +8,7 @@ include("input_validate.php"); $keyval=$_GET["My_key"]; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $type_n=array(); diff --git a/sourcecodes/cross_valid.php b/sourcecodes/cross_valid.php index 8adbcdfe..9ed8ab07 100644 --- a/sourcecodes/cross_valid.php +++ b/sourcecodes/cross_valid.php @@ -46,8 +46,9 @@ function test_input($data) { } ?> + <?php -$varName_file = "/var/lib/genenet/bnw/".$keyval."name.txt"; +$varName_file = "/tmp/bnw/".$keyval."name.txt"; $varName_line = file_get_contents($varName_file); $varNamesArr = explode("\t",$varName_line); ?> @@ -55,6 +56,7 @@ $varNamesArr = explode("\t",$varName_line); + <!-- Site navigation menu --> <ul class="navbar2"> <li class="noHover"><p>Network ID:<br><?php print($keyval);?></p></li> @@ -74,14 +76,13 @@ $varNamesArr = explode("\t",$varName_line); <?php // $filename1="./data/".$keyval."looCV.txt"; // $filename2="./data/".$keyval."looCV_temp.txt"; -// $dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; -$filename1=$keyval."looCV.txt"; -$filename2=$keyval."looCV_temp.txt"; - $plotly_file=$keyval."loo_plotly.html"; -// $plotly_file_local = "./data/".$keyval."loo_plotly.html"; -// $pred_file_local = "./data/".$keyval."looCV.txt"; -if(file_exists($dir.$filename2)) + $dir="/tmp/bnw/"; +$filename1=$dir.$keyval."looCV.txt"; +$filename2=$dir.$keyval."looCV_temp.txt"; + $plotly_file=$dir.$keyval."loo_plotly.html"; + $plotly_file_local = "./data/".$keyval."loo_plotly.html"; + $pred_file_local = "./data/".$keyval."looCV.txt"; +if(file_exists($filename2)) {?> <br> <h2> Leave-one-out cross-validation results are being calculated</h2> @@ -90,25 +91,17 @@ if(file_exists($dir.$filename2)) <br> <?php } - else if(file_exists($dir.$filename1)) - { - $file_data = file_get_contents($dir.$plotly_file); - - ?> + else if(file_exists($filename1)) + {?> <div> - <object width="800" height="500" data=<?=$file_data?> + <object type="text/html" data=<?php print($plotly_file_local);?> width="800" height="500" > </object> </div> -<?php -$table_text = json_encode(file("file://".$dir.$filename1)); -?> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error,raw) { + d3.text("<?php print($pred_file_local);?>", function(error,raw) { var dsv=d3.dsvFormat("\t") - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data=dsv.parse(data2) + var data=dsv.parse(raw) var caption_text=data.pop() if (error) throw error; tabulate_caption("#table_div1",data,caption_text.CaseRow); @@ -116,7 +109,7 @@ $table_text = json_encode(file("file://".$dir.$filename1)); </script> </div> <br> - <a class=button2 href=<?php print("reroute.php?".$filename1);?>>Download cross-validation results</a> + <a class=button2 href=<?php print($pred_file_local);?>>Download cross-validation results</a> <br> <br> <h3>Perform leave-one-out cross-validation of another network variable<br></h3> @@ -139,8 +132,7 @@ $table_text = json_encode(file("file://".$dir.$filename1)); } else { ?> <h2>Perform leave-one-out cross-validation of network</h2> - -<p align="justify" style='font-size:18px'> +<p align="justify" style='font-size:18px'> Select the variable that you want to examine the predictions of below. <br> <br> diff --git a/sourcecodes/cv_plotly.py b/sourcecodes/cv_plotly.py index 05d0621d..c22e0dcc 100644 --- a/sourcecodes/cv_plotly.py +++ b/sourcecodes/cv_plotly.py @@ -1,7 +1,9 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 +#!/home/jziebart/python/Python-2.7.15/python import os import sys +#sys.path.append('/home/jziebart/.local/bin') +#sys.path.append('/home/jziebart/.local/lib') import plotly import plotly.graph_objs as go @@ -17,10 +19,9 @@ f=open(filename,"r") lines=f.readlines() #Read the last line to get the variable name line = lines.pop() -#line = map(string.strip,line.strip().split(" ")) -line = line.strip().split(" ") +line = map(string.strip,line.strip().split(" ")) varName = line[3][:-1] -plot_title = varName+" LOOCV" +plot_title = "<br>"+varName+" LOOCV" #remove header line header = lines.pop(0) @@ -28,11 +29,9 @@ header = lines.pop(0) typefile = netID+"type.txt" tf=open(typefile,"r") line=tf.readline() -#varnames = map(string.strip,line.strip().split("\t")) -varnames = line.strip().split("\t") +varnames = map(string.strip,line.strip().split("\t")) line=tf.readline() -#vartypes = map(string.strip,line.strip().split("\t")) -vartypes = line.strip().split("\t") +vartypes = map(string.strip,line.strip().split("\t")) varindex = varnames.index(varName) cd_type = int(vartypes[varindex]) @@ -48,8 +47,7 @@ if cd_type == 1: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) x.append(float(line[1])) y.append(float(line[2])) # line=f.readline() @@ -62,11 +60,7 @@ if cd_type == 1: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", - xaxis=dict( + xaxis=dict( autorange=True, title='Actual values', titlefont=dict( @@ -92,8 +86,7 @@ if cd_type == 1: else: #Make bar chart for discrete data #Get names of states - #header = map(string.strip,header.strip().split("\t")) - header = header.strip().split("\t") + header = map(string.strip,header.strip().split("\t")) states = header[2:] #Read the data actual = [] @@ -101,8 +94,7 @@ else: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) actual.append(line[1]) predict_x = line[2:] predict_x = [float(x) for x in predict_x] @@ -153,10 +145,6 @@ else: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", xaxis=dict( autorange=True, title='State', diff --git a/sourcecodes/cv_predictions.php b/sourcecodes/cv_predictions.php index 65915534..54a565ed 100644 --- a/sourcecodes/cv_predictions.php +++ b/sourcecodes/cv_predictions.php @@ -32,8 +32,7 @@ $keyval=valid_keyval($_GET["My_key"]); <li>This feature has recently been added to BNW and is still being tested. Please inform us of any issues.<br> Its use is briefly described <a href="help.php#crossvalid" target="_blank">here</a>.<br><br></li> <?php -// $dir="/tmp/bnw/"; - $dir="/var/lib/genenet/bnw/"; + $dir="/tmp/bnw/"; $loo_file1=$dir.$keyval."looCV_temp.txt"; $loo_file2=$dir.$keyval."looCV.txt"; if(file_exists($loo_file1)) @@ -54,7 +53,7 @@ if(file_exists($loo_file1)) ?> <?php $kfold_file1=$dir.$keyval."kfoldCV_temp.txt"; - $kfold_file2=$dir.$keyval."kfold_plotly.html"; + $kfold_file2=$dir.$keyval."kfoldCV.txt"; if(file_exists($kfold_file1)) {?> <li> <a class=button3 href="cv_predictions.php?My_key=<?php print($keyval);?>">k-fold cross-validation predictions are being calculated.<br>Click here to update status.</a> diff --git a/sourcecodes/data/LRlnetwork.json b/sourcecodes/data/LRlnetwork.json deleted file mode 100644 index 7ee3b56f..00000000 --- a/sourcecodes/data/LRlnetwork.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "nodes": [ - { - "data": { - "id": "1", - "label": "Node1" - } - } - ] -} diff --git a/sourcecodes/data/old/Backupfiles/evidencemodified b/sourcecodes/data/old/Backupfiles/evidencemodified deleted file mode 100644 index 9b3f7563..00000000 --- a/sourcecodes/data/old/Backupfiles/evidencemodified +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/Backupfiles/initialstructure b/sourcecodes/data/old/Backupfiles/initialstructure deleted file mode 100644 index 9ecf1bc7..00000000 --- a/sourcecodes/data/old/Backupfiles/initialstructure +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/Backupfiles/newintervention b/sourcecodes/data/old/Backupfiles/newintervention deleted file mode 100644 index d818a943..00000000 --- a/sourcecodes/data/old/Backupfiles/newintervention +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/Backupfiles/temp_evidence_file b/sourcecodes/data/old/Backupfiles/temp_evidence_file deleted file mode 100644 index b687ceaf..00000000 --- a/sourcecodes/data/old/Backupfiles/temp_evidence_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified \ No newline at end of file diff --git a/sourcecodes/data/old/Backupfiles/temp_intervention_file b/sourcecodes/data/old/Backupfiles/temp_intervention_file deleted file mode 100644 index cdf5ce0f..00000000 --- a/sourcecodes/data/old/Backupfiles/temp_intervention_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/newintervention \ No newline at end of file diff --git a/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure b/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure deleted file mode 100644 index 5d1c323d..00000000 --- a/sourcecodes/data/old/Backupfiles/temp_shell_file_initial_structure +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure \ No newline at end of file diff --git a/sourcecodes/data/old/evidencemodified b/sourcecodes/data/old/evidencemodified deleted file mode 100644 index 9b3f7563..00000000 --- a/sourcecodes/data/old/evidencemodified +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/example_sci_bk/Lluban.txt b/sourcecodes/data/old/example_sci_bk/Lluban.txt deleted file mode 100644 index 38108f00..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluban.txt +++ /dev/null @@ -1,15 +0,0 @@ -From To -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Genotype -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 -Phenotype Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 diff --git a/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt b/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt deleted file mode 100644 index 79295d7e..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt +++ /dev/null @@ -1,503 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 -2 -1.0008 -0.44837 0.21808 -1.196 -1 -0.29368 -0.53043 -1.0893 -0.10136 -2 0.70835 0.72886 -0.18098 -0.42907 -1 0.63703 0.86428 1.7013 0.1425 -1 -1.2402 -0.69712 -1.7002 -0.71634 -1 -1.1952 0.27155 -0.79413 -1.0965 -2 0.62914 0.94265 1.8385 0.6135 -1 -1.91 -2.379 -3.1094 -1.0924 -2 -0.83436 -0.90968 -1.3598 1.335 -1 0.15685 0.4766 1.2891 -1.3309 -2 0.7047 1.0623 1.9811 1.2821 -1 0.59747 -0.023123 0.88555 -0.8844 -1 -1.0557 -1.5548 -1.3016 -0.77687 -2 1.5206 2.0289 0.90366 1.8089 -1 0.65525 -0.47226 -1.1824 0.41863 -2 -0.39262 0.382 -0.64829 0.40947 -2 0.14966 0.22972 0.33797 0.69647 -1 -1.8836 -0.68534 -0.99941 -0.78961 -1 0.48181 0.01241 1.2145 0.16835 -2 1.4673 2.0438 2.4674 2.5234 -1 -1.3242 -0.80218 -1.6446 -0.31044 -1 -1.2471 -2.0351 -1.0296 -1.937 -1 0.23695 -0.01724 -0.32851 -0.16484 -1 -0.13986 -0.6065 -0.8491 -0.95538 -2 0.90888 1.0365 2.7222 1.3507 -1 -0.30556 -1.1546 -0.86033 -2.2006 -2 0.5391 0.99532 0.96947 1.1575 -2 1.1235 0.37982 0.64439 0.94362 -2 1.7073 1.9303 2.8018 1.9158 -1 -0.20553 -0.074104 -0.50073 -1.0697 -1 -0.27415 0.23076 -0.27564 -0.11286 -1 -1.304 -1.1213 -0.71793 -1.3462 -2 0.54315 0.55846 0.87411 1.2432 -1 -1.0659 -0.38067 -1.4372 -2.0927 -1 0.21278 -1.0115 -1.0984 -0.72751 -1 -2.9061 -1.3118 -3.8372 -2.0448 -2 -0.69608 -0.61145 -1.0037 0.12181 -1 0.66835 0.018886 -1.0081 -1.4165 -1 0.32575 -0.51767 1.0187 -0.40914 -2 0.65837 1.2791 1.8388 2.2906 -2 0.37574 0.21618 -0.89435 1.2643 -1 0.13513 -0.31405 -0.16057 0.77712 -2 0.16054 0.40635 0.036165 1.6374 -1 1.9393 1.5717 2.6922 1.1933 -1 -0.59118 -0.47154 -0.20293 -1.5576 -1 -0.35938 -0.49565 -0.20837 0.61043 -2 -0.57133 0.15921 -0.44158 0.43312 -1 0.31835 0.49002 2.2029 0.17685 -1 -0.0093708 -0.85889 -1.0934 -1.6905 -1 -0.90501 -1.4637 -1.5526 -1.828 -2 0.11531 -0.022781 0.88843 0.8607 -1 0.34978 -0.34306 0.95301 -0.056177 -2 -0.22236 -0.13023 0.37608 0.18027 -1 -0.90103 -0.38393 -1.1513 -0.78153 -2 0.66848 0.81005 1.3945 3.3654 -2 0.10539 0.59781 0.77864 0.63865 -1 -1.15 -1.4531 -2.929 -1.6867 -1 0.20842 -0.0039076 -0.12879 -0.31459 -2 0.52155 1.248 1.0411 1.9656 -2 0.041926 0.86223 1.2222 1.0289 -1 -0.70875 -0.15791 -1.1581 -0.77456 -1 -1.1701 -0.57889 -0.8843 -0.11873 -2 0.98106 1.0805 0.95484 2.1834 -2 0.26676 0.7527 0.61491 1.9024 -1 -0.64765 0.19831 -1.4399 1.3127 -2 0.92209 2.2111 1.208 2.7402 -2 -0.93755 -0.26009 0.54448 0.20265 -2 1.2403 1.8468 1.6169 1.8359 -1 -0.1313 0.14288 -0.48278 -0.96105 -1 -0.7222 -0.25191 -1.2122 -0.59027 -2 -0.57013 -0.061267 -0.5438 0.18234 -1 -1.5355 -1.1998 -2.6613 -0.2634 -2 0.86507 0.60361 1.2411 -0.29711 -1 -0.60117 -0.7424 -0.79575 -0.5736 -1 -0.91776 -1.5669 -2.1735 -0.56602 -2 0.9917 2.3088 1.7993 2.645 -1 0.17017 0.53321 0.84278 -1.4458 -2 -0.22306 0.262 -0.86259 0.87407 -1 -0.42107 -0.69813 -0.48166 -1.009 -1 0.46913 -0.76457 0.11077 -0.21258 -1 0.066036 -0.48665 -0.74847 0.38785 -1 0.16465 -0.57268 0.19043 0.23 -1 -1.2044 -2.2027 -2.9688 -2.5546 -1 -0.3031 -2.0277 -1.3027 -2.6541 -2 -0.20063 0.3886 1.2227 0.84669 -2 -0.23897 0.0036995 -1.4547 0.37173 -1 2.197 0.41411 0.68339 -1.2721 -2 1.9922 2.748 3.0416 3.1268 -1 -1.7922 -1.2233 -3.1352 -0.98514 -2 0.66968 0.81377 1.9112 1.7507 -2 1.048 1.3718 1.5938 1.4847 -1 0.56532 -0.97153 -0.91123 -2.4761 -2 -0.53609 -0.30043 -0.65398 -0.38562 -2 1.0012 1.3344 2.0595 2.8441 -1 -3.4639 -2.4231 -3.9055 -2.3575 -1 0.79272 -0.78962 -0.40706 -1.1306 -1 0.78178 0.32152 0.79399 0.14086 -2 -0.28587 0.20138 0.78238 2.1602 -2 1.4137 1.6184 2.2458 2.1799 -2 1.409 1.6079 2.4053 2.0587 -2 -0.049571 1.1163 2.0792 0.99457 -1 -1.394 -0.67782 -2.2302 -0.33872 -2 0.5374 1.8476 2.205 2.0025 -1 -1.4988 -0.90782 -1.4206 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mode 100644 index 88bbd3ba..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt +++ /dev/null @@ -1,10 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Genotype -> Gene3; -Genotype -> Gene1; -Gene3 -> Phenotype; -Gene2 -> Gene3; -Gene2 -> Phenotype; -Gene1 -> Gene2; -} \ No newline at end of file diff --git a/sourcecodes/data/old/example_sci_bk/Lluk.txt b/sourcecodes/data/old/example_sci_bk/Lluk.txt deleted file mode 100644 index 83b33d23..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluk.txt +++ /dev/null @@ -1 +0,0 @@ -1000 diff --git a/sourcecodes/data/old/example_sci_bk/Llumap.txt b/sourcecodes/data/old/example_sci_bk/Llumap.txt deleted file mode 100644 index 958281d5..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llumap.txt +++ /dev/null @@ -1,5 +0,0 @@ -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/old/example_sci_bk/Llumapdata.txt b/sourcecodes/data/old/example_sci_bk/Llumapdata.txt deleted file mode 100644 index d684ea06..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llumapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene1 Gene2 Gene3 Phenotype diff --git a/sourcecodes/data/old/example_sci_bk/Lluname.txt b/sourcecodes/data/old/example_sci_bk/Lluname.txt deleted file mode 100644 index f3a1f5bf..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt deleted file mode 100644 index bdc07cbd..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt +++ /dev/null @@ -1,433 +0,0 @@ -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1 0.4860 -2 0.5140 -Gene1 1 -250 150 -1 1 -1 3 --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 0.2633 --0.8401 0.2797 --0.7700 0.2956 --0.7000 0.3110 --0.6300 0.3256 --0.5599 0.3392 --0.4899 0.3517 --0.4199 0.3629 --0.3498 0.3726 --0.2798 0.3808 --0.2098 0.3873 --0.1397 0.3920 --0.0697 0.3948 -0.0003 0.3958 -0.0704 0.3948 -0.1404 0.3920 -0.2104 0.3872 -0.2805 0.3807 -0.3505 0.3726 -0.4205 0.3628 -0.4906 0.3516 -0.5606 0.3391 -0.6306 0.3254 -0.7007 0.3108 -0.7707 0.2955 -0.8407 0.2795 -0.9108 0.2631 -0.9808 0.2465 -1.0508 0.2299 -1.1209 0.2133 -1.1909 0.1969 -1.2609 0.1810 -1.3310 0.1655 -1.4010 0.1507 -1.4710 0.1365 -1.5411 0.1230 -1.6111 0.1103 -1.6811 0.0985 -1.7512 0.0875 -1.8212 0.0774 -1.8912 0.0681 -1.9613 0.0596 -2.0313 0.0520 -2.1013 0.0451 -2.1714 0.0389 -2.2414 0.0334 -2.3114 0.0286 -2.3815 0.0243 -2.4515 0.0206 -2.5215 0.0173 -2.5916 0.0145 -2.6616 0.0121 -2.7316 0.0101 -2.8017 0.0083 -2.8717 0.0068 -2.9417 0.0056 -3.0118 0.0046 -3.0818 0.0037 -3.1518 0.0030 -3.2219 0.0024 -3.2919 0.0019 -3.3619 0.0015 -3.4320 0.0012 -3.5020 0.0009 -Gene2 1 -250 150 -1 2 -2 4 5 --3.5862 0.0008 --3.5124 0.0010 --3.4385 0.0013 --3.3647 0.0016 --3.2909 0.0020 --3.2171 0.0026 --3.1432 0.0032 --3.0694 0.0041 --2.9956 0.0050 --2.9218 0.0062 --2.8479 0.0077 --2.7741 0.0094 --2.7003 0.0114 --2.6264 0.0138 --2.5526 0.0166 --2.4788 0.0199 --2.4050 0.0237 --2.3311 0.0281 --2.2573 0.0331 --2.1835 0.0388 --2.1097 0.0453 --2.0358 0.0526 --1.9620 0.0607 --1.8882 0.0696 --1.8143 0.0795 --1.7405 0.0903 --1.6667 0.1021 --1.5929 0.1147 --1.5190 0.1282 --1.4452 0.1426 --1.3714 0.1578 --1.2976 0.1736 --1.2237 0.1900 --1.1499 0.2069 --1.0761 0.2241 --1.0022 0.2414 --0.9284 0.2587 --0.8546 0.2758 --0.7808 0.2924 --0.7069 0.3084 --0.6331 0.3236 --0.5593 0.3377 --0.4855 0.3506 --0.4116 0.3621 --0.3378 0.3719 --0.2640 0.3800 --0.1901 0.3863 --0.1163 0.3905 --0.0425 0.3927 -0.0313 0.3929 -0.1052 0.3910 -0.1790 0.3870 -0.2528 0.3811 -0.3266 0.3732 -0.4005 0.3636 -0.4743 0.3524 -0.5481 0.3397 -0.6220 0.3258 -0.6958 0.3108 -0.7696 0.2949 -0.8434 0.2783 -0.9173 0.2613 -0.9911 0.2440 -1.0649 0.2267 -1.1387 0.2095 -1.2126 0.1925 -1.2864 0.1760 -1.3602 0.1601 -1.4341 0.1449 -1.5079 0.1304 -1.5817 0.1167 -1.6555 0.1039 -1.7294 0.0920 -1.8032 0.0811 -1.8770 0.0711 -1.9508 0.0620 -2.0247 0.0537 -2.0985 0.0464 -2.1723 0.0398 -2.2462 0.0340 -2.3200 0.0288 -2.3938 0.0243 -2.4676 0.0205 -2.5415 0.0171 -2.6153 0.0142 -2.6891 0.0117 -2.7629 0.0097 -2.8368 0.0079 -2.9106 0.0064 -2.9844 0.0052 -3.0583 0.0042 -3.1321 0.0034 -3.2059 0.0027 -3.2797 0.0021 -3.3536 0.0017 -3.4274 0.0013 -3.5012 0.0010 -3.5750 0.0008 -3.6489 0.0006 -3.7227 0.0005 -3.7965 0.0004 -Gene3 1 -250 150 -2 1 3 -1 5 --4.3571 0.0001 --4.2762 0.0001 --4.1954 0.0001 --4.1145 0.0001 --4.0336 0.0002 --3.9527 0.0002 --3.8719 0.0003 --3.7910 0.0004 --3.7101 0.0006 --3.6293 0.0008 --3.5484 0.0010 --3.4675 0.0013 --3.3866 0.0018 --3.3058 0.0023 --3.2249 0.0029 --3.1440 0.0037 --3.0632 0.0047 --2.9823 0.0059 --2.9014 0.0074 --2.8205 0.0092 --2.7397 0.0113 --2.6588 0.0139 --2.5779 0.0170 --2.4971 0.0206 --2.4162 0.0248 --2.3353 0.0297 --2.2544 0.0354 --2.1736 0.0419 --2.0927 0.0493 --2.0118 0.0576 --1.9310 0.0669 --1.8501 0.0773 --1.7692 0.0887 --1.6883 0.1012 --1.6075 0.1147 --1.5266 0.1292 --1.4457 0.1447 --1.3648 0.1610 --1.2840 0.1781 --1.2031 0.1958 --1.1222 0.2139 --1.0414 0.2323 --0.9605 0.2507 --0.8796 0.2688 --0.7987 0.2866 --0.7179 0.3036 --0.6370 0.3197 --0.5561 0.3345 --0.4753 0.3479 --0.3944 0.3597 --0.3135 0.3695 --0.2326 0.3773 --0.1518 0.3828 --0.0709 0.3861 -0.0100 0.3870 -0.0908 0.3855 -0.1717 0.3817 -0.2526 0.3756 -0.3335 0.3673 -0.4143 0.3570 -0.4952 0.3449 -0.5761 0.3311 -0.6569 0.3160 -0.7378 0.2996 -0.8187 0.2824 -0.8996 0.2645 -0.9804 0.2463 -1.0613 0.2279 -1.1422 0.2095 -1.2230 0.1915 -1.3039 0.1740 -1.3848 0.1570 -1.4657 0.1409 -1.5465 0.1256 -1.6274 0.1114 -1.7083 0.0981 -1.7891 0.0859 -1.8700 0.0747 -1.9509 0.0646 -2.0318 0.0555 -2.1126 0.0474 -2.1935 0.0402 -2.2744 0.0340 -2.3552 0.0285 -2.4361 0.0237 -2.5170 0.0197 -2.5979 0.0162 -2.6787 0.0132 -2.7596 0.0108 -2.8405 0.0087 -2.9213 0.0070 -3.0022 0.0056 -3.0831 0.0044 -3.1640 0.0035 -3.2448 0.0027 -3.3257 0.0021 -3.4066 0.0016 -3.4874 0.0013 -3.5683 0.0010 -3.6492 0.0007 -3.7301 0.0006 -Phenotype 1 -250 150 -2 3 4 -0 --3.5574 0.0010 --3.4806 0.0013 --3.4037 0.0016 --3.3268 0.0021 --3.2499 0.0026 --3.1731 0.0033 --3.0962 0.0042 --3.0193 0.0052 --2.9425 0.0065 --2.8656 0.0080 --2.7887 0.0098 --2.7118 0.0120 --2.6350 0.0146 --2.5581 0.0176 --2.4812 0.0212 --2.4044 0.0253 --2.3275 0.0300 --2.2506 0.0354 --2.1737 0.0416 --2.0969 0.0486 --2.0200 0.0564 --1.9431 0.0651 --1.8663 0.0748 --1.7894 0.0854 --1.7125 0.0970 --1.6356 0.1096 --1.5588 0.1230 --1.4819 0.1374 --1.4050 0.1526 --1.3282 0.1685 --1.2513 0.1850 --1.1744 0.2021 --1.0975 0.2195 --1.0207 0.2370 --0.9438 0.2545 --0.8669 0.2718 --0.7901 0.2887 --0.7132 0.3049 --0.6363 0.3202 --0.5594 0.3344 --0.4826 0.3473 --0.4057 0.3587 --0.3288 0.3684 --0.2520 0.3763 --0.1751 0.3822 --0.0982 0.3860 --0.0213 0.3877 -0.0555 0.3872 -0.1324 0.3846 -0.2093 0.3798 -0.2861 0.3731 -0.3630 0.3644 -0.4399 0.3539 -0.5168 0.3418 -0.5936 0.3283 -0.6705 0.3136 -0.7474 0.2979 -0.8242 0.2813 -0.9011 0.2643 -0.9780 0.2468 -1.0549 0.2293 -1.1317 0.2118 -1.2086 0.1945 -1.2855 0.1777 -1.3623 0.1614 -1.4392 0.1458 -1.5161 0.1310 -1.5930 0.1170 -1.6698 0.1039 -1.7467 0.0918 -1.8236 0.0806 -1.9004 0.0704 -1.9773 0.0612 -2.0542 0.0529 -2.1311 0.0454 -2.2079 0.0388 -2.2848 0.0329 -2.3617 0.0278 -2.4385 0.0234 -2.5154 0.0195 -2.5923 0.0162 -2.6692 0.0134 -2.7460 0.0110 -2.8229 0.0090 -2.8998 0.0073 -2.9766 0.0059 -3.0535 0.0047 -3.1304 0.0038 -3.2073 0.0030 -3.2841 0.0024 -3.3610 0.0019 -3.4379 0.0015 -3.5147 0.0011 -3.5916 0.0009 -3.6685 0.0007 -3.7454 0.0005 -3.8222 0.0004 -3.8991 0.0003 -3.9760 0.0002 -4.0528 0.0002 -4.1297 0.0001 diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt deleted file mode 100644 index 7e6f0d97..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt +++ /dev/null @@ -1,433 +0,0 @@ -1 -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1.0000 1.0000 -Gene1 1 -250 150 -1 1 -1 3 --3.5013 0.0000 --3.4313 0.0000 --3.3613 0.0000 --3.2912 0.0000 --3.2212 0.0000 --3.1512 0.0000 --3.0811 0.0000 --3.0111 0.0000 --2.9411 0.0000 --2.8710 0.0000 --2.8010 0.0000 --2.7310 0.0000 --2.6609 0.0000 --2.5909 0.0000 --2.5209 0.0001 --2.4508 0.0002 --2.3808 0.0004 --2.3108 0.0007 --2.2407 0.0014 --2.1707 0.0026 --2.1007 0.0046 --2.0306 0.0079 --1.9606 0.0133 --1.8906 0.0217 --1.8205 0.0344 --1.7505 0.0529 --1.6805 0.0791 --1.6104 0.1147 --1.5404 0.1615 --1.4704 0.2207 --1.4003 0.2928 --1.3303 0.3771 --1.2603 0.4715 --1.1902 0.5723 --1.1202 0.6743 --1.0502 0.7713 --0.9801 0.8564 --0.9101 0.9232 --0.8401 0.9660 --0.7700 0.9813 --0.7000 0.9676 --0.6300 0.9263 --0.5599 0.8608 --0.4899 0.7765 --0.4199 0.6800 --0.3498 0.5781 --0.2798 0.4771 --0.2098 0.3822 --0.1397 0.2973 --0.0697 0.2244 -0.0003 0.1645 -0.0704 0.1170 -0.1404 0.0808 -0.2104 0.0542 -0.2805 0.0353 -0.3505 0.0223 -0.4205 0.0137 -0.4906 0.0081 -0.5606 0.0047 -0.6306 0.0026 -0.7007 0.0014 -0.7707 0.0008 -0.8407 0.0004 -0.9108 0.0002 -0.9808 0.0001 -1.0508 0.0000 -1.1209 0.0000 -1.1909 0.0000 -1.2609 0.0000 -1.3310 0.0000 -1.4010 0.0000 -1.4710 0.0000 -1.5411 0.0000 -1.6111 0.0000 -1.6811 0.0000 -1.7512 0.0000 -1.8212 0.0000 -1.8912 0.0000 -1.9613 0.0000 -2.0313 0.0000 -2.1013 0.0000 -2.1714 0.0000 -2.2414 0.0000 -2.3114 0.0000 -2.3815 0.0000 -2.4515 0.0000 -2.5215 0.0000 -2.5916 0.0000 -2.6616 0.0000 -2.7316 0.0000 -2.8017 0.0000 -2.8717 0.0000 -2.9417 0.0000 -3.0118 0.0000 -3.0818 0.0000 -3.1518 0.0000 -3.2219 0.0000 -3.2919 0.0000 -3.3619 0.0000 -3.4320 0.0000 -3.5020 0.0000 -Gene2 1 -250 150 -1 2 -2 4 5 --3.5862 0.0000 --3.5124 0.0000 --3.4385 0.0000 --3.3647 0.0000 --3.2909 0.0000 --3.2171 0.0001 --3.1432 0.0001 --3.0694 0.0002 --2.9956 0.0003 --2.9218 0.0005 --2.8479 0.0008 --2.7741 0.0012 --2.7003 0.0018 --2.6264 0.0028 --2.5526 0.0041 --2.4788 0.0060 --2.4050 0.0087 --2.3311 0.0124 --2.2573 0.0175 --2.1835 0.0242 --2.1097 0.0329 --2.0358 0.0441 --1.9620 0.0583 --1.8882 0.0759 --1.8143 0.0974 --1.7405 0.1230 --1.6667 0.1530 --1.5929 0.1874 --1.5190 0.2262 --1.4452 0.2689 --1.3714 0.3148 --1.2976 0.3631 --1.2237 0.4126 --1.1499 0.4617 --1.0761 0.5089 --1.0022 0.5525 --0.9284 0.5908 --0.8546 0.6224 --0.7808 0.6458 --0.7069 0.6600 --0.6331 0.6644 --0.5593 0.6588 --0.4855 0.6434 --0.4116 0.6190 --0.3378 0.5866 --0.2640 0.5475 --0.1901 0.5034 --0.1163 0.4558 --0.0425 0.4066 -0.0313 0.3573 -0.1052 0.3092 -0.1790 0.2636 -0.2528 0.2213 -0.3266 0.1830 -0.4005 0.1491 -0.4743 0.1197 -0.5481 0.0946 -0.6220 0.0736 -0.6958 0.0565 -0.7696 0.0426 -0.8434 0.0317 -0.9173 0.0233 -0.9911 0.0168 -1.0649 0.0119 -1.1387 0.0084 -1.2126 0.0058 -1.2864 0.0039 -1.3602 0.0026 -1.4341 0.0017 -1.5079 0.0011 -1.5817 0.0007 -1.6555 0.0005 -1.7294 0.0003 -1.8032 0.0002 -1.8770 0.0001 -1.9508 0.0001 -2.0247 0.0000 -2.0985 0.0000 -2.1723 0.0000 -2.2462 0.0000 -2.3200 0.0000 -2.3938 0.0000 -2.4676 0.0000 -2.5415 0.0000 -2.6153 0.0000 -2.6891 0.0000 -2.7629 0.0000 -2.8368 0.0000 -2.9106 0.0000 -2.9844 0.0000 -3.0583 0.0000 -3.1321 0.0000 -3.2059 0.0000 -3.2797 0.0000 -3.3536 0.0000 -3.4274 0.0000 -3.5012 0.0000 -3.5750 0.0000 -3.6489 0.0000 -3.7227 0.0000 -3.7965 0.0000 -Gene3 1 -250 150 -2 1 3 -1 5 --4.3571 0.0002 --4.2762 0.0002 --4.1954 0.0003 --4.1145 0.0004 --4.0336 0.0005 --3.9527 0.0007 --3.8719 0.0010 --3.7910 0.0013 --3.7101 0.0017 --3.6293 0.0022 --3.5484 0.0028 --3.4675 0.0036 --3.3866 0.0046 --3.3058 0.0059 --3.2249 0.0074 --3.1440 0.0093 --3.0632 0.0115 --2.9823 0.0143 --2.9014 0.0175 --2.8205 0.0214 --2.7397 0.0260 --2.6588 0.0313 --2.5779 0.0374 --2.4971 0.0445 --2.4162 0.0526 --2.3353 0.0617 --2.2544 0.0719 --2.1736 0.0833 --2.0927 0.0958 --2.0118 0.1095 --1.9310 0.1243 --1.8501 0.1403 --1.7692 0.1572 --1.6883 0.1750 --1.6075 0.1936 --1.5266 0.2127 --1.4457 0.2322 --1.3648 0.2518 --1.2840 0.2713 --1.2031 0.2904 --1.1222 0.3088 --1.0414 0.3263 --0.9605 0.3424 --0.8796 0.3570 --0.7987 0.3698 --0.7179 0.3806 --0.6370 0.3890 --0.5561 0.3951 --0.4753 0.3987 --0.3944 0.3996 --0.3135 0.3980 --0.2326 0.3937 --0.1518 0.3869 --0.0709 0.3778 -0.0100 0.3665 -0.0908 0.3532 -0.1717 0.3381 -0.2526 0.3216 -0.3335 0.3039 -0.4143 0.2852 -0.4952 0.2660 -0.5761 0.2464 -0.6569 0.2268 -0.7378 0.2074 -0.8187 0.1884 -0.8996 0.1700 -0.9804 0.1524 -1.0613 0.1358 -1.1422 0.1201 -1.2230 0.1056 -1.3039 0.0922 -1.3848 0.0800 -1.4657 0.0690 -1.5465 0.0591 -1.6274 0.0502 -1.7083 0.0425 -1.7891 0.0357 -1.8700 0.0297 -1.9509 0.0246 -2.0318 0.0203 -2.1126 0.0166 -2.1935 0.0135 -2.2744 0.0109 -2.3552 0.0087 -2.4361 0.0070 -2.5170 0.0055 -2.5979 0.0043 -2.6787 0.0034 -2.7596 0.0026 -2.8405 0.0020 -2.9213 0.0015 -3.0022 0.0012 -3.0831 0.0009 -3.1640 0.0007 -3.2448 0.0005 -3.3257 0.0004 -3.4066 0.0003 -3.4874 0.0002 -3.5683 0.0001 -3.6492 0.0001 -3.7301 0.0001 -Phenotype 1 -250 150 -2 3 4 -0 --3.5574 0.0004 --3.4806 0.0006 --3.4037 0.0008 --3.3268 0.0012 --3.2499 0.0016 --3.1731 0.0022 --3.0962 0.0030 --3.0193 0.0040 --2.9425 0.0054 --2.8656 0.0071 --2.7887 0.0093 --2.7118 0.0121 --2.6350 0.0155 --2.5581 0.0198 --2.4812 0.0250 --2.4044 0.0313 --2.3275 0.0389 --2.2506 0.0479 --2.1737 0.0584 --2.0969 0.0706 --2.0200 0.0846 --1.9431 0.1005 --1.8663 0.1184 --1.7894 0.1381 --1.7125 0.1597 --1.6356 0.1831 --1.5588 0.2081 --1.4819 0.2343 --1.4050 0.2615 --1.3282 0.2893 --1.2513 0.3173 --1.1744 0.3448 --1.0975 0.3714 --1.0207 0.3966 --0.9438 0.4197 --0.8669 0.4402 --0.7901 0.4576 --0.7132 0.4716 --0.6363 0.4816 --0.5594 0.4875 --0.4826 0.4891 --0.4057 0.4864 --0.3288 0.4794 --0.2520 0.4684 --0.1751 0.4535 --0.0982 0.4353 --0.0213 0.4140 -0.0555 0.3904 -0.1324 0.3648 -0.2093 0.3379 -0.2861 0.3102 -0.3630 0.2822 -0.4399 0.2545 -0.5168 0.2275 -0.5936 0.2016 -0.6705 0.1770 -0.7474 0.1541 -0.8242 0.1329 -0.9011 0.1136 -0.9780 0.0963 -1.0549 0.0809 -1.1317 0.0673 -1.2086 0.0556 -1.2855 0.0455 -1.3623 0.0368 -1.4392 0.0296 -1.5161 0.0236 -1.5930 0.0186 -1.6698 0.0146 -1.7467 0.0113 -1.8236 0.0087 -1.9004 0.0066 -1.9773 0.0050 -2.0542 0.0037 -2.1311 0.0028 -2.2079 0.0020 -2.2848 0.0015 -2.3617 0.0011 -2.4385 0.0008 -2.5154 0.0005 -2.5923 0.0004 -2.6692 0.0003 -2.7460 0.0002 -2.8229 0.0001 -2.8998 0.0001 -2.9766 0.0001 -3.0535 0.0000 -3.1304 0.0000 -3.2073 0.0000 -3.2841 0.0000 -3.3610 0.0000 -3.4379 0.0000 -3.5147 0.0000 -3.5916 0.0000 -3.6685 0.0000 -3.7454 0.0000 -3.8222 0.0000 -3.8991 0.0000 -3.9760 0.0000 -4.0528 0.0000 -4.1297 0.0000 diff --git a/sourcecodes/data/old/example_sci_bk/Llunlevels.txt b/sourcecodes/data/old/example_sci_bk/Llunlevels.txt deleted file mode 100644 index 714e56bd..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llunlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype 1 2 - diff --git a/sourcecodes/data/old/example_sci_bk/Llunnode.txt b/sourcecodes/data/old/example_sci_bk/Llunnode.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llunnode.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/old/example_sci_bk/Llunrows.txt b/sourcecodes/data/old/example_sci_bk/Llunrows.txt deleted file mode 100644 index c15fb720..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llunrows.txt +++ /dev/null @@ -1 +0,0 @@ -501 diff --git a/sourcecodes/data/old/example_sci_bk/Lluparent.txt b/sourcecodes/data/old/example_sci_bk/Lluparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt deleted file mode 100644 index bcf72d97..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt +++ /dev/null @@ -1,6 +0,0 @@ -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/old/example_sci_bk/Llustructure_input_temp.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt deleted file mode 100644 index 95aa7a5d..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt +++ /dev/null @@ -1,6 +0,0 @@ -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/old/example_sci_bk/Llustructure_old.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt deleted file mode 100644 index 5b464577..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt +++ /dev/null @@ -1,5 +0,0 @@ -Genotype 0.4860 0.5140 -Gene3 0.0001 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0006 0.0008 0.0010 0.0013 0.0018 0.0023 0.0029 0.0037 0.0047 0.0059 0.0074 0.0092 0.0113 0.0139 0.0170 0.0206 0.0248 0.0297 0.0354 0.0419 0.0493 0.0576 0.0669 0.0773 0.0887 0.1012 0.1147 0.1292 0.1447 0.1610 0.1781 0.1958 0.2139 0.2323 0.2507 0.2688 0.2866 0.3036 0.3197 0.3345 0.3479 0.3597 0.3695 0.3773 0.3828 0.3861 0.3870 0.3855 0.3817 0.3756 0.3673 0.3570 0.3449 0.3311 0.3160 0.2996 0.2824 0.2645 0.2463 0.2279 0.2095 0.1915 0.1740 0.1570 0.1409 0.1256 0.1114 0.0981 0.0859 0.0747 0.0646 0.0555 0.0474 0.0402 0.0340 0.0285 0.0237 0.0197 0.0162 0.0132 0.0108 0.0087 0.0070 0.0056 0.0044 0.0035 0.0027 0.0021 0.0016 0.0013 0.0010 0.0007 0.0006 -Gene1 0.0009 0.0012 0.0015 0.0019 0.0024 0.0030 0.0037 0.0046 0.0056 0.0069 0.0083 0.0101 0.0121 0.0145 0.0174 0.0206 0.0243 0.0286 0.0335 0.0389 0.0451 0.0520 0.0597 0.0682 0.0775 0.0876 0.0986 0.1105 0.1231 0.1366 0.1508 0.1657 0.1811 0.1971 0.2134 0.2300 0.2467 0.2633 0.2797 0.2956 0.3110 0.3256 0.3392 0.3517 0.3629 0.3726 0.3808 0.3873 0.3920 0.3948 0.3958 0.3948 0.3920 0.3872 0.3807 0.3726 0.3628 0.3516 0.3391 0.3254 0.3108 0.2955 0.2795 0.2631 0.2465 0.2299 0.2133 0.1969 0.1810 0.1655 0.1507 0.1365 0.1230 0.1103 0.0985 0.0875 0.0774 0.0681 0.0596 0.0520 0.0451 0.0389 0.0334 0.0286 0.0243 0.0206 0.0173 0.0145 0.0121 0.0101 0.0083 0.0068 0.0056 0.0046 0.0037 0.0030 0.0024 0.0019 0.0015 0.0012 0.0009 -Phenotype 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0042 0.0052 0.0065 0.0080 0.0098 0.0120 0.0146 0.0176 0.0212 0.0253 0.0300 0.0354 0.0416 0.0486 0.0564 0.0651 0.0748 0.0854 0.0970 0.1096 0.1230 0.1374 0.1526 0.1685 0.1850 0.2021 0.2195 0.2370 0.2545 0.2718 0.2887 0.3049 0.3202 0.3344 0.3473 0.3587 0.3684 0.3763 0.3822 0.3860 0.3877 0.3872 0.3846 0.3798 0.3731 0.3644 0.3539 0.3418 0.3283 0.3136 0.2979 0.2813 0.2643 0.2468 0.2293 0.2118 0.1945 0.1777 0.1614 0.1458 0.1310 0.1170 0.1039 0.0918 0.0806 0.0704 0.0612 0.0529 0.0454 0.0388 0.0329 0.0278 0.0234 0.0195 0.0162 0.0134 0.0110 0.0090 0.0073 0.0059 0.0047 0.0038 0.0030 0.0024 0.0019 0.0015 0.0011 0.0009 0.0007 0.0005 0.0004 0.0003 0.0002 0.0002 0.0001 -Gene2 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0041 0.0050 0.0062 0.0077 0.0094 0.0114 0.0138 0.0166 0.0199 0.0237 0.0281 0.0331 0.0388 0.0453 0.0526 0.0607 0.0696 0.0795 0.0903 0.1021 0.1147 0.1282 0.1426 0.1578 0.1736 0.1900 0.2069 0.2241 0.2414 0.2587 0.2758 0.2924 0.3084 0.3236 0.3377 0.3506 0.3621 0.3719 0.3800 0.3863 0.3905 0.3927 0.3929 0.3910 0.3870 0.3811 0.3732 0.3636 0.3524 0.3397 0.3258 0.3108 0.2949 0.2783 0.2613 0.2440 0.2267 0.2095 0.1925 0.1760 0.1601 0.1449 0.1304 0.1167 0.1039 0.0920 0.0811 0.0711 0.0620 0.0537 0.0464 0.0398 0.0340 0.0288 0.0243 0.0205 0.0171 0.0142 0.0117 0.0097 0.0079 0.0064 0.0052 0.0042 0.0034 0.0027 0.0021 0.0017 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004 diff --git a/sourcecodes/data/old/example_sci_bk/Lluthr.txt b/sourcecodes/data/old/example_sci_bk/Lluthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/old/example_sci_bk/Llutier.txt b/sourcecodes/data/old/example_sci_bk/Llutier.txt deleted file mode 100644 index da7084fb..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llutier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,1,Genotype,Tier2,3,Gene1,Gene2,Gene3,Tier3,1,Phenotype, \ No newline at end of file diff --git a/sourcecodes/data/old/example_sci_bk/Llutype.txt b/sourcecodes/data/old/example_sci_bk/Llutype.txt deleted file mode 100644 index 9ea66ce4..00000000 --- a/sourcecodes/data/old/example_sci_bk/Llutype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 diff --git a/sourcecodes/data/old/example_sci_bk/Lluvar.txt b/sourcecodes/data/old/example_sci_bk/Lluvar.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluvar.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/old/example_sci_bk/Lluvardata.txt b/sourcecodes/data/old/example_sci_bk/Lluvardata.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluvardata.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/old/example_sci_bk/Lluvarname.txt b/sourcecodes/data/old/example_sci_bk/Lluvarname.txt deleted file mode 100644 index 3fe283bd..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluvarname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype \ No newline at end of file diff --git a/sourcecodes/data/old/example_sci_bk/Lluwhite.txt b/sourcecodes/data/old/example_sci_bk/Lluwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/old/example_sci_bk/Lluwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh deleted file mode 100644 index ee0dde13..00000000 --- a/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified Llu -fi -exit diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh deleted file mode 100644 index adde14dd..00000000 --- a/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Llu -fi -exit diff --git a/sourcecodes/data/old/examplecar/OVIban.txt b/sourcecodes/data/old/examplecar/OVIban.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/old/examplecar/OVIban.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt b/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt deleted file mode 100644 index 3a2846cf..00000000 --- a/sourcecodes/data/old/examplecar/OVIcontinuous_input.txt +++ /dev/null @@ -1,1004 +0,0 @@ -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 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1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 6.89466 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.30596 2 2 2 1 1 3 1 1 2 2 1 -2 1 2 1 1 1 1 6.80188 1 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 4.86438 1 3 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.90783 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.971687 2 3 2 1 1 1 2 2 1 1 1 -2 1 2 1 1 2 1 1.88183 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.17229 1 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.927847 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.36548 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.00101 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.28421 1 1 1 1 2 1 2 2 1 1 1 -1 1 1 1 1 1 1 1.86953 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 9.0133 1 2 2 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.439457 2 2 2 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 4.34038 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.32347 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 6.60777 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.806183 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 7.83139 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.49472 1 1 1 1 2 2 1 1 1 1 1 -2 1 2 1 1 1 1 0.942534 1 2 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.70449 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.0436 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.93414 1 3 3 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 2.13185 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.262005 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 12.7252 1 2 2 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 0.465012 1 1 1 1 1 1 2 2 1 1 1 -1 1 2 1 1 1 1 0.455832 1 1 1 1 1 3 1 1 1 1 1 -2 1 1 1 1 1 1 5.52702 1 1 1 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 4.37922 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 8.52767 1 2 2 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 2.53081 1 2 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.34317 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.24552 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.39164 2 3 3 1 2 1 1 2 1 1 1 -2 1 1 1 1 1 1 0.635824 1 1 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 0.810242 2 3 3 2 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 20.3734 1 2 2 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 0.314643 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.93743 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.55162 2 3 3 1 2 3 1 2 1 1 1 -1 1 2 1 1 1 1 0.729802 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.0873788 2 3 3 1 2 2 1 1 1 1 1 -1 1 1 1 1 1 1 2.09206 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.834649 2 3 3 1 2 3 1 1 1 1 1 -1 1 2 1 1 1 1 9.7003 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 4.45689 1 1 1 1 1 2 1 1 2 1 1 -2 1 1 1 1 1 1 0.802165 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 5.66099 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.61237 1 1 1 1 1 3 1 1 2 2 1 -1 1 1 1 1 1 1 2.97608 1 1 1 2 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.48756 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.87253 2 2 2 2 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 7.42702 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.209732 2 3 3 2 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.55715 2 2 2 1 1 2 2 2 1 1 1 -2 1 2 1 1 1 1 0.207224 2 2 2 1 2 1 1 1 1 1 1 -2 1 1 1 1 2 1 7.37554 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.11792 2 3 3 2 2 1 2 2 1 1 1 -2 1 1 1 1 1 1 1.53867 1 1 1 1 1 1 2 2 2 1 2 -2 1 2 1 1 2 1 0.0302816 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.28003 1 1 1 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 2.9777 2 3 3 1 2 1 2 1 2 2 1 -1 1 1 1 1 1 1 0.0199808 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.29523 1 3 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 2 1 1.64431 2 3 3 1 2 1 1 2 1 1 1 -1 1 1 1 1 1 1 1.65059 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.37525 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 1.73187 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 1.01163 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 1.87413 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.35695 2 2 2 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 0.273621 2 3 3 1 1 3 1 1 1 1 1 -2 1 1 1 1 2 1 3.43754 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.69945 2 2 2 1 1 3 1 1 1 1 1 -1 1 1 1 1 1 1 6.24086 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.112064 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.88415 1 2 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.06286 2 2 2 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.17353 2 3 3 1 2 1 1 2 1 1 1 -1 1 1 1 1 1 1 1.49488 1 1 1 2 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 8.26156 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.29956 2 3 3 1 2 1 1 1 2 1 2 -2 1 2 1 1 2 1 5.02241 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.79705 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.41045 1 2 2 1 2 2 1 2 1 1 1 -2 1 2 1 1 1 1 3.62587 1 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.03338 2 3 3 1 2 3 1 1 2 2 1 -2 1 1 1 1 1 1 1.32098 1 1 1 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 2.90188 1 1 1 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 2.5172 2 2 2 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 1.59161 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 1.51327 1 2 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.61682 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.582747 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.78714 1 1 1 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 3.90871 2 3 3 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 2.12194 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.85085 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.63259 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 1.90261 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.12473 2 3 3 2 2 2 1 1 1 1 1 -1 1 2 1 1 1 1 0.744409 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.553062 2 3 3 1 2 3 2 2 1 1 1 -2 1 2 1 1 2 1 4.13517 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 5.34859 1 3 1 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 4.14217 2 2 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.68854 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.47433 1 1 1 1 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 4.04289 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 4.64514 2 2 2 1 1 1 1 2 1 1 1 -2 1 1 1 1 1 1 3.52575 1 1 1 2 1 1 1 1 2 2 1 -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/old/examplecar/OVIgraphviz.txt b/sourcecodes/data/old/examplecar/OVIgraphviz.txt deleted file mode 100644 index 2aaaecb2..00000000 --- a/sourcecodes/data/old/examplecar/OVIgraphviz.txt +++ /dev/null @@ -1,70 +0,0 @@ -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/old/examplecar/OVIk.txt b/sourcecodes/data/old/examplecar/OVIk.txt deleted file mode 100644 index d00491fd..00000000 --- a/sourcecodes/data/old/examplecar/OVIk.txt +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/sourcecodes/data/old/examplecar/OVImap.txt b/sourcecodes/data/old/examplecar/OVImap.txt deleted file mode 100644 index eda717d2..00000000 --- a/sourcecodes/data/old/examplecar/OVImap.txt +++ /dev/null @@ -1,19 +0,0 @@ -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/old/examplecar/OVImapdata.txt b/sourcecodes/data/old/examplecar/OVImapdata.txt deleted file mode 100644 index d1eac895..00000000 --- a/sourcecodes/data/old/examplecar/OVImapdata.txt +++ /dev/null @@ -1 +0,0 @@ -BatVolt PlugVolt StMotor Alter MFuse Charging Starter Cranks Dist GasFilter GasTank Fuel AirFilter Air Plugs SpkQual Starts Timing BatAge diff --git a/sourcecodes/data/old/examplecar/OVIname.txt b/sourcecodes/data/old/examplecar/OVIname.txt deleted file mode 100644 index e7901e87..00000000 --- a/sourcecodes/data/old/examplecar/OVIname.txt +++ /dev/null @@ -1 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter diff --git a/sourcecodes/data/old/examplecar/OVInet_figure.txt b/sourcecodes/data/old/examplecar/OVInet_figure.txt deleted file mode 100644 index ceed746e..00000000 --- a/sourcecodes/data/old/examplecar/OVInet_figure.txt +++ /dev/null @@ -1,237 +0,0 @@ -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/old/examplecar/OVInet_figure_new.txt b/sourcecodes/data/old/examplecar/OVInet_figure_new.txt deleted file mode 100644 index bd2ec975..00000000 --- a/sourcecodes/data/old/examplecar/OVInet_figure_new.txt +++ /dev/null @@ -1,138 +0,0 @@ -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/old/examplecar/OVInnode.txt b/sourcecodes/data/old/examplecar/OVInnode.txt deleted file mode 100644 index d6b24041..00000000 --- a/sourcecodes/data/old/examplecar/OVInnode.txt +++ /dev/null @@ -1 +0,0 @@ -19 diff --git a/sourcecodes/data/old/examplecar/OVInrows.txt b/sourcecodes/data/old/examplecar/OVInrows.txt deleted file mode 100644 index 7d802a3e..00000000 --- a/sourcecodes/data/old/examplecar/OVInrows.txt +++ /dev/null @@ -1 +0,0 @@ -1002 diff --git a/sourcecodes/data/old/examplecar/OVIparent.txt b/sourcecodes/data/old/examplecar/OVIparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/old/examplecar/OVIparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/old/examplecar/OVIstructure_input.txt b/sourcecodes/data/old/examplecar/OVIstructure_input.txt deleted file mode 100644 index cad732f3..00000000 --- a/sourcecodes/data/old/examplecar/OVIstructure_input.txt +++ /dev/null @@ -1,20 +0,0 @@ -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/old/examplecar/OVIstructure_input_temp.txt b/sourcecodes/data/old/examplecar/OVIstructure_input_temp.txt deleted file mode 100644 index 09d40aa3..00000000 --- a/sourcecodes/data/old/examplecar/OVIstructure_input_temp.txt +++ /dev/null @@ -1,20 +0,0 @@ -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 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 0.000000 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 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 diff --git a/sourcecodes/data/old/examplecar/OVIstructure_old.txt b/sourcecodes/data/old/examplecar/OVIstructure_old.txt deleted file mode 100644 index 22f14ba3..00000000 --- a/sourcecodes/data/old/examplecar/OVIstructure_old.txt +++ /dev/null @@ -1,19 +0,0 @@ -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/old/examplecar/OVIthr.txt b/sourcecodes/data/old/examplecar/OVIthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/old/examplecar/OVIthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/old/examplecar/OVItype.txt b/sourcecodes/data/old/examplecar/OVItype.txt deleted file mode 100644 index 0b76081c..00000000 --- a/sourcecodes/data/old/examplecar/OVItype.txt +++ /dev/null @@ -1,2 +0,0 @@ -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/old/examplecar/OVIvar.txt b/sourcecodes/data/old/examplecar/OVIvar.txt deleted file mode 100644 index dec2bf5d..00000000 --- a/sourcecodes/data/old/examplecar/OVIvar.txt +++ /dev/null @@ -1 +0,0 @@ -19 \ No newline at end of file diff --git a/sourcecodes/data/old/examplecar/OVIvardata.txt b/sourcecodes/data/old/examplecar/OVIvardata.txt deleted file mode 100644 index e595bf94..00000000 --- a/sourcecodes/data/old/examplecar/OVIvardata.txt +++ /dev/null @@ -1 +0,0 @@ --1.3159 \ No newline at end of file diff --git a/sourcecodes/data/old/examplecar/OVIvarname.txt b/sourcecodes/data/old/examplecar/OVIvarname.txt deleted file mode 100644 index 2453221d..00000000 --- a/sourcecodes/data/old/examplecar/OVIvarname.txt +++ /dev/null @@ -1 +0,0 @@ -BatAge \ No newline at end of file diff --git a/sourcecodes/data/old/examplecar/OVIwhite.txt b/sourcecodes/data/old/examplecar/OVIwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/old/examplecar/OVIwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh b/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh deleted file mode 100644 index dab5c39a..00000000 --- a/sourcecodes/data/old/examplecar/old/OVIrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified OVI -fi -exit diff --git a/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh b/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh deleted file mode 100644 index d47ae324..00000000 --- a/sourcecodes/data/old/examplecar/old/OVIrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure OVI -fi -exit diff --git a/sourcecodes/data/old/examplezoo/fSfban.txt b/sourcecodes/data/old/examplezoo/fSfban.txt deleted file mode 100644 index 9197eeec..00000000 --- a/sourcecodes/data/old/examplezoo/fSfban.txt +++ /dev/null @@ -1,261 +0,0 @@ -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/old/examplezoo/fSfcontinuous_input.txt b/sourcecodes/data/old/examplezoo/fSfcontinuous_input.txt deleted file mode 100644 index 340ad4f6..00000000 --- a/sourcecodes/data/old/examplezoo/fSfcontinuous_input.txt +++ /dev/null @@ -1,104 +0,0 @@ -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/old/examplezoo/fSfgraphviz.txt b/sourcecodes/data/old/examplezoo/fSfgraphviz.txt deleted file mode 100644 index 701801c6..00000000 --- a/sourcecodes/data/old/examplezoo/fSfgraphviz.txt +++ /dev/null @@ -1,61 +0,0 @@ -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/old/examplezoo/fSfk.txt b/sourcecodes/data/old/examplezoo/fSfk.txt deleted file mode 100644 index f599e28b..00000000 --- a/sourcecodes/data/old/examplezoo/fSfk.txt +++ /dev/null @@ -1 +0,0 @@ -10 diff --git a/sourcecodes/data/old/examplezoo/fSfmap.txt b/sourcecodes/data/old/examplezoo/fSfmap.txt deleted file mode 100644 index 4a123441..00000000 --- a/sourcecodes/data/old/examplezoo/fSfmap.txt +++ /dev/null @@ -1,17 +0,0 @@ -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/old/examplezoo/fSfmapdata.txt b/sourcecodes/data/old/examplezoo/fSfmapdata.txt deleted file mode 100644 index 19d91997..00000000 --- a/sourcecodes/data/old/examplezoo/fSfmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair diff --git a/sourcecodes/data/old/examplezoo/fSfname.txt b/sourcecodes/data/old/examplezoo/fSfname.txt deleted file mode 100644 index c68267c4..00000000 --- a/sourcecodes/data/old/examplezoo/fSfname.txt +++ /dev/null @@ -1 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type diff --git a/sourcecodes/data/old/examplezoo/fSfnet_figure.txt b/sourcecodes/data/old/examplezoo/fSfnet_figure.txt deleted file mode 100644 index 0c8f9428..00000000 --- a/sourcecodes/data/old/examplezoo/fSfnet_figure.txt +++ /dev/null @@ -1,130 +0,0 @@ -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/old/examplezoo/fSfnnode.txt b/sourcecodes/data/old/examplezoo/fSfnnode.txt deleted file mode 100644 index 98d9bcb7..00000000 --- a/sourcecodes/data/old/examplezoo/fSfnnode.txt +++ /dev/null @@ -1 +0,0 @@ -17 diff --git a/sourcecodes/data/old/examplezoo/fSfnrows.txt b/sourcecodes/data/old/examplezoo/fSfnrows.txt deleted file mode 100644 index 257e5632..00000000 --- a/sourcecodes/data/old/examplezoo/fSfnrows.txt +++ /dev/null @@ -1 +0,0 @@ -102 diff --git a/sourcecodes/data/old/examplezoo/fSfparent.txt b/sourcecodes/data/old/examplezoo/fSfparent.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/old/examplezoo/fSfparent.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/old/examplezoo/fSfstructure_input.txt b/sourcecodes/data/old/examplezoo/fSfstructure_input.txt deleted file mode 100644 index c49d600b..00000000 --- a/sourcecodes/data/old/examplezoo/fSfstructure_input.txt +++ /dev/null @@ -1,18 +0,0 @@ -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/old/examplezoo/fSfstructure_input_temp.txt b/sourcecodes/data/old/examplezoo/fSfstructure_input_temp.txt deleted file mode 100644 index 8910aaee..00000000 --- a/sourcecodes/data/old/examplezoo/fSfstructure_input_temp.txt +++ /dev/null @@ -1,18 +0,0 @@ -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/old/examplezoo/fSfstructure_old.txt b/sourcecodes/data/old/examplezoo/fSfstructure_old.txt deleted file mode 100644 index bf00f5d5..00000000 --- a/sourcecodes/data/old/examplezoo/fSfstructure_old.txt +++ /dev/null @@ -1,16 +0,0 @@ -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/old/examplezoo/fSfthr.txt b/sourcecodes/data/old/examplezoo/fSfthr.txt deleted file mode 100644 index aec258df..00000000 --- a/sourcecodes/data/old/examplezoo/fSfthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.8 diff --git a/sourcecodes/data/old/examplezoo/fSftier.txt b/sourcecodes/data/old/examplezoo/fSftier.txt deleted file mode 100644 index ca417b31..00000000 --- a/sourcecodes/data/old/examplezoo/fSftier.txt +++ /dev/null @@ -1 +0,0 @@ -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/old/examplezoo/fSftype.txt b/sourcecodes/data/old/examplezoo/fSftype.txt deleted file mode 100644 index 41c0f73e..00000000 --- a/sourcecodes/data/old/examplezoo/fSftype.txt +++ /dev/null @@ -1,2 +0,0 @@ -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/old/examplezoo/fSfwhite.txt b/sourcecodes/data/old/examplezoo/fSfwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/old/examplezoo/fSfwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh b/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh deleted file mode 100644 index f20a9a29..00000000 --- a/sourcecodes/data/old/examplezoo/old/fSfrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure fSf -fi -exit diff --git a/sourcecodes/data/old/examplezoo/standardized_data.txt b/sourcecodes/data/old/examplezoo/standardized_data.txt deleted file mode 100644 index 0975061e..00000000 --- a/sourcecodes/data/old/examplezoo/standardized_data.txt +++ /dev/null @@ -1,102 +0,0 @@ -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 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -2 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 2 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 1 2 1 2 2 2 2 2 2 1 1 2 2 1 -1 1 1 1 2 2 1 2 1 2 2 2 1 2 1 1 2 -2 1 2 1 1 2 1 2 2 2 1 2 1 2 1 1 2 -1 1 1 1 1 2 1 2 2 2 1 2 1 2 1 1 2 -1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 1 1 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 1 1 1 2 2 2 2 2 2 1 1 2 2 1 -2 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 2 1 1 2 2 2 2 2 2 1 1 2 2 1 -1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 1 1 1 2 2 2 2 2 2 1 1 2 2 1 -1 1 2 2 1 2 1 2 2 2 2 2 2 2 1 1 2 -1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 2 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 1 1 1 2 1 2 1 2 2 2 1 2 1 1 2 -1 1 1 2 2 1 2 2 2 2 2 2 1 1 2 2 1 -1 1 1 1 2 2 1 2 1 2 2 2 1 2 1 1 2 -1 1 2 1 2 1 2 2 2 2 2 2 1 1 2 2 1 -1 1 1 1 1 2 1 2 2 2 2 2 1 2 1 1 2 -1 1 1 1 2 1 2 2 1 2 2 2 1 1 2 2 1 -1 1 2 1 1 2 1 2 2 2 1 3 1 2 1 1 2 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 1 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 1 2 1 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 1 2 1 1 1 1 3 1 1 1 7 1 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 1 2 2 1 2 1 3 1 2 1 5 1 -1 2 2 2 1 1 2 2 1 2 1 3 1 2 1 5 1 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2 -1 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 1 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 1 2 2 1 2 2 3 1 2 1 5 1 -1 1 2 1 1 2 1 2 1 2 2 3 1 2 1 1 2 -1 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 2 2 2 2 2 2 3 1 1 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -2 1 1 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 1 2 1 1 2 2 1 2 1 3 1 2 1 5 1 -1 1 1 1 1 1 2 2 2 2 2 3 1 1 1 3 1 -1 1 2 1 1 1 2 2 1 2 2 3 1 2 1 3 1 -1 1 1 1 1 2 1 2 1 2 2 3 1 2 1 1 2 -1 1 2 1 1 2 1 2 2 2 2 3 1 2 1 1 2 -1 1 2 2 1 1 2 1 1 1 1 4 1 1 1 7 1 -1 1 2 2 1 1 2 1 1 1 1 5 1 1 1 7 1 -1 1 1 1 1 1 2 2 1 1 1 5 1 1 1 6 1 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 1 -2 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 2 1 2 1 2 2 1 1 1 5 1 1 1 6 1 -1 1 2 2 1 1 2 1 1 1 1 5 1 1 1 7 1 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 1 1 1 1 2 2 1 1 1 5 1 1 1 6 1 -1 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 2 2 1 1 2 1 2 1 1 6 1 1 1 7 1 -1 2 2 1 1 1 1 2 1 1 2 6 1 1 1 7 1 diff --git a/sourcecodes/data/old/initialstructure b/sourcecodes/data/old/initialstructure deleted file mode 100644 index 9ecf1bc7..00000000 --- a/sourcecodes/data/old/initialstructure +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/newintervention b/sourcecodes/data/old/newintervention deleted file mode 100644 index d818a943..00000000 --- a/sourcecodes/data/old/newintervention +++ /dev/null Binary files differdiff --git a/sourcecodes/data/old/temp_evidence_file b/sourcecodes/data/old/temp_evidence_file deleted file mode 100644 index b687ceaf..00000000 --- a/sourcecodes/data/old/temp_evidence_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified \ No newline at end of file diff --git a/sourcecodes/data/old/temp_intervention_file b/sourcecodes/data/old/temp_intervention_file deleted file mode 100644 index cdf5ce0f..00000000 --- a/sourcecodes/data/old/temp_intervention_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/newintervention \ No newline at end of file diff --git a/sourcecodes/data/old/temp_shell_file_initial_structure b/sourcecodes/data/old/temp_shell_file_initial_structure deleted file mode 100644 index 5d1c323d..00000000 --- a/sourcecodes/data/old/temp_shell_file_initial_structure +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure \ No newline at end of file diff --git a/sourcecodes/data/sample_input.txt b/sourcecodes/data/sample_input.txt deleted file mode 100644 index 5d900d3c..00000000 --- a/sourcecodes/data/sample_input.txt +++ /dev/null @@ -1,42 +0,0 @@ -Genotype Trait1 Trait2 Trait3 Phenotype -A 0.969 3 3.25 1.0 -NA 0.925 1.6 2.46 1.03 -B 0.427 NA 4.20 0.83 -A 0.877 8.3 3.76 0.96 -A 0.914 4.4 3.69 1.04 -A 0.560 4.9 2.60 0.98 -B 0.383 13.1 4.27 0.81 -B 0.101 18.6 5.08 0.77 -B 0.106 18.9 4.91 0.80 -A 0.894 2.5 2.69 0.99 -B 0.067 19.8 4.87 0.84 -A 0.921 2.9 4.12 1.03 -A 0.938 0.7 4.36 0.98 -B 0.658 15.7 4.53 0.88 -A 0.9 4.8 2.60 0.91 -A 0.790 10.4 2.39 0.89 -B 0.295 8.6 4.24 0.85 -A 0.317 12.2 4.44 0.88 -B 0.032 20.2 5.05 0.81 -B 0.603 23.4 4.28 0.80 -A 0.939 3.6 2.34 0.95 -B 0.978 0.4 3.49 0.88 -B 0.1 23.2 4.67 0.76 -B 0.036 32.6 4.93 0.82 -B 0.660 9.2 3.82 0.92 -B 0.078 35.8 4.51 0.85 -B 0.186 20.7 5.04 0.77 -B 0.071 35.6 4.57 0.79 -B 0.239 15.4 4.33 0.94 -B 0.205 24.5 5.05 0.77 -B 0.062 13.4 4.59 0.83 -A 0.599 5 4.18 0.96 -B 0.324 13.2 4.25 0.85 -B 0.876 14.2 2.92 0.86 -B 0.146 15.6 4.57 0.9 -B 0.257 22.5 5.21 0.75 -B 0.033 31.1 4.63 0.71 -B 0.297 36.1 3.88 0.79 -A 0.872 4.2 4.09 0.85 -A 0.909 4.3 3.65 0.97 -B 0.100 28.3 4.46 0.75 diff --git a/sourcecodes/delete_cv_pred.sh b/sourcecodes/delete_cv_pred.sh index b756e2b6..04bb0b77 100644 --- a/sourcecodes/delete_cv_pred.sh +++ b/sourcecodes/delete_cv_pred.sh @@ -1,22 +1,15 @@ #!/bin/bash #cd ./data/ -#cd /tmp/bnw/ -cd /var/lib/genenet/bnw/ +cd /tmp/bnw/ temp='looCV_temp.txt' rm $1$temp temp='looCV.txt' rm $1$temp -rm $1$temp -temp='loo_plotly.html' temp='kfoldCV_temp.txt' rm $1$temp temp='kfoldCV.txt' rm $1$temp -temp='kfold_plotly.html' -rm $1$temp temp='ts_upload.txt' rm $1$temp temp='ts_output.txt' rm $1$temp -temp='ts_plotly.html' -rm $1$temp diff --git a/sourcecodes/enter_netID.php~ b/sourcecodes/enter_netID.php~ deleted file mode 100644 index c58e63f3..00000000 --- a/sourcecodes/enter_netID.php~ +++ /dev/null @@ -1,74 +0,0 @@ -<!DOCTYPE HTML> -<html> - -<?php - -include("header_new.inc"); -include("input_validate.php"); - -$netID = ""; -$netIDErr = ""; -if ($_SERVER["REQUEST_METHOD"] == "POST") { - if (empty($_POST["netID"])) { - $netIDErr = "Entering a network ID is required"; - } else { - // $netID = valid_keyval($_POST["netID"]); - $netIDErr = "1"; - $netID = test_input($_POST["netID"]); - // $netIDErr = "1"; - // check if name only contains letters - if (strlen($netID)!=3) { - $netIDErr = "Network ID must be three letters"; - } - if (!preg_match('/^[a-zA-Z]+$/',$netID)) { - $netIDErr = "Only letters are allowed"; - } - } -} - -function test_input($data) { - $data = trim($data); - $data = stripslashes($data); - $data = htmlspecialchars($data); - return $data; -} -?> - - -<!-- Site navigation menu --> -<ul class="navbar"> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> -</ul> - -<div id="outer"> -<!-- Main content --> -<h2>Enter network ID from previously used network</h2> -<p align="justify"> -<br> Networks that have previously been generated in BNW can be accessed by entering the network ID in the input box below. The network ID is currently a three character string that can be found on the left hand menu of any network page. Network files are periodically deleted from BNW so it is possible that older networks may no longer be active. -<br> -<br> -<p><span class="error"></span></p> -<FORM METHOD="post" ACTION="<?php echo htmlspecialchars($_SERVER["PHP_SELF"]);?>"> - Network ID:<INPUT TYPE="text" name="netID" value="<?php echo $netID;?>" style="padding: 2px 5px; border: 2px solid; border-color: black black black black; font-family: Georgia, ..., serif; font-size: 18px; -display: block; height: 30px; width: 100px;"><span class="error"> <?php echo $netIDErr;?></span> -<br><input type="submit" name="submit" value="Submit" style="display: block; height: 30px; width:100px; font-family: Georgia, ..., serif; font-size: 16px;"> -</FORM> -</p> -<br> - -<?php -if ($netIDErr=="1") -{ - $keyval=$netID; -?> -<script> - window.open("layout_svg_no.php?My_key=<?php print($keyval);?>",'_self',false); -</script> -<?php -} -?> - -</div> -</body> -</html> \ No newline at end of file diff --git a/sourcecodes/example.php b/sourcecodes/example.php index d831b32d..47570aa2 100644 --- a/sourcecodes/example.php +++ b/sourcecodes/example.php @@ -1,8 +1,8 @@ <?php include("input_validate.php"); $oldkeyval=$_GET["My_key"]; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; + $type_n=array(); diff --git a/sourcecodes/examplefilecopy.sh b/sourcecodes/examplefilecopy.sh index b10aca42..d99865f7 100644 --- a/sourcecodes/examplefilecopy.sh +++ b/sourcecodes/examplefilecopy.sh @@ -7,5 +7,5 @@ do new=${f//$2/$3} # take action on each file. $f store current file name # echo "new Processing $new file..." - cp $f /var/lib/genenet/bnw/$new -done + cp $f /tmp/bnw/$new +done \ No newline at end of file diff --git a/sourcecodes/execute_bn_gom.php b/sourcecodes/execute_bn_gom.php index 1de6f9f6..8a728a24 100644 --- a/sourcecodes/execute_bn_gom.php +++ b/sourcecodes/execute_bn_gom.php @@ -5,8 +5,7 @@ $keyval=valid_keyval($_GET["My_key"]); //////////////execute c codes for local score/////////////////// //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $pfile=$dir.$keyval."parent.txt"; $parentf=file_get_contents("$pfile"); diff --git a/sourcecodes/executionprogress.php b/sourcecodes/executionprogress.php index 7c5d3163..c50a8c83 100644 --- a/sourcecodes/executionprogress.php +++ b/sourcecodes/executionprogress.php @@ -7,8 +7,7 @@ include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; //number of parents $pfile=$dir.$keyval."parent.txt"; diff --git a/sourcecodes/executionprogress_default.php b/sourcecodes/executionprogress_default.php index 0cc09b81..e609bfa4 100644 --- a/sourcecodes/executionprogress_default.php +++ b/sourcecodes/executionprogress_default.php @@ -7,8 +7,7 @@ include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; //number of parents $pfile=$dir.$keyval."parent.txt"; diff --git a/sourcecodes/filecopy.sh b/sourcecodes/filecopy.sh index fa8560de..79e51980 100644 --- a/sourcecodes/filecopy.sh +++ b/sourcecodes/filecopy.sh @@ -1,7 +1,6 @@ #!/bin/bash #cd ./data/ -#cd /tmp/bnw/ -cd /var/lib/genenet/bnw/ +cd /tmp/bnw/ FILES=$1* for f in $FILES do diff --git a/sourcecodes/graphviz_structure.php b/sourcecodes/graphviz_structure.php index 0708971f..1e866bc4 100644 --- a/sourcecodes/graphviz_structure.php +++ b/sourcecodes/graphviz_structure.php @@ -25,10 +25,8 @@ $keyval=valid_keyval($_GET["My_key"]); //$matfile="./data/".$keyval."structure_input.txt"; //$fout=fopen("./data/".$keyval."graphviz.txt","w"); -//$matfile="/tmp/bnw/".$keyval."structure_input.txt"; -//$fout=fopen("/tmp/bnw/".$keyval."graphviz.txt","w"); -$matfile="/var/lib/genenet/bnw/".$keyval."structure_input.txt"; -$fout=fopen("/var/lib/genenet/bnw/".$keyval."graphviz.txt","w"); +$matfile="/tmp/bnw/".$keyval."structure_input.txt"; +$fout=fopen("/tmp/bnw/".$keyval."graphviz.txt","w"); $matrix1=file_get_contents("$matfile"); $str_arrmat=array(); @@ -47,8 +45,7 @@ fwrite($fout,"$initialstring"); //$g_file_name="./data/".$keyval."grviz_name_file.txt"; -//$g_file_name="/tmp/bnw/".$keyval."grviz_name_file.txt"; -$g_file_name="/var/lib/genenet/bnw/".$keyval."grviz_name_file.txt"; +$g_file_name="/tmp/bnw/".$keyval."grviz_name_file.txt"; $grviz_name_file=fopen($g_file_name,"w"); for($i=0;$i<$n;$i++) @@ -81,9 +78,30 @@ for($i=1;$i<=$n;$i++) } fwrite($fout,"$endstring"); - -shell_exec('./run_scripts/run_octave '.$keyval); +//fwrite($fouttemp,"$endstring"); +//shell_exec('/usr/bin/dot -Tpng -o /var/www/html/compbio/BNW/graphviz.jpg /var/www/html/compbio/BNW/graphviztemp.txt'); + +//$file1="./data/".$keyval."run_initialstructure.sh"; +//$initiallines=file_get_contents("./data/temp_shell_file_initial_structure"); +$file1="/tmp/bnw/".$keyval."run_initialstructure.sh"; +$initiallines=file_get_contents("/tmp/bnw/temp_shell_file_initial_structure"); +$all_lines="$initiallines"."$keyval\nfi\nexit"; +$fp = fopen($file1,"w"); +fwrite($fp, "$all_lines\n"); +fclose($fp); +//prepare and execute shell script for matlab with a write lock +//$cmd="./runmat.sh $keyval"; +//system($cmd); +//$str_temp="./data/".$keyval."structure_input_temp.txt"; +//$str_temp="/tmp/bnw/".$keyval."structure_input_temp.txt"; +//if (file_exists($str_temp)) { + shell_exec('./run_scripts/run_octave '.$keyval); +//} else { + // shell_exec('cp ./data/'.$keyval.'structure_input.txt ./data/'.$keyval.'structure_input_temp.txt'); +// shell_exec('cp /tmp/bnw/'.$keyval.'structure_input.txt /tmp/bnw/'.$keyval.'structure_input_temp.txt'); +// shell_exec('./run_scripts/run_octave '.$keyval); +//} ?> <script> window.open("layout_svg_no.php?My_key=<?php print($keyval);?>",'_self',false); diff --git a/sourcecodes/header_new.inc b/sourcecodes/header_new.inc index 317b99b5..74183a8e 100644 --- a/sourcecodes/header_new.inc +++ b/sourcecodes/header_new.inc @@ -3,7 +3,7 @@ <META HTTP-EQUIV="Cache-Control" CONTENT="no-cache"> <META HTTP-EQUIV="Pragma" CONTENT="no-cache"> <META HTTP-EQUIV="Expires" CONTENT="0"> - + <title>Bayesian Network Webserver</title> <link rel="stylesheet" href="my_new_style.css"> diff --git a/sourcecodes/home_upload.php b/sourcecodes/home_upload.php index e9d459dc..930ac966 100644 --- a/sourcecodes/home_upload.php +++ b/sourcecodes/home_upload.php @@ -26,4 +26,4 @@ include("header_new.inc"); <br> </div> </body> -</html> +</html> \ No newline at end of file diff --git a/sourcecodes/input_check.php b/sourcecodes/input_check.php index 832b8faa..442acf81 100644 --- a/sourcecodes/input_check.php +++ b/sourcecodes/input_check.php @@ -10,10 +10,8 @@ if($_GET["My_key"]!="") if($_POST["My_key"]!="") $keyval=valid_keyval($_POST["My_key"]); -$dir = "/var/lib/genenet/bnw/"; - -$input_table_file=$keyval."input_table.txt"; -$input_data_file=$keyval."continuous_input_orig.txt"; +$input_table_file="./data/".$keyval."input_table.txt"; +$input_data_file="./data/".$keyval."continuous_input_orig.txt"; ?> @@ -34,15 +32,10 @@ $input_data_file=$keyval."continuous_input_orig.txt"; <div class="table_div"> <p class=basic_header>Description of network variables:</p> <div class="d3_table" id="table_div1"> - <?php - $table_text = json_encode(file("file://".$dir.$input_table_file)); - ?> -<script type="text/javascript"> - d3.text("", function(error, raw){ + <script type="text/javascript"> + d3.text("<?php print($input_table_file);?>", function(error, raw){ var dsv = d3.dsvFormat("\t") - var data1 = <?php echo $table_text?>; - var data2 = data1.join("") - var data = dsv.parse(data2) + var data = dsv.parse(raw) var caption_text = data.pop(); if (error) throw error; tabulate_caption("#table_div1",data,caption_text.Variable); @@ -52,16 +45,11 @@ $input_data_file=$keyval."continuous_input_orig.txt"; <br> <div class="d3_table" id="table_div2"> - <?php - $table_text = json_encode(file("file://".$dir.$input_data_file)); - ?> <script type="text/javascript"> - d3.text("", function(error, raw){ + d3.text("<?php print($input_data_file);?>", function(error, raw){ var dsv = d3.dsvFormat("\t") - var data1 = <?php echo $table_text?>; - var data2 = data1.join("") - var data = dsv.parse(data2) + var data = dsv.parse(raw) var caption_text = "Input data file:"; if (error) throw error; tabulate_caption("#table_div2",data,caption_text); @@ -72,7 +60,7 @@ $input_data_file=$keyval."continuous_input_orig.txt"; - <a class=button2 href="<?php print("reroute.php?".$input_data_file);?>">Download original input file<br></a> + <a class=button2 href="<?php print($input_data_file);?>">Download original input file<br></a> <br> <br><br> </div> diff --git a/sourcecodes/kfold_cv.php b/sourcecodes/kfold_cv.php index 16de2d5c..f162c796 100644 --- a/sourcecodes/kfold_cv.php +++ b/sourcecodes/kfold_cv.php @@ -1,10 +1,10 @@ <head> -<meta http-equiv='cache-control' content='no-cache'> -<meta http-equiv='expires' content='0'> +<meta http-equiv='cache-control' content='no-cache'> +<meta http-equiv='expires' content='0'> <meta http-equiv='pragma' content='no-cache'> <script src="./scripts/d3.v4.min.js"></script> <script src="./scripts/create_table.js"></script> -<?php +<?php include("header_new.inc"); include("header_batchsearch.inc"); include("input_validate.php"); @@ -47,7 +47,7 @@ function test_input($data) { ?> <?php -$varName_file = "/var/lib/genenet/bnw/".$keyval."name.txt"; +$varName_file = "/tmp/bnw/".$keyval."name.txt"; $varName_line = file_get_contents($varName_file); $varNamesArr = explode("\t",$varName_line); ?> @@ -76,44 +76,39 @@ $varNamesArr = explode("\t",$varName_line); <?php // $filename1="./data/".$keyval."kfoldCV.txt"; // $filename2="./data/".$keyval."kfoldCV_temp.txt"; - $dir="/var/lib/genenet/bnw/"; - $filename1=$keyval."kfoldCV.txt"; - $filename2=$keyval."kfoldCV_temp.txt"; -$plotly_file=$keyval."kfold_plotly.html"; -//$plotly_file_local="./data/".$keyval."kfold_plotly.html"; -//$pred_file_local="./data/".$keyval."kfoldCV.txt"; - -if(file_exists($dir.$filename2)) + $dir="/tmp/bnw/"; + $filename1=$dir.$keyval."kfoldCV.txt"; + $filename2=$dir.$keyval."kfoldCV_temp.txt"; +$plotly_file=$dir.$keyval."kfold_plotly.html"; +$plotly_file_local="./data/".$keyval."kfold_plotly.html"; +$pred_file_local="./data/".$keyval."kfoldCV.txt"; + +if(file_exists($filename2)) {?> <br> <h2> k-fold cross-validation results are being calculated</h2> <br> <?php } - else if(file_exists($dir.$plotly_file)) - { - $table_text = json_encode(file("file://".$dir.$filename1)); - //$plotly_data=file_get_contents("file://".$dir.$plotly_file); -?> + else if(file_exists($filename1)) + {?> <div> - <object width="800" height="500" data=<?php include($dir.$plotly_file)?> + <object type="text/html" data=<?php print($plotly_file_local);?> width="800" height="500" > </object> </div> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error,raw) { + d3.text("<?php print($pred_file_local);?>", function(error,raw) { var dsv=d3.dsvFormat("\t") - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data=dsv.parse(data2) - var caption_text=data.pop() - if (error) throw error; - tabulate_caption("#table_div1",data,caption_text.CaseRow); - }); + var data=dsv.parse(raw) + var caption_text=data.pop() + if (error) throw error; + tabulate_caption("#table_div1",data,caption_text.CaseRow); + }); </script> </div> <br> - <a class=button2 href=<?php print("reroute.php?".$filename1);?>>Download cross-validation results</a> + <a class=button2 href=<?php print($pred_file_local);?>>Download cross-validation results</a> <br> <br> <h3>Perform k-fold cross-validation of another network variable</h3><br> @@ -146,8 +141,9 @@ if(file_exists($dir.$filename2)) } else { ?> <h2>Perform k-fold cross-validation of network</h2> -<p align="justify"> - To perform cross-validation, select the name of the variable that you want to test <br>the predictions of and the number of folds below. <br><br> +<p align="justify"> + To perform cross-validation, select the name of the variable that you want to test <br>the predictions of and the number of folds below. +<br><br> <FORM METHOD="post" ACTION="<?php echo htmlspecialchars($_SERVER["PHP_SELF"]);?>"> <p style='font-size:18px'>Select variable name:</p> <select style='font-size:18px' Name="varName"> diff --git a/sourcecodes/kfold_plotly.py b/sourcecodes/kfold_plotly.py index 102d01d2..66f08143 100644 --- a/sourcecodes/kfold_plotly.py +++ b/sourcecodes/kfold_plotly.py @@ -1,13 +1,15 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python +#!/home/jziebart/python/Python-2.7.15/python import os import sys +#sys.path.append('/home/jziebart/.local/bin') +#sys.path.append('/home/jziebart/.local/lib') + import plotly import plotly.graph_objs as go import csv import string - netID = sys.argv[-1] outfile = netID+"kfold_plotly.html" @@ -17,12 +19,11 @@ f=open(filename,"r") #Read the first line to get the variable name lines=f.readlines() line = lines.pop() -#line = map(string.strip,line.strip().split(" ")) -line = line.strip().split(" ") +line = map(string.strip,line.strip().split(" ")) #print line varName = line[3][:-1] #print varName -plot_title = varName+' k-fold validation' +plot_title = '<br>'+varName+' k-fold validation' #print plot_title header = lines.pop(0) @@ -30,11 +31,9 @@ header = lines.pop(0) typefile = netID+"type.txt" tf=open(typefile,"r") line=tf.readline() -#varnames = map(string.strip,line.strip().split("\t")) -varnames = line.strip().split("\t") +varnames = map(string.strip,line.strip().split("\t")) line=tf.readline() -#vartypes = map(string.strip,line.strip().split("\t")) -vartypes = line.strip().split("\t") +vartypes = map(string.strip,line.strip().split("\t")) varindex = varnames.index(varName) cd_type = int(vartypes[varindex]) @@ -50,8 +49,7 @@ if cd_type == 1: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) x.append(float(line[2])) y.append(float(line[3])) # line=f.readline() @@ -64,10 +62,6 @@ if cd_type == 1: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", xaxis=dict( autorange=True, title='Actual values', @@ -97,8 +91,7 @@ else: # for i in range(5): # line = f.readline() #Get names of states - #header = map(string.strip,header.strip().split("\t")) - header = header.strip().split("\t") + header = map(string.strip,header.strip().split("\t")) states = header[3:] #Read the data actual = [] @@ -106,8 +99,7 @@ else: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) actual.append(line[2]) predict_x = line[3:] predict_x = [float(x) for x in predict_x] @@ -155,10 +147,6 @@ else: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", xaxis=dict( autorange=True, title='State', diff --git a/sourcecodes/layout.php b/sourcecodes/layout.php index aef275ca..5441c489 100644 --- a/sourcecodes/layout.php +++ b/sourcecodes/layout.php @@ -9,8 +9,7 @@ include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $vf1=$dir.$keyval."var.txt"; $vf2=$dir.$keyval."varname.txt"; @@ -74,9 +73,9 @@ function calcHeight() <ul class="navbar_ac"> <li><a href="parameter_display.php?My_key=<?php print($keyval);?>" target='_blank'>View parameters</a> <li><a href="violin.php?My_key=<?php print($keyval);?>" target='_blank'>View violin plots of distributions</a> - <li><a href="matrix_new.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> + <li><a href="matrix.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> <?php -$filename1="/var/lib/genenet/bnw/".$keyval."slsettings.txt"; +$filename1="/tmp/bnw/".$keyval."slsettings.txt"; if(file_exists($filename1)) {?> <li><a href="review_settings.php?My_key=<?php print($keyval);?>" target="_blank">View structure learning settings</a> diff --git a/sourcecodes/layout_cyto.php b/sourcecodes/layout_cyto.php index 85d8835a..b939f79a 100644 --- a/sourcecodes/layout_cyto.php +++ b/sourcecodes/layout_cyto.php @@ -2,6 +2,11 @@ <head> +<!-- +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css"> +--> + <link rel="stylesheet" href="./scripts/cytoscape.js-panzoom.css"> <link rel="stylesheet" href="./scripts/font-awesome.css"> @@ -12,17 +17,15 @@ include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; +$dir="./data/"; //In this case, $dir is used by the json command so it is interpreted and turned into /tmp/bnw/ automatically //$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; -$input_json=$keyval."network.json"; +$input_json=$dir.$keyval."network.json"; $output_png=$keyval."modified_network.png"; //In this section, $dir is used by php, so we need to use /tmp/bnw -//$thrfile="/tmp/bnw/".$keyval."thr.txt"; -$thrfile="/var/lib/genenet/bnw/".$keyval."thr.txt"; +$thrfile="/tmp/bnw/".$keyval."thr.txt"; if(file_exists($thrfile)) { $thr=file_get_contents("$thrfile"); @@ -33,6 +36,14 @@ if(file_exists($thrfile)) ?> +<!-- +<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js"></script> +<script src="https://unpkg.com/dagre@0.7.4/dist/dagre.js"></script> +<script src="https://cdn.jsdelivr.net/npm/cytoscape-dagre@2.2.2/cytoscape-dagre.min.js"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js"></script> +--> <script src="./scripts/jquery.min.js"></script> <script src="./scripts/cytoscape.min.js"></script> <script src="./scripts/dagre.js"></script> @@ -76,11 +87,6 @@ display: none; </style> -<?php -$json_text = json_encode(file("file://".$dir.$input_json)); -?> - - <script> // var default_layout = { name: 'breadthfirst', @@ -97,16 +103,11 @@ var default_layout = { name: 'dagre', padding: 30, spacingFactor: 1.25 } - - //$.getJSON("<?php print($input_json);?>",function (data) { - $.getJSON("./data/LRlnetwork.json",function (dumm) { + $.getJSON("<?php print($input_json);?>",function (data) { + //$.getJSON("./data/cwHnetwork.json",function (data) { // console.log(data); // document.addEventListener('DOMContentLoaded', function(){ - var data1 = <?php echo $json_text?>; -// console.log(data1); - var data2 = data1.join(""); - var data = JSON.parse(data2); var cy = window.cy = cytoscape({ container: document.getElementById('cy'), elements: data, @@ -367,8 +368,7 @@ $('#pos_slide').change(function (e) { <li><a id="addEdge" href="#">Add edge between selected nodes</a></li> <li><a id="deleteEdge" href="#">Remove selected edges</a></li> <?php - //$filename1="/tmp/bnw/".$keyval."structure_input_temp.txt"; - $filename1="/var/lib/genenet/bnw/".$keyval."structure_input_temp.txt"; + $filename1="/tmp/bnw/".$keyval."structure_input_temp.txt"; if(file_exists($filename1)) {?> <li><a id="weightFilter" href="#">Filter edges by weight:</a> @@ -399,4 +399,4 @@ if(file_exists($filename1)) </body> -</html> +</html> \ No newline at end of file diff --git a/sourcecodes/layout_cyto.php~ b/sourcecodes/layout_cyto.php~ deleted file mode 100644 index 272ae961..00000000 --- a/sourcecodes/layout_cyto.php~ +++ /dev/null @@ -1,402 +0,0 @@ -<!DOCTYPE html> -<head> - - -<!-- -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css"> ---> - -<link rel="stylesheet" href="./scripts/cytoscape.js-panzoom.css"> -<link rel="stylesheet" href="./scripts/font-awesome.css"> - - -<?php - -include("header_new.inc"); -include("input_validate.php"); -$keyval=valid_keyval($_GET["My_key"]); - -$dir="./data/"; -//In this case, $dir is used by the json command so it is interpreted and turned into /tmp/bnw/ automatically -//$dir="/tmp/bnw/"; - -$input_json=$dir.$keyval."network.json"; -$output_png=$keyval."modified_network.png"; - -//In this section, $dir is used by php, so we need to use /tmp/bnw -$thrfile="/tmp/bnw/".$keyval."thr.txt"; -if(file_exists($thrfile)) - { - $thr=file_get_contents("$thrfile"); - $thr=trim($thr); - } else { - $thr=0.5; -} -?> - - -<!-- -<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js"></script> -<script src="https://unpkg.com/dagre@0.7.4/dist/dagre.js"></script> -<script src="https://cdn.jsdelivr.net/npm/cytoscape-dagre@2.2.2/cytoscape-dagre.min.js"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js"></script> ---> -<script src="./scripts/jquery.min.js"></script> -<script src="./scripts/cytoscape.min.js"></script> -<script src="./scripts/dagre.js"></script> -<script src="./scripts/cytoscape-dagre.min.js"></script> -<script src="./scripts/cytoscape-panzoom.js"></script> -<script src="./scripts/lodash.js"></script> - - -<style type = "text/css"> - -#cy { - width: 80%; - height: 80%; -position: absolute; -/*float: top;*/ -top: 3em; -left: 9em; -overflow: auto; -border: 2px solid; -border-radius: 0.5em; -} - - -#loading { -position: absolute; -display: block; -top: 10%; -width: 45%; -color: #000; -font-size: 8em; -text-align: center; -} - -#loading.loaded { -display: none; -} - -#filterOut { - color: black; -} - -</style> - -<script> - - // var default_layout = { name: 'breadthfirst', - // directed: true, - // maximal: true, - // grid: true, - // spacingFactor: 1, - // fit: true, //whether to fit the viewport to the graph - // padding: 10 // the padding on fit - //} - -var default_layout = { name: 'dagre', - fit: true, - padding: 30, - spacingFactor: 1.25 - } - - $.getJSON("<?php print($input_json);?>",function (data) { - //$.getJSON("./data/cwHnetwork.json",function (data) { - // console.log(data); - // document.addEventListener('DOMContentLoaded', function(){ - var cy = window.cy = cytoscape({ - container: document.getElementById('cy'), - elements: data, - layout: default_layout, - style: [ - { - selector: 'node', - style: { - 'label': 'data(label)', - 'font-size': 20, - 'shape': 'roundrectangle', - 'text-halign': 'center', - 'text-valign': 'center', - 'width': 'label', - 'height': 'label', - 'padding': '6px', - 'color': 'black', - 'background-color': 'white', - 'border-style': 'solid', - 'border-color': 'black', - 'border-width': '2px' - } - }, - { - selector: '.selected1', - style:{ - 'color': 'green', - 'shape': 'ellipse', - 'background-color': '#DCDCDC', - 'border-color': 'green', - 'border-width': '2px', - 'border-style': 'dashed' - } - }, - { - selector: '.selected2', - style:{ - 'color': 'red', - 'shape': 'octagon', - 'border-color': 'red', - 'border-width': '2px', - 'background-color': '#DCDCDC', - 'border-style': 'dashed' - } - }, - { - selector: 'edge', - style: { - 'line-color': 'black', - 'curve-style': 'bezier', - //'target-endpoint': 'outside-to-node-or-label', - 'width': '3px', - 'target-arrow-shape': 'triangle', - 'target-arrow-color': 'black', - 'control-point-step-size': '140px', - 'arrow-scale': '2' - } - }, - { - selector: '.selected3', - style:{ - 'line-color': 'red', - 'target-arrow-color': 'red', - 'line-style': 'dashed' - } - } - ] - }); - // }); - - - - //window.onload=function() { - - var eles = cy.filter(); //var containing all elements so they can be restored after being removed - - // the default values of each option are outlined below: - var defaults = { - zoomFactor: 0.05, // zoom factor per zoom tick - zoomDelay: 45, // how many ms between zoom ticks - minZoom: 0.1, // min zoom level - maxZoom: 10, // max zoom level - fitPadding: 30, // padding when fitting - panSpeed: 10, // how many ms in between pan ticks - panDistance: 10, // max pan distance per tick - panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction) - panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed) - panInactiveArea: 8, // radius of inactive area in pan drag box - panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0 - zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution) - fitSelector: undefined, // selector of elements to fit - animateOnFit: function(){ // whether to animate on fit - return false; - }, - fitAnimationDuration: 1000, // duration of animation on fit - - // icon class names - sliderHandleIcon: 'fa fa-minus', - zoomInIcon: 'fa fa-plus', - zoomOutIcon: 'fa fa-minus', - resetIcon: 'fa fa-expand', - }; - - - - cy.panzoom( defaults ); - - $("#loading").addClass("loaded"); - -//This is probably more complex than it needs to be; -// the goal is to ensure: -// 1) No more than two nodes can be selected at a time. -// 2) Only one parent node (selected1) and only one child node (selected2) -// can be selected -cy.on('tap', 'node', function(event) { - if(cy.filter("node.selected1").length == 0) { - event.target.addClass('selected1'); - event.target.removeClass('selected2'); - } else { - event.target.removeClass('selected1'); - if(cy.filter("node.selected1").length == 1) { - if(cy.filter("node.selected2").length == 0) { - event.target.addClass('selected2'); - } else { - event.cy.filter("node.selected2").removeClass("selected2"); - } - } else { - event.cy.filter("node.selected1").removeClass("selected1"); - event.cy.filter("node.selected2").removeClass("selected2"); - } - } - }); -//The code below works with older versions of Cytoscape.js (before v3) -//cy.on('tap', 'node', function(event) { -// if(cy.filter("node.selected1").length == 0) { -// event.cyTarget.addClass('selected1'); -// event.cyTarget.removeClass('selected2'); -// } else { -// event.cyTarget.removeClass('selected1'); -// if(cy.filter("node.selected1").length == 1) { -// if(cy.filter("node.selected2").length == 0) { -// event.cyTarget.addClass('selected2'); -// } else { -// event.cy.filter("node.selected2").removeClass("selected2"); -// } -// } else { -// event.cy.filter("node.selected1").removeClass("selected1"); -// event.cy.filter("node.selected2").removeClass("selected2"); -// } -// } -// }); - - -$("#addEdge").click(function (e) { - if(cy.filter("node.selected1").length !=1) - return; - if(cy.filter("node.selected1").length !=1) - return; - var edge = new Object(); - edge.group = 'edges'; - edge.data = {source: cy.filter("node.selected1")[0].data('id'), target: cy.$("node.selected2")[0].data('id'), weight: 1}; - cy.add(edge); - cy.filter("node.selected1").removeClass('selected1',false); - cy.filter("node.selected2").removeClass('selected2',false); - }); - - -//cy.on('tap', 'edge', function(event) { -// event.cyTarget.toggleClass('selected3'); -// }); - -cy.on('tap', 'edge', function(event) { - event.target.toggleClass('selected3'); - }); - -$("#deleteEdge").click(function (e) { - var tEdges = cy.filter("edge.selected3"); - for (var i = 0; i < tEdges.length; i++) - { - cy.remove(tEdges[i]); - } - eles = cy.filter(); - }); - - -//$("#saveNetwork").click(function (e) { -// console.log(cy.elements().jsons()); -//}); - -$("#downloadNetwork").click(function (e) { - var png64 = cy.png(); - $(this).attr('href',png64); - $(this).attr('download',"<?php print($output_png);?>"); - }); - -$("#saveNetwork").click(function (e) { - //var jsonObject = JSON.stringify(cy.elements().jsons()); - - $("#loading").removeClass("loaded"); - var node_labs = cy.nodes().map(function (ele) { - return ele.data('label'); - }); - var sources = cy.edges().map(function (ele) { - return ele.data('source'); - }); - var targets = cy.edges().map(function (ele) { - return ele.data('target'); - }); - var weights = cy.edges().map(function (ele) { - return ele.data('weight'); - }); - - var old_key = "<?php print($keyval);?>"; - $.post("modified_network.php", { - old_key : old_key, - nnodes : node_labs.length, - node_labs : JSON.stringify(node_labs), - nedges : sources.length, - sources : JSON.stringify(sources), - targets : JSON.stringify(targets), - weights : JSON.stringify(weights) - }, - function( data ) { - window.location.href = data; - }); - // $.post("modified_network.php", { - // str : old_key, - //json : jsonObject - // }, -}); - - - - - -$('#pos_slide').change(function (e) { - eles.restore(); - pos_slide_val = $('#pos_slide').val(); - cy.$("edge[weight < " + pos_slide_val + "]").remove(); - }); - -// }; -}); - - - -</script> - - - - -</head> - - -<body> -<!-- Site navigation menu --> -<ul class="navbar"> - <li><a id="addEdge" href="#">Add edge between selected nodes</a></li> - <li><a id="deleteEdge" href="#">Remove selected edges</a></li> -<?php - $filename1="/tmp/bnw/".$keyval."structure_input_temp.txt"; -if(file_exists($filename1)) - {?> - <li><a id="weightFilter" href="#">Filter edges by weight:</a> - <form name="weightValue"> - <output name="filterOut" id="filterOut" style="color:black"><?php print($thr);?></output><br> - <input type="range" name="weightOutputName" id= "pos_slide" min="<?php print($thr);?>" max="1" value ="<?php print($thr);?>" step="0.01" list="weight" style="display: inline; width: 120px" oninput="filterOut.value = pos_slide.value"> - </form> - </li> -<?php - } -?> - <li><a id="saveNetwork" href="#">Use modified network</a></li> -</ul> -<ul class="navbar2"> - <li class="noHover"><p>Network ID:<br><?php print($keyval);?></p></li> - <li><a id="downloadNetwork" href="#">Save network as PNG</a></li> -</ul> -<ul class="navbar2"> - <li><a href="add_remove_howto.htm" target='_blank'>About this page</a> - <li><a href="help.php" target='_blank'>Help</a> - <li><a href="../home.php">Home</a> -</ul> - -<div id="cy"></div> -<div id="loading"> - <span class="fa fa-refresh fa-spin"></spin> -</div> - -</body> - -</html> \ No newline at end of file diff --git a/sourcecodes/layout_svg_no.php b/sourcecodes/layout_svg_no.php index f32b4054..f7268788 100644 --- a/sourcecodes/layout_svg_no.php +++ b/sourcecodes/layout_svg_no.php @@ -14,10 +14,9 @@ include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; -$dir="/var/lib/genenet/bnw/"; +$dir="./data/"; -$svg_file=$keyval."network_no_edge.svg"; +$svg_file=$dir.$keyval."network_no_edge.svg"; $png_file=$keyval."network_no_edge.png"; @@ -60,8 +59,7 @@ function calcHeight() <div class="panel"> <ul class="navbar_ac"> <?php -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $filename1=$dir.$keyval."structure_input_temp.txt"; if(file_exists($filename1)) {?> @@ -70,15 +68,16 @@ if(file_exists($filename1)) } ?> <button id='saveButton' class="button1">Save network as PNG</button> -<button id='saveButton_svg' class="button1">Save network as SVG</button> +<a href="<?php print($svg_file);?>" download><button type="submit" class="button1">Save network as SVG</button></a> </ul> </div> <button class="accordion">More about network <i class="fa fa-angle-down" style="font-size: 18px;"></i></button> <div class="panel"> <ul class="navbar_ac"> - <li><a href="matrix_new.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> + <li><a href="matrix.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> <li><a href="parameter_display.php?My_key=<?php print($keyval);?>" target="_blank">View network parameters</a> <?php +$dir="/tmp/bnw/"; $filename1=$dir.$keyval."slsettings.txt"; if(file_exists($filename1)) {?> @@ -113,35 +112,61 @@ if(file_exists($filename1)) //onload = "makeDraggable(evt)"; -<?php -$svg_xml = json_encode(file("file://".$dir.$svg_file)); -?> -d3.xml("", function(dumm){ - var data1 = <?php echo $svg_xml;?>; - var data2 = data1.join("") - parser = new DOMParser(); - documentFragment = parser.parseFromString(data2,"text/xml"); + +d3.xml("<?php print($svg_file);?>", function(error, documentFragment){ + if (error) {console.log(error); return;} + var svgNode = documentFragment .getElementsByTagName("svg")[0]; d3.select("#svg_div").node().appendChild(svgNode); + // nodes = d3.selectAll('.node'); + // links = d3.selectAll('.edge'); width = svgNode.getBBox().width*5; height = svgNode.getBBox().height*5; -}); + // nodes + // .call(d3.drag() + // .on("start",dragstarted) + // .on("drag",dragged) + // .on("end",dragended)); + + // links + // .call(d3.drag() + // .on("start",dragstarted) + // .on("drag",dragged) + // .on("end",dragended)); + + + //function dragstarted(d) { + // d3.select(this).raise().classed("active", true); + //} + + //function dragged(d) { + //this.x = this.x || 0; + //this.y = this.y || 0; + //this.x += d3.event.dx; + //this.y += d3.event.dy; + //d3.select(this) + // .attr("transform","translate(" + this.x + "," + this.y + ")"); + //} + + //function dragended(d) { + //d3.select(this).classed("active", false); + //} + + //console.log(svgNode); + //console.log(nodes); + //console.log(links); + + }); </script> <script> - d3.select('#saveButton_svg').on('click',function() { - var svgString = getSVGString(d3.select("#svg_div").select('svg').node()); - var svgBlob = new Blob([svgString],{type:"image/svg+xml;charset=utf-8"}); - saveAs(svgBlob,"<?php echo $svg_file; ?>"); -}); - d3.select('#saveButton').on('click', function(){ var svgString = getSVGString(d3.select("#svg_div").select('svg').node()); diff --git a/sourcecodes/layout_svg_wt.php b/sourcecodes/layout_svg_wt.php index 3f4bc6f0..f2bd630a 100644 --- a/sourcecodes/layout_svg_wt.php +++ b/sourcecodes/layout_svg_wt.php @@ -13,10 +13,9 @@ include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; -$dir="/var/lib/genenet/bnw/"; +$dir="./data/"; -$svg_file=$keyval."network.svg"; +$svg_file=$dir.$keyval."network.svg"; $png_file=$keyval."network.png"; @@ -37,6 +36,12 @@ function calcHeight() //--> </script> +<!-- +<script src="http://d3js.org/d3.v4.min.js" charset="utf-8"></script> +<script src="http://d3js.org/d3-selection-multi.v1.js"></script> +<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script> +<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script> +--> <script src="./scripts/d3.v4.min.js" charset="utf-8"></script> <script src="./scripts/d3-selection-multi.v1.js"></script> <script src="./scripts/canvas-toBlob.js"></script> @@ -53,14 +58,14 @@ function calcHeight() <ul class="navbar_ac"> <li><a href="layout_svg_no.php?My_key=<?php print($keyval);?>">Hide edge weights</a></li> </li> -<button id='saveButton' class="button1">Save network as PNG</button> -<button id='saveButton_svg' class="button1">Save network as SVG</button> +<button id='saveButton' class="button1">Save network image as PNG</button> +<a href="<?php print($svg_file);?>" download><button type="submit" class="button1">Save network image as SVG</button></a> </ul> </div> <button class="accordion">More about network <i class="fa fa-angle-down" style="font-size: 18px;"></i></button> <div class="panel"> <ul class="navbar_ac"> - <li><a href="matrix_new.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> + <li><a href="matrix.php?My_key=<?php print($keyval);?>" target="_blank">View structure matrix</a> <li><a href="parameter_display.php?My_key=<?php print($keyval);?>" target="_blank">View network parameters</a> <li><a href="review_settings.php?My_key=<?php print($keyval);?>" target="_blank">View structure learning settings</a> <li><a href="input_check.php?My_key=<?php print($keyval);?>" target="_blank">View input data and descriptions</a> @@ -91,22 +96,56 @@ function calcHeight() <script> -<?php -$svg_xml = json_encode(file("file://".$dir.$svg_file)); -?> -d3.xml("", function(dumm){ - var data1 = <?php echo $svg_xml;?>; - var data2 = data1.join(""); - parser = new DOMParser(); - documentFragment = parser.parseFromString(data2,"text/xml"); + + +d3.xml("<?php print($svg_file);?>", function(error, documentFragment){ + if (error) {console.log(error); return;} + + var svgNode = documentFragment .getElementsByTagName("svg")[0]; d3.select("#svg_div").node().appendChild(svgNode); + //nodes = d3.selectAll('.node'); + //links = d3.selectAll('.edge'); width = svgNode.getBBox().width*5; height = svgNode.getBBox().height*5; + // nodes + // .call(d3.drag() + // .on("start",dragstarted) + // .on("drag",dragged) + // .on("end",dragended)); + + // links + // .call(d3.drag() + // .on("start",dragstarted) + // .on("drag",dragged) + // .on("end",dragended)); + + + //function dragstarted(d) { + // d3.select(this).raise().classed("active", true); + //} + + //function dragged(d) { + // this.x = this.x || 0; + // this.y = this.y || 0; + // this.x += d3.event.dx; + // this.y += d3.event.dy; + // d3.select(this) + // .attr("transform","translate(" + this.x + "," + this.y + ")"); + //} + + //function dragended(d) { + // d3.select(this).classed("active", false); + //} + +//console.log(svgNode); +//console.log(nodes); +//console.log(links); + }); </script> @@ -114,12 +153,6 @@ d3.xml("", function(dumm){ <script> - d3.select('#saveButton_svg').on('click',function() { - var svgString = getSVGString(d3.select("#svg_div").select('svg').node()); - var svgBlob = new Blob([svgString],{type:"image/svg+xml;charset=utf-8"}); - saveAs(svgBlob,"<?php echo $svg_file;?>"); -}); - d3.select('#saveButton').on('click', function(){ var svgString = getSVGString(d3.select("#svg_div").select('svg').node()); diff --git a/sourcecodes/mat_structure.php b/sourcecodes/mat_structure.php index c1f0d82b..29bdb854 100644 --- a/sourcecodes/mat_structure.php +++ b/sourcecodes/mat_structure.php @@ -2,8 +2,7 @@ function structure_change($keyval) { //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $matfile=$dir.$keyval."varname.txt"; $namelist=file_get_contents("$matfile"); $matfilestruct=$dir.$keyval."structure_input.txt"; @@ -77,4 +76,4 @@ for($l=0;$l<=$i;$l++) //return $matfilestruct; } -?> +?> \ No newline at end of file diff --git a/sourcecodes/matrix.php b/sourcecodes/matrix.php index aaf58028..b5e1e89d 100644 --- a/sourcecodes/matrix.php +++ b/sourcecodes/matrix.php @@ -1,189 +1,76 @@ +<head> +<script src="./scripts/d3.v4.min.js"></script> +<script src="./scripts/create_table.js"></script> <?php +include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; -$dir="/tmp/bnw/"; +$dir="./data/"; +//$dir="/tmp/bnw/"; -$matfile=$dir.$keyval."structure_input_temp.txt"; -$fpw=fopen($dir.$keyval."Model_Averaging_Scores.txt","w"); -$matrix1=file_get_contents("$matfile"); //file("$matfile"); -fwrite($fpw,$matrix1); -fclose($fpw); -$str_arrmat=array(); -$str_arrmat=explode("\n",$matrix1); -$datamat=array(); -$data_cell=array(); - -$dataname=array(); -$dataname=explode("\t",$str_arrmat[0]); -$n=count($dataname); - - - - - -//echo $m_line; - - -if($matrix1!="") -{?> - <h2> Model Averaging Scores </h2> - <br><table width="90%" align="center" style="background-color:" bordercolor="" border=1 cellspacing="0" cellpadding="0"> - -<tr> -<th> -Name -</th> -<?php +$score_file = $dir.$keyval."structure_input_temp.txt"; +$mat_file = $dir.$keyval."structure_input.txt"; +?> -foreach($dataname as $cell1) -{ - $cell1=trim($cell1); - ?> -<th> <?php print($cell1); ?> </th> +</head> + + +<!-- Site navigation menu --> +<ul class="navbar2"> + <li class="noHover"><p>Network ID:<br><?php print($keyval);?></p></a></li> + <li><a href="about_this_page.php#matrix">About this page</a> + <li><a href="help.php">Help</a> + <li><a href="home.php">Home</a> +</ul> + +<body> + <div class="table_div"> + <div class="d3_table" id="table_div1"> + <script type="text/javascript"> + d3.text("<?php print($mat_file);?>", function(error, raw){ + var dsv = d3.dsvFormat("\t") + var data = dsv.parse(raw) + var caption_text = "Structure matrix"; + if (error) throw error; + tabulate_header_row("#table_div1",data,caption_text); + }); +</script> +</div> + <a class=button2 href="<?php print($mat_file);?>">Download structure matrix</a> +<br> +<br> <?php - -} +$filename1="/tmp/bnw/".$keyval."structure_input_temp.txt"; +if(file_exists($filename1)) + { ?> -</tr> -<?php - - for($i=0;$i<$n;$i++) - { - $ii=$i+1; - $datamat=explode("\t",$str_arrmat[$ii]); - - ?> - <tr> - <th> - <?php print trim($dataname[$i]); ?> - </th> - <?php - $dpr=trim($dataname[$i]); - - - foreach($datamat as $cell) - { - $cell=trim($cell); - if($cell!="") - { - ?> - <td> - <?php print $cell; ?> - </td> - <?php - - } - } - ?> - <tr> - <?php - - } - ?> - </table> - -<a href=<?php $d="./data/".$keyval."Model_Averaging_Scores.txt"; print($d);?>>download</a> - -<?php - -} - -/////////////////////////////////Second////////////////////////////////////////////////////////// - - -$matfile=$dir.$keyval."structure_input.txt"; -//echo $matfile; + <div class="d3_table" id="table_div2"> -$fpw=fopen($dir.$keyval."Structure_matrix.txt","w"); + <script type="text/javascript"> -$matrix1=file_get_contents("$matfile"); //file("$matfile"); + d3.text("<?php print($score_file);?>", function(error, raw){ + var dsv = d3.dsvFormat("\t") + var data = dsv.parse(raw) + var caption_text = "Model averaging scores"; + if (error) throw error; + tabulate_header_row("#table_div2",data,caption_text); + }); -fwrite($fpw,$matrix1); -fclose($fpw); +</script> + </div> - - - -$str_arrmat=array(); -$str_arrmat=explode("\n",$matrix1); -$datamat=array(); -$data_cell=array(); - -$dataname=array(); -$dataname=explode("\t",$str_arrmat[0]); -$n=count($dataname); - - - - - -//echo $m_line; - - -if($matrix1!="") -{?> - <h2> Structure Matrix </h2> - <br><table width="90%" align="center" style="background-color:" bordercolor="" border=1 cellspacing="0" cellpadding="0"> - -<tr> -<th> -Name -</th> -<?php - - -foreach($dataname as $cell1) -{ - $cell1=trim($cell1); - ?> -<th> <?php print($cell1); ?> </th> + <a class=button2 href="<?php print($score_file);?>">Download model averaging scores<br></a> +<br> <?php - -} + } ?> -</tr> -<?php - - for($i=0;$i<$n;$i++) - { - $ii=$i+1; - $datamat=explode("\t",$str_arrmat[$ii]); - - ?> - <tr> - <th> - <?php print trim($dataname[$i]); ?> - </th> - <?php - $dpr=trim($dataname[$i]); - - - foreach($datamat as $cell) - { - $cell=trim($cell); - if($cell!="") - { - ?> - <td> - <?php print $cell; ?> - </td> - <?php - - } - } - ?> - <tr> - <?php - - } - ?> - </table> -<?php +<br> +<br> +<br> +<br> +<br> +</div> +</body> -} -?> -<a href=<?php $d="./data/".$keyval."Structure_matrix.txt"; print($d);?>>download<br></a> -<input type=button onClick="self.close();" value="Close this window"> \ No newline at end of file diff --git a/sourcecodes/matrix_new.php b/sourcecodes/matrix_new.php deleted file mode 100644 index 22ea851a..00000000 --- a/sourcecodes/matrix_new.php +++ /dev/null @@ -1,84 +0,0 @@ -<head> -<script src="./scripts/d3.v4.min.js"></script> -<script src="./scripts/create_table.js"></script> -<?php -include("header_new.inc"); -include("input_validate.php"); -$keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; - -$score_file = $keyval."structure_input_temp.txt"; -$mat_file = $keyval."structure_input.txt"; - -?> - -</head> - - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li class="noHover"><p>Network ID:<br><?php print($keyval);?></p></a></li> - <li><a href="about_this_page.php#matrix">About this page</a> - <li><a href="help.php">Help</a> - <li><a href="home.php">Home</a> -</ul> - -<body> -<?php -$table_text =json_encode(file("file://".$dir.$mat_file)); -?> - <div class="table_div"> - <div class="d3_table" id="table_div1"> - <script type="text/javascript"> - d3.text("", function(error, raw){ - var dsv = d3.dsvFormat("\t") - var data1 = <?php echo $table_text?>; - var data2 = data1.join("") - var data = dsv.parse(data2) - var caption_text = "Structure matrix"; - if (error) throw error; - tabulate_header_row("#table_div1",data,caption_text); - }); -</script> -</div> - <a class=button2 target="_blank" href="<?php print("reroute.php?".$mat_file);?>">Download structure matrix</a> -<br> -<br> -<?php -if(file_exists($dir.$score_file)) - { -$table_text1a = json_encode(file("file://".$dir.$score_file)) -?> - <div class="d3_table" id="table_div2"> - - <script type="text/javascript"> - - d3.text("", function(error, raw_temp){ - var dsv = d3.dsvFormat("\t") - var data1a = <?php echo $table_text1a?>; - var data2a = data1a.join(""); - var data = dsv.parse(data2a) - var caption_text = "Model averaging scores"; - if (error) throw error; - tabulate_header_row("#table_div2",data,caption_text); - }); - -</script> - </div> - - <a class=button2 target="_blank" href="<?php print("reroute.php?".$score_file);?>">Download model averaging scores<br></a> -<br> -<?php - } -?> -<br> -<br> -<br> -<br> -<br> -</div> -</body> - - diff --git a/sourcecodes/modified_network.php b/sourcecodes/modified_network.php index 35f7a54a..9f38335c 100644 --- a/sourcecodes/modified_network.php +++ b/sourcecodes/modified_network.php @@ -28,8 +28,7 @@ if($_POST["My_key"]!="") //$filename = "./data/".$old_key."modify_edge.txt"; -//$filename = "/tmp/bnw/".$old_key."modify_edge.txt"; -$filename = "/var/lib/genenet/bnw/".$old_key."modify_edge.txt"; +$filename = "/tmp/bnw/".$old_key."modify_edge.txt"; $file = fopen($filename,'w'); //fwrite($file,$json); diff --git a/sourcecodes/modify_edges.php b/sourcecodes/modify_edges.php deleted file mode 100644 index 6d0c7838..00000000 --- a/sourcecodes/modify_edges.php +++ /dev/null @@ -1,950 +0,0 @@ -<?php - -///////This code will allow users to group variables in tier. getcombineDescription() function combined all data and take you to "tier_description_processing_gom.php" for preparation of ban and whitelist ////////// - -include("header_new.inc"); -include("runtime_check.php"); -include("input_validate.php"); -$keyval=$_GET["My_key"]; - -$dir="./data/"; - -$type_n=array(); - -//Get number of tier data and key value for changes in number of tier - -if(isset($_POST["nm_tier"])) -{ - $type_n=explode("|",$_POST["nm_tier"]); -} -else if(isset($_POST["nm_parent"])) -{ - $type_n=explode("|",$_POST["nm_parent"]); -} -else if(isset($_POST["nm_k"])) -{ - $type_n=explode("|",$_POST["nm_k"]); -} -else if(isset($_POST["nm_thr"])) -{ - $type_n=explode("|",$_POST["nm_thr"]); -} - -$parent_number=trim($type_n[0]); -$k_number=trim($type_n[1]); -$tier_number=trim($type_n[2]); -$structure_thr=trim($type_n[3]); - - -if($keyval=="") - $keyval=$type_n[4]; - - -if($parent_number=="") -{ - $parent_number=4; -} - -if($k_number=="") -{ - $k_number=1; -} - -if($tier_number=="") -{ - $tier_number=3; -} -if($structure_thr=="") -{ - $structure_thr=0.5; -} - - - -$nf=$dir.$keyval."nnode.txt"; -$node=trim(file_get_contents("$nf")); -$maxplist=$node-1; - -//print default number of parents -$pfile=$dir.$keyval."parent.txt"; -$parentf=fopen($pfile,"w"); -fwrite($parentf,"$parent_number\n"); - -//print default number of k for model averaging -$kfile=$dir.$keyval."k.txt"; -$kf=fopen($kfile,"w"); -fwrite($kf,"$k_number\n"); - -//print model averaging threshold -$thrfile=$dir.$keyval."thr.txt"; -$kf=fopen($thrfile,"w"); -fwrite($kf,"$structure_thr\n"); - -//////////////////Check execution time////////////////////////////////////////////// -$keyval=valid_keyval($keyval); -$runtime=exe_time($keyval,$parent_number,$k_number); - -//print("Runtime is $runtime"); - -?> -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p onClick="getcombineDescription(ntiers,'ban_from','ban_to','white_from','white_to','<?php print($keyval);?>')"><a href="javascript:void(0)" >View modified structure </p> - <li><a href="javascript:void(0);" -NAME="InputCheck" title="InputCheck" - onClick=window.open("input_check.php?My_key=<?php print($keyval);?>","Rat//ting","width=950,height=270,0,status=0,");>View uploaded variables and data</a> -</ul> -<ul class="navbar"> - <li><a href="help.php#constraint_interface" target="_blank">How to use this page</a> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> - -</ul> - - - -<div id="outernew"> - - - -<?php - - -if(isset($HTTP_POST_VARS["bantext"])) -{ - $ban_search=$HTTP_POST_VARS["searchkey"]; -} - -if(isset($HTTP_POST_VARS["whitetext"])) -{ - $white_search=$HTTP_POST_VARS["searchkey"]; -} - -?> - -<!DOCTYPE html> -<html> -<head> -<title>Drag and Drop test</title> -<style type="text/css"> - #nodelist{ - width:200px; - font-weight:bold; - border: 2px solid; - } - #tiers{ - position:absolute; - left:215px; - white-space: nowrap; - min-width: 3000px; - float:top; - } - - #int_box1{ - white-space: nowrap; - min-width: 10000px; - } - #int_box2{ - white-space: nowrap; - min-width: 10000px; - } - #int_box3{ - white-space: nowrap; - min-width: 10000px; - } - #int_box4{ - white-space: nowrap; - min-width: 10000px; - } - - #outer_tier_desc{ - margin-top: 100px; - } - - #outer_tier_desc1{ - width:2000px; - margin-top: 20px; - } - - #outer_box_lists{ - margin-top: 100px; - } - #nodelist2{ - width:200px; - font-weight:bold; - border: 2px solid; - float:left; - } - #ban_outer { - position:absolute; - left: 215px; - width:449px; - border: 2px solid; - background-color:#C0C0C0; - font-weight:bold; - margin-left:15px; - } - #ban_from { - width:200px; - border:2px solid; - margin-left:15px; - } - #ban_to { - width:200px; - border:2px solid; - margin-left:15px; - } - #white_outer { - position:absolute; - left:700px; - width:449px; - border: 2px solid; - background-color:#C0C0C0; - font-weight:bold; - } - #white_from { - width:200px; - border:2px solid; - margin-left:15px; - } - #white_to { - width:200px; - border:2px solid; - margin-left:15px; - } - - - .tier { - width:200px; - border: 2px solid; - font-weight:bold; - float:left; - background-color:#FFFFFF; - margin-left:5px; - display: inline-block; - } - .int { - border: 2px solid; - font-weight:bold; - float:left; - background-color:#FFFFFF; - margin-left:0px; - display: inline-block; - } - .int1 { - border: 2px solid; - background-color:#FFFFFF; - clear: left; - float:left; - margin-left:0px; - display: inline-block; - } - .node1 { - width:150px; - height:30px; - float:left; - margin-left:10px; - margin-top:10px; - border: 2px dashed; - background-color:#C0C0C0; - } - .node2 { - width:150px; - height:30px; - float:left; - margin-left:10px; - margin-top:10px; - border: 2px dashed; - background-color:#EAE822; - } - -</style> - -<script type="text/javascript"> - -//There are three groups of functions here: -//The first group is involved with dragging and dropping nodes -// between different locations. -//The second group is involved with creating the divs that are needed -// based on the number of nodes and number of tiers and organizing -// them on the webpage. -//The third group determines which divs the nodes are located in -// to group the nodes into tiers and make ban and white lists. - - -//Drag and drop functions: -function drag(drop_target, e) { - e.dataTransfer.setData('Text', drop_target.id); - } - -function drop(drop_target, e) { - var id = e.dataTransfer.getData('Text'); - drop_target.appendChild(document.getElementById(id)); - e.preventDefault(); - } - -function dropCopy(ev) { - ev.stopPropagation(); - ev.preventDefault(); - var src = ev.dataTransfer.getData("Text"); - var orig = document.getElementById(src); - var pid = orig.parentNode.id; - var target_id = ev.target.id; - //document.write(pid); - if (pid != target_id){ - var origclone = orig.cloneNode(true); - var newid = src+"a"; - origclone.setAttribute('id',newid); - document.getElementById(pid).appendChild(origclone); - ev.target.appendChild(orig); - } - else { - document.write(pid,target_id); - } - return false; -} - - - - -function loadFunction(nnodes,ntiers) { - // makeNodeList(nnodes,'nodelist','tr'); - // makeNodes(nnodes,'nodelist'); - // makeTiers(nnodes,ntiers); - makeNodes(nnodes,'nodelist2','bw'); - // makeTierDesc1(ntiers); - // makeTierDesc2(ntiers); - //makeTierDesc3(ntiers); - //makeTierDesc4(ntiers); - makeBWLists(nnodes); -} - - -//Function to make the NodeList. It is similar to the above function. -function makeNodeList(nnodes,nlist) { - var element1 = document.createElement('div'); - var newheight = 45*nnodes + 40; - newheight = newheight+'px'; - element1.setAttribute('id',nlist); - element1.setAttribute('ondrop','drop(this, event)'); - element1.setAttribute('ondragenter','return false'); - element1.setAttribute('ondragover','return false'); - element1.style.height=(newheight); - element1.innerHTML = "Nodes<br>"; - document.getElementById('tier_box').appendChild(element1); -} - - -//This is the function that makes the nodes. It is called when the -// page loads. The nodes are placed in the "nodelist" div. -//Will need to mofidy this function to pass it a list of the node -// names. The inner html is what is used in the later functions -// that make the tier list, banlist, and white list. -function makeNodes(nnodes,nlist,suffix) { - -<?php $xyz=1; -$nm=$dir."$keyval"."name.txt"; - -$namelist=file_get_contents("$nm"); -$str_arrname=array(); -$str_arrname=explode("\n",$namelist); -$dataname=array(); -$dataname=explode("\t",$str_arrname[0]); - for ($i=1;$i<=$node;$i++){ -$ii=$i-1; -$npr=trim($dataname[$ii]); -?> - i="<?php print($i);?>"; - var newname = 'node'+i; - var element1 = document.createElement('div'); - element1.setAttribute('draggable','true'); - element1.setAttribute('class','node1'); - element1.setAttribute('ondragstart','drag(this, event)'); - element1.setAttribute('id',newname+suffix); - element1.setAttribute('ondragover','return false'); - element1.innerHTML = "<?php print($npr);?>"; - document.getElementById(nlist).appendChild(element1); - <?php } - ?> - } - - -//Function to make the Tiers. It is similar to the above function. -function makeTiers(nnodes,ntiers) { - for (i=1;i<=ntiers;i++){ - var newname = 'Tier'+i; - var element1 = document.createElement('div'); - //var newpos = i*205; - //newpos = 'left: '+newpos+'px'; - var newheight = nnodes*45 + 40; - newheight = newheight+'px'; - //var newstyle = newpos + newheight; - element1.setAttribute('class','tier'); - element1.setAttribute('id',newname); - element1.setAttribute('ondrop','drop(this, event)'); - element1.setAttribute('ondragenter','return false'); - element1.setAttribute('ondragover','return false'); - //element1.setAttribute('style',newpos); - element1.style.height=(newheight); - element1.innerHTML = newname +"<br>"; - document.getElementById('tiers').appendChild(element1); - } - var newwidth = ntiers*205 + 20; - newwidth = newwidth+'px'; - document.getElementById('tiers').style.width=newwidth; -} - - - -function makeTierDesc1(ntiers) { - var element1 = document.createElement('div'); - var newheight = '20px'; - var newwidth = '220px'; - element1.setAttribute('id','int_box1_first'); - element1.setAttribute('class','int'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - //element1.innerHTML = "st<br>"; - document.getElementById('int_box1').appendChild(element1); - for (i=1;i<=ntiers;i++) { - var newname = 'int_box1'+i; - var newheight = '20px'; - var newwidth = '205px'; - //var newwidth = ntiers*65 + 20; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "  Tier"+i+"<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box1').appendChild(element1); - } - -} -function makeTierDesc2(ntiers) { - var element1 = document.createElement('div'); - var newheight = '50px'; - var newwidth = '220px'; - element1.setAttribute('id','int_box2_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Are within tier <br>interactions allowed?<br>"; - document.getElementById('int_box2').appendChild(element1); - for (i=1;i<=ntiers;i++) { - var newname = 'int_box2'+i; - var newheight = '50px'; - var newwidth = '205px'; - //var newwidth = ntiers*65 + 20; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box2').appendChild(element1); - //create form to hold yes/no radio boxes - var form1 = document.createElement('form'); - //form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>"; - var radio_yes = document.createElement('input'); - radio_yes.setAttribute('type','radio'); - radio_yes.setAttribute('name',"r_yes_no_"+newname); - radio_yes.setAttribute('id',"r_yes_"+newname); - - radio_yes.value = "r_yes_"+newname; - radio_yes.setAttribute('checked','checked'); - form1.appendChild(radio_yes); - var yes_label = document.createElement('label'); - yes_label.setAttribute('for',radio_yes.id); - yes_label.innerHTML = "Yes     "; - form1.appendChild(yes_label); - var radio_no = document.createElement('input'); - radio_no.setAttribute('type','radio'); - radio_no.setAttribute('name',"r_yes_no_"+newname); - radio_no.setAttribute('id',"r_no_"+newname); - radio_no.value = "r_no_"+newname; - form1.appendChild(radio_no); - var no_label = document.createElement('label'); - no_label.setAttribute('for',radio_no.id); - no_label.innerHTML = "No<br>"; - form1.appendChild(no_label); - element1.appendChild(form1); - // alert(radio_yes.value); - // alert(radio_yes.checked); - // alert(radio_no.value); - // alert(radio_no.checked); - } - -} - -function makeTierDesc3(ntiers) { - var element1 = document.createElement('div'); - var newwidth = '220px'; - var newheight = ntiers*10 + 25; - newheight = newheight + 'px'; - //var newheight = '50px'; - //var newwidth = '250px'; - element1.setAttribute('id','int_box3_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Which tiers contain nodes that <br>can be the parents of this tier?<br>"; - document.getElementById('int_box3').appendChild(element1); - for (i=1;i<=ntiers;i++) { - var newname = 'int_box3'+i; - //var newheight = '50px'; - var newwidth = '205px'; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box3').appendChild(element1); - //create form to hold allowed parents - var form2 = document.createElement('form'); - //form2.innerHTML = "Which tiers can be the "+ - // "parents of the nodes in Tier"+i+"?<br>"; - var k = 0; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - k = k + 1; - var pbox = document.createElement('input'); - pbox.setAttribute('type','checkbox'); - // pbox.setAttribute('name',"par_"+i); - pbox.setAttribute('name',"par_"+i+"_"+j); - pbox.setAttribute('id',"par_"+i+"_"+j); - pbox.value = "par_"+i+"_"+j; - if (j<i) { - pbox.setAttribute('checked','checked'); - } - var plabel = document.createElement('label'); - plabel.setAttribute('for',pbox.id); - if (k%2 == 0) { - plabel.innerHTML = "Tier"+j+"  <br>"; - } else { - plabel.innerHTML = "Tier"+j+"  "; - } - form2.appendChild(pbox); - form2.appendChild(plabel); - } - } - element1.appendChild(form2); - } -} - -function makeTierDesc4(ntiers) { - var element1 = document.createElement('div'); - //var newheight = '50px'; - var newwidth = '220px'; - var newheight = ntiers*10 + 25; - newheight = newheight + 'px'; - element1.setAttribute('id','int_box4_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Which tiers contain nodes that<br> can be the children of this tier?<br>"; - document.getElementById('int_box4').appendChild(element1); - for (i=1;i<=ntiers;i++) { - var newname = 'int_box4'+i; - //var newheight = '50px'; - //var newwidth = ntiers*65 + 20; - var newwidth = '205px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box4').appendChild(element1); - //create form to hold allowed children - var form3 = document.createElement('form'); - //form3.innerHTML = "Nodes in which tiers can be <br>the children of this tier?<br>"; - var k = 0; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - k = k + 1; - var cbox = document.createElement('input'); - cbox.setAttribute('type','checkbox'); - //cbox.setAttribute('name',"child_"+i); - cbox.setAttribute('name',"child_"+i+"_"+j); - cbox.setAttribute('id',"child_"+i+"_"+j); - - cbox.value = "child_"+i+"_"+j; - if (j>i) { - cbox.setAttribute('checked','checked'); - } - var clabel = document.createElement('label'); - clabel.setAttribute('for',cbox.id); - if (k%2 == 0) { - clabel.innerHTML = "Tier"+j+"  <br>"; - } - else - { - clabel.innerHTML = "Tier"+j+"  "; - } - form3.appendChild(cbox); - form3.appendChild(clabel); - } - } - element1.appendChild(form3); - } -} - - - -//Old function to make section of page that allows for tier description. -//Replaced by the four functions above. -function makeTierDesc(ntiers) { - for (i=1;i<=ntiers;i++) { - //var i = 2; - var newname = 'desc_tier'+i; - - //create the outer division to hold the other boxes - var out_div = document.createElement('div'); - out_div.setAttribute('id',newname); - if (i==1) { - out_div.innerHTML = "Tier"+i+"<br>"; - } else { - out_div.innerHTML = "<br><br>Tier"+i+"<br>"; - } - document.getElementById('outer_tier_desc').appendChild(out_div); - - //create form to hold yes/no radio boxes - var form1 = document.createElement('form'); - form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>"; - var radio_yes = document.createElement('input'); - radio_yes.setAttribute('type','radio'); - radio_yes.setAttribute('name',"r_yes_no_"+newname); - radio_yes.setAttribute('id',"r_yes_"+newname); - - radio_yes.value = "r_yes_"+newname; - radio_yes.setAttribute('checked','checked'); - form1.appendChild(radio_yes); - var yes_label = document.createElement('label'); - yes_label.setAttribute('for',radio_yes.id); - yes_label.innerHTML = "Yes "; - form1.appendChild(yes_label); - var radio_no = document.createElement('input'); - radio_no.setAttribute('type','radio'); - radio_no.setAttribute('name',"r_yes_no_"+newname); - radio_no.setAttribute('id',"r_no_"+newname); - radio_no.value = "r_no_"+newname; - form1.appendChild(radio_no); - var no_label = document.createElement('label'); - no_label.setAttribute('for',radio_no.id); - no_label.innerHTML = "No<br>"; - form1.appendChild(no_label); - out_div.appendChild(form1); - // alert(radio_yes.value); - // alert(radio_yes.checked); - // alert(radio_no.value); - // alert(radio_no.checked); - - - //create form to hold allowed parents - var form2 = document.createElement('form'); - form2.innerHTML = "Which tiers can be the "+ - "parents of the nodes in Tier"+i+"?<br>"; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - var pbox = document.createElement('input'); - pbox.setAttribute('type','checkbox'); - // pbox.setAttribute('name',"par_"+i); - pbox.setAttribute('name',"par_"+i+"_"+j); - pbox.setAttribute('id',"par_"+i+"_"+j); - pbox.value = "par_"+i+"_"+j; - if (j<i) { - pbox.setAttribute('checked','checked'); - } - var plabel = document.createElement('label'); - plabel.setAttribute('for',pbox.id); - plabel.innerHTML = "Tier"+j; - form2.appendChild(pbox); - form2.appendChild(plabel); - } - } - out_div.appendChild(form2); - - // alert(pbox.value); - // alert(pbox.checked); - - - - //create form to hold allowed children - var form3 = document.createElement('form'); - form3.innerHTML = "Which tiers can be the "+ - "children of the nodes in Tier"+i+"?<br>"; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - var cbox = document.createElement('input'); - cbox.setAttribute('type','checkbox'); - //cbox.setAttribute('name',"child_"+i); - cbox.setAttribute('name',"child_"+i+"_"+j); - cbox.setAttribute('id',"child_"+i+"_"+j); - - cbox.value = "child_"+i+"_"+j; - if (j>i) { - cbox.setAttribute('checked','checked'); - } - var clabel = document.createElement('label'); - clabel.setAttribute('for',cbox.id); - clabel.innerHTML = "Tier"+j; - form3.appendChild(cbox); - form3.appendChild(clabel); - } - } - out_div.appendChild(form3); - //var break = document.createElement('div'); - //break.innerHTML = "<br>"; - //out_div.appendChild(break); - //out_div.appendChild(break); - // alert(cbox.value); - // alert(cbox.checked); - - } -} - -//Function to give the divs for the ban and white lists the correct -// dimensions. -function makeBWLists(nnodes) { - var newheight = 45*nnodes + 40; - var nlheight = newheight+'px'; - document.getElementById('nodelist2').style.height=nlheight; - var inheight = newheight*2; - var outheight = inheight + 50; - inheight=inheight+'px'; - outheight = outheight+'px'; - document.getElementById('ban_outer').style.height=outheight; - document.getElementById('white_outer').style.height=outheight; - document.getElementById('ban_from').style.height=inheight; - document.getElementById('ban_to').style.height=inheight; - document.getElementById('white_from').style.height=inheight; - document.getElementById('white_to').style.height=inheight; - -} - - -//Functions that get the locations of the nodes to group the -// nodes into tiers and make ban and white lists. -//Will probably need to add a function to get the tier description information. -//Might be able to do that with just php though? -function getNodesInTiers(ntiers) { - output = ntiers+",\n"; - for (i=1;i<=ntiers;i++){ - var newname = 'Tier'+i; - children = document.getElementById(newname).childNodes; - temp = children.length - 2; - temp = newname + ",\t" +temp+ ",\t" - for (j=2;j<children.length;j++){ - temp = temp + children[j].innerHTML + ",\t" - } - output = output + temp +"\n" - } - - - return output; - - // window.open("http://compbio.uthsc.edu/BNServer/tier.php?tier="+output,"Ratting","width=950,height=270,0,status=0,"); - -} - -function getNodesInList(from_div,to_div) { - children_from = document.getElementById(from_div).childNodes; - children_to = document.getElementById(to_div).childNodes; - if(children_from.length == children_to.length){ - temp = ""; - for (i=2;i<children_from.length;i++){ - temp = temp+children_from[i].innerHTML; - temp = temp+",\t"+children_to[i].innerHTML+",\n"; - } - - - - } - else - { - alert('Error in node list'); - temp=""; - } - return temp; -} - - -//Functions that get the description of the tiers. -function getDescribeTiers(ntiers) { - output = ""; - for (i=1;i<=ntiers;i++) { - temp=""; - var newname = 'int_box2'+i; - - var temp_id_yes="r_yes_"+newname; - var temp_id_no="r_no_"+newname; - - temp_yes = document.getElementById(temp_id_yes); - temp_no = document.getElementById(temp_id_no); - - // temp = temp + temp_yes.value + ",\t" - temp = temp + temp_yes.checked + ",\t" - - // temp = temp + temp_no.value + ",\t" - temp = temp + temp_no.checked + ",\t" - - for (j=1;j<=ntiers;j++) { - if(j!=i) - { - var pbox_id="par_"+i+"_"+j; - var cbox_id="child_"+i+"_"+j; - temp_p = document.getElementById(pbox_id); - temp_c = document.getElementById(cbox_id); - - temp = temp + temp_p.checked + ",\t" - - temp = temp + temp_c.checked + ",\t" - - - } - } - // alert(temp); - - output = output + temp +"\n" - -} - - - // window.open("http://compbio.uthsc.edu/BNServer/tierdescription.php?tierdesc="+output,"Ratting","width=950,height=270,0,status=0,"); - return output; - -} - - -//Combined all three function together and then execute structure learning - -function getcombineDescription(ntiers,ban_from,ban_to,white_from,white_to,keyv) -{ - // var tier=getNodesInTiers(ntiers); - // var tierdesc=getDescribeTiers(ntiers); - ntiers = 1; - var tier = ""; - var tierdesc = ""; - var ban=getNodesInList(ban_from,ban_to); - var white=getNodesInList(white_from,white_to); - window.open("modify_edges_processing.php?ban="+ban+"&white="+white +"&My_key="+keyv,'_self',false); -} - -function clearBWLists() -{ - var element = document.getElementById('ban_from'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('ban_to'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('white_from'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('white_to'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } -} - - - - - -</script> -</head> - - -<script type="text/javascript"> - var nnodes =<?php print($node);?>; - var ntiers = <?php print($tier_number);?>; -</script> - -<body onload="loadFunction(nnodes,ntiers)"> - - -</br> - - -<!--- - <p><h3>2. Assign variables to tiers:<br></h3> - </p> - <br> - <div id="tier_box"> - <div id="tiers"></div> - - </div> - - - <div id="outer_tier_desc1"> - <p><h3>3. Define interactions allowed between tiers:<br></h3> - </p> - <br> - <div id="int_box1"> - </div> - <br> - <div id="int_box2"> - </div> - <br> - <div id="int_box3"> - </div> - <br> - <div id="int_box4"> - </div> - </div> - <br> - <br> - <br> - ----> - <div id="outer_box_lists"> - <p><h3>Specify edges to remove or add:<br></h3> - </p> - <br> - <div><input type="button" value="Clear lists of banned and required edges" onClick="clearBWLists()"/></div><br> - <div id="nodelist2" ondrop="return false" - ondragcenter="return false" ondragover="return false" >Nodes<br> - </div> - - <div id="ban_outer">Edges to remove<br> - <div id="ban_from" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">From<br></div> - <div id="ban_to" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">To<br></div> - </div> - <div id="white_outer">Edges to add<br> - <div id="white_from" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">From<br></div> - <div id="white_to" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">To<br></div> - </div> - </div> - - - - - <br> - <br> - - - -</body> -</div> -</html> - diff --git a/sourcecodes/modify_edges_processing.php b/sourcecodes/modify_edges_processing.php deleted file mode 100644 index 98bf3f87..00000000 --- a/sourcecodes/modify_edges_processing.php +++ /dev/null @@ -1,234 +0,0 @@ -<?php -include("input_validate.php"); -$keyval=valid_keyval($_GET["My_key"]); - -function get_tier($keyval) -{ - -$tier=trim($_GET['tier']); -$dir="./data/"; -$tf=$dir.$keyval."del_var.txt"; -$fpvar = fopen("$tf","w"); - -fwrite($fpvar,"$tier"); -fclose($fpvar); -} - - -function enter_ban_list($t1,$s1,$t2,$s2,$tier_d,$fpvar) -{ - - for ($i=0;$i<$s1;$i++) - { - $data_val_1=$tier_d[$t1][$i]; - - for ($j=0;$j<$s2;$j++) - { - $data_val_2=$tier_d[$t2][$j]; - if($data_val_1!=$data_val_2) - { - - fprintf($fpvar,"%s\t%s\n",$data_val_1,$data_val_2); - - - } - - } - - } - - -} - - - -function describe_tier($fpvar,$keyval) -{ - - -$tierdesc=trim($_GET['tierdesc']); -$dir="./data/"; -$tf=$dir.$keyval."tier.txt"; -$tier=file_get_contents("$tf"); - -$tier_data=array(); -$tier_size=array(); -$tier_d=array(); -$tier_data=explode(",",$tier); - -$tn=$tier_data[0]; -$count=0; - -for ($i=0;$i<$tn;$i++) -{ - $count+=2; - $tier_size[$i]=$tier_data[$count]; - - $rs=$tier_size[$i]; - for ($j=0;$j<$rs;$j++) - { - $count++; - $tier_d[$i][$j]=$tier_data[$count]; - - - } - -} - - - -$data=array(); -$data=explode(",",$tierdesc); -$n=count($data); -$nn=0; -$di=0; -for ($i=0;$i<$tn;$i++) -{ - -$d_y=trim($data[$di]); -$di++; -$d_n=trim($data[$di]); - -if($d_n=="true") //put data in banlist -{ - $s1=$tier_size[$i]; - enter_ban_list($i,$s1,$i,$s1,$tier_d,$fpvar); - -} -$di++; - - - for ($j=0;$j<$tn;$j++) - { - if($j!=$i) - { - $p_d=trim($data[$di]); - $di++; - - if($p_d=="false") //put data in banlist - { - $s1=$tier_size[$j]; - $s2=$tier_size[$i]; - //echo $tier_size[$j]; - enter_ban_list($j,$s1,$i,$s2,$tier_d,$fpvar); - } - - - - $c_d=trim($data[$di]); - $di++; - if($c_d=="false") //put data in banlist - { - $s1=$tier_size[$i]; - $s2=$tier_size[$j]; - // echo $tier_size[$j]; - enter_ban_list($i,$s1,$j,$s2,$tier_d,$fpvar); - } - - - } - } - -} - - -} - - -function banlist($fpvar) -{ -$ban=trim($_GET['ban']); -$data=array(); -$data=explode(",",$ban); -$n=count($data); -$nn=0; -for ($i=0;$i<$n;$i+=2) -{ - $ii=$i+1; - $d1=trim($data[$i]); - $d2=trim($data[$ii]); - - if($d1!="" && $d2!="") - { - fprintf($fpvar,"%s\t%s\n",$d1,$d2); - $nn++; - } - -} - -} - -function whitelist($fpvar) -{ - -$white=trim($_GET['white']); - - - -$data=array(); -$data=explode(",",$white); -$n=count($data); -$nn=0; -for ($i=0;$i<$n;$i+=2){ -$ii=$i+1; -$d1=trim($data[$i]); -$d2=trim($data[$ii]); - -if($d1!="" && $d2!="") -{ - fprintf($fpvar,"%s\t%s\n",$d1,$d2); - $nn++; -} - -} - - -} - - -/////////////////////Call functions////////////////////// - - - -$dir="./data/"; - -$sid1=$dir.$keyval."del_edge"; -$sid2=$dir.$keyval."add_edge"; - -$Textban=$sid1.".txt"; -$Textwhite=$sid2.".txt"; -$fpb = fopen($Textban,"w"); -$fpw = fopen($Textwhite,"w"); -$datpost="From\tTo\n"; -fwrite($fpb,"$datpost"); -fwrite($fpw,"$datpost"); - -get_tier($keyval); - - -//describe_tier($fpb,$keyval); -banlist($fpb); -whitelist($fpw); - - -$oldkey=$keyval; - -///Generate new random key -$alphas=array(); -$alphas = array_merge(range('A', 'Z'), range('a', 'z')); - -$al1=rand(0,51); -$al2=rand(0,51); -$al3=rand(0,51); - -$alpha="$alphas[$al1]"."$alphas[$al2]"."$alphas[$al3]"; -$keyval=$alpha; - -shell_exec('./run_scripts/run_mod_edges '.$oldkey.' '.$keyval); - - -////////////////////////////////////execute structurelearning///////////////////////////////////////////////////////////////////////////////////////////// -?> -<script> -window.open("graphviz_structure.php?My_key=<?php print($keyval);?>",'_self',false); -</script> \ No newline at end of file diff --git a/sourcecodes/modify_structure_learning.php b/sourcecodes/modify_structure_learning.php index 35e805d5..1b0a70ef 100644 --- a/sourcecodes/modify_structure_learning.php +++ b/sourcecodes/modify_structure_learning.php @@ -7,9 +7,7 @@ function get_tier($keyval) $tier=trim($_GET['tier']); //$dir="./data/"; -//$dir="/tmp/bnw/"; - -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."del_var.txt"; $fpvar = fopen("$tf","w"); @@ -233,4 +231,4 @@ shell_exec('./run_scripts/run_prep_input '.$keyval); ?> <script> window.open("bn_after_upload_gom.php?My_key=<?php print($keyval);?>",'_self',false); -</script> +</script> \ No newline at end of file diff --git a/sourcecodes/net_structure.php b/sourcecodes/net_structure.php index 12126e45..dfe14b99 100644 --- a/sourcecodes/net_structure.php +++ b/sourcecodes/net_structure.php @@ -9,30 +9,29 @@ include("input_validate.php"); $searchID=""; $UploadValue="NO"; -$TextFile=$_FILES["MyFile"]["name"]; - -if($_GET["My_key"]!="") - $keyval=$_GET["My_key"]; +$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; if($_POST["My_key"]!="") $keyval=$_POST["My_key"]; +if($_GET["My_key"]!="") + $keyval=$_GET["My_key"]; + $keyval=valid_keyval($keyval); $sid="structure_input"; //$dir="./data/"; -//$dir="/tmp/bnw/".$keyval; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/".$keyval; -$TextinFile=$dir.$keyval.$sid.".txt"; +$TextinFile=$dir.$sid.".txt"; //$TextinFileFinal=$dir.$sid.".txt"; //$TextinFile=$dir.$sid."_temp.txt"; -if(isset($_POST["searchkey"])) +if(isset($HTTP_POST_VARS["searchkey"])) { - $searchID=$_POST["searchkey"]; + $searchID=$HTTP_POST_VARS["searchkey"]; } @@ -49,14 +48,14 @@ if($searchID=="") <?php } -if(isset($_POST["MyUpload"])) +if(isset($HTTP_POST_VARS["MyUpload"])) { - $UploadValue=$_POST["MyUpload"]; + $UploadValue=$HTTP_POST_VARS["MyUpload"]; if ($UploadValue=="YES") { if($TextFile!="") { - $sta=move_uploaded_file($_FILES['MyFile']['tmp_name'],$TextinFile); + $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); if(!$sta) { echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; diff --git a/sourcecodes/net_structure.php.bk b/sourcecodes/net_structure.php.bk deleted file mode 100644 index 395c6112..00000000 --- a/sourcecodes/net_structure.php.bk +++ /dev/null @@ -1,132 +0,0 @@ -<?php -include("header_new.inc"); -include("header_batchsearch.inc"); -include("input_validate.php"); -////////////////continuous/////////////// -$searchID=""; -$UploadValue="NO"; -$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; - -if($_POST["My_key"]!="") - $keyval=$_POST["My_key"]; - -if($_GET["My_key"]!="") - $keyval=$_GET["My_key"]; - -$keyval=valid_keyval($keyval); - -$sid="structure_input"; -//$dir="./data/$keyval"; -$dir="/tmp/bnw/$keyval"; - -$TextinFileFinal=$dir.$sid.".txt"; - -$TextinFile=$dir.$sid."_temp.txt"; - -$TextinFilenamelist=$dir."name.txt"; - -if(isset($HTTP_POST_VARS["searchkey"])) -{ - $searchID=$HTTP_POST_VARS["searchkey"]; -} - -if(isset($HTTP_POST_VARS["MyUpload"])) -{ - $UploadValue=$HTTP_POST_VARS["MyUpload"]; - if ($UploadValue=="YES") - { - if($TextFile!="") - { - $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); - if(!$sta) - { - echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; - flush(); - exit(); - } - else - { - $searchID=file_get_contents("$TextinFile"); - //fclose($fh); - unlink($TextinFile); - - } - - } - - else - { - echo "<script type='text/javascript'> window.alert ('Sorry, please select upload file.')</script>"; - } - } -} - -if($searchID!="") -{ -?> - -<!-- Site navigation menu --> -<ul class="navbar"> - <li><a href="graphviz_structure.php?My_key=<?php print($keyval);?>">Display structure</a> -</ul> -<ul class="navbar"> - <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> -</ul> -<div id="outernew_load"> -</div> -<?php -} -else -{ - -?> -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> - <li><a href="help.php" target='_blank'>Help</a> - <li><a href="home.php">Home</a> -</ul> -<?php -} -?> - -<div id="outernew"> - -<h2>Upload network structure</h2> -<FORM name="key_search" id="in_form" enctype="multipart/form-data" ACTION="net_structure.php" METHOD=POST> -<INPUT style="background-color:#FFFFFF;color:#0000FF" type="file" name="MyFile" id="MyFile_id" class="inputfile" onchange="upload_submit()" > -<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > -<INPUT TYPE="hidden" name="MyUpload" value="NO"> -<textarea name="searchkey" style="display:none"><?PHP print($searchID)?> </textarea> -<br><br> -<INPUT TYPE="submit" value=" Load example structure " onclick="return demo_str();">    -<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > -</FORM> - -</div> -<script> - function upload_submit() { - Upload(); - document.getElementById("in_form").submit(); -} -</script> - - -<?php - $str_arr=array(); - $searchID=trim($searchID); - $str_arr=explode("\n",$searchID); - $data=array(); - - $fpmain = fopen($TextinFileFinal,"w"); - - foreach($str_arr as $line) - { - $line=trim($line); - fwrite($fpmain, "$line\n"); - - } - -?> diff --git a/sourcecodes/net_structure.php~ b/sourcecodes/net_structure.php~ deleted file mode 100644 index d4462962..00000000 --- a/sourcecodes/net_structure.php~ +++ /dev/null @@ -1,136 +0,0 @@ -<?php - //Going to modify this so it just writes the uploaded data to a file. - //Standardization and determining other factors will be performed in - // a Matlab/Octave script. - -include("header_new.inc"); -include("header_batchsearch.inc"); -include("input_validate.php"); - -$searchID=""; -$UploadValue="NO"; -$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; - -if($_POST["My_key"]!="") - $keyval=$_POST["My_key"]; - -if($_GET["My_key"]!="") - $keyval=$_GET["My_key"]; - -$keyval=valid_keyval($keyval); - -$sid="structure_input"; -//$dir="./data/"; -$dir="/tmp/bnw/".$keyval; - -$TextinFile=$dir.$sid.".txt"; - -//$TextinFileFinal=$dir.$sid.".txt"; - -//$TextinFile=$dir.$sid."_temp.txt"; - -if(isset($HTTP_POST_VARS["searchkey"])) -{ - $searchID=$HTTP_POST_VARS["searchkey"]; - -} - -if($searchID=="") -{ -?> - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> -</ul> -<?php -} - -if(isset($HTTP_POST_VARS["MyUpload"])) -{ - $UploadValue=$HTTP_POST_VARS["MyUpload"]; - if ($UploadValue=="YES") - { - if($TextFile!="") - { - $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); - if(!$sta) - { - echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; - flush(); - exit(); - } - else - { - $searchID=file_get_contents("$TextinFile"); - //unlink($TextinFile); - } - } - else - { - echo "<script type='text/javascript'> window.alert ('Sorry, please select upload file.')</script>"; - } - } -} - -?> -<div id="outernew"> -<h2><font>Upload structure file</font></h2> -<FORM name="key_search" id="in_form" enctype="multipart/form-data" ACTION="net_structure.php" METHOD=POST> -<INPUT style="background-color:#FFFFFF;" type="file" name="MyFile" id="MyFile_id" class="inputfile" onchange="upload_submit()" > -<label for="MyFile_id">Choose a file. . .</label> - <INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > -<INPUT TYPE="hidden" name="MyUpload" value="NO"> - <textarea name="searchkey" style="display:none;"><?PHP print($searchID)?> </textarea> -<br><br> - <INPUT TYPE="submit" class=button2 value=" Load example structure " onclick="return demo_str();">    - <INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > -</FORM> -</div> -<script> - function upload_submit() { - Upload(); - document.getElementById("in_form").submit(); - } -</script> - -<?php - -if($searchID!="") - { - if ($UploadValue=="NO") - { - $str_arr=array(); - $searchID=trim($searchID); - $str_arr=explode("\n",$searchID); - $data=array(); - - $fpmain = fopen($TextinFile,"w"); - - foreach($str_arr as $line) - { - $line=trim($line); - fwrite($fpmain, "$line\n"); - - } - } -?> -<ul class="navbar2"> - <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> -</ul> -<div id="outernew_load"> -<br> -<a class=button3 href="graphviz_structure.php?My_key=<?php print($keyval);?>">Display uploaded network</a> -<br> -<?php -} -?> - -</body> -</html> - - diff --git a/sourcecodes/network_layout_evd.php b/sourcecodes/network_layout_evd.php index 7d97483a..32e1b7bf 100644 --- a/sourcecodes/network_layout_evd.php +++ b/sourcecodes/network_layout_evd.php @@ -28,8 +28,7 @@ foreach($leve_l as $l) /////////////Read data from net_figure file///////////// //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $keyval=valid_keyval($_GET["My_key"]); @@ -240,7 +239,7 @@ $nedges=$ii; <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=utf-8"/> -<script type="text/javascript" src="https://www.google.com/jsapi"></script> +<script type="text/javascript" src="http://www.google.com/jsapi"></script> <script type="text/javascript"> google.load('visualization', '1', {packages: ['corechart']}); </script> diff --git a/sourcecodes/network_layout_evd_2.php b/sourcecodes/network_layout_evd_2.php index ed9ce502..7703daab 100644 --- a/sourcecodes/network_layout_evd_2.php +++ b/sourcecodes/network_layout_evd_2.php @@ -27,8 +27,7 @@ foreach($leve_l as $l) $keyval=valid_keyval($_GET["My_key"]); //////////////////////////Entered evidences////////////////////////////////////////// //$dir="./data/"; -//$dir ="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir ="/tmp/bnw/"; $lfile=$dir.$keyval."nlevels.txt"; $levelmap=file_get_contents($lfile); @@ -378,7 +377,7 @@ $nedges=$ii; <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=utf-8"/> -<script type="text/javascript" src="https://www.google.com/jsapi"></script> +<script type="text/javascript" src="http://www.google.com/jsapi"></script> <script type="text/javascript"> google.load('visualization', '1', {packages: ['corechart']}); </script> diff --git a/sourcecodes/network_layout_inv.php b/sourcecodes/network_layout_inv.php index 7442026f..d457212e 100644 --- a/sourcecodes/network_layout_inv.php +++ b/sourcecodes/network_layout_inv.php @@ -24,8 +24,7 @@ foreach($leve_l as $l) $keyval=valid_keyval($_GET["My_key"]); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $lfile=$dir.$keyval."nlevels.txt"; $levelmap=file_get_contents($lfile); @@ -234,7 +233,7 @@ $nedges=$ii; <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=utf-8"/> -<script type="text/javascript" src="https://www.google.com/jsapi"></script> +<script type="text/javascript" src="http://www.google.com/jsapi"></script> <script type="text/javascript"> google.load('visualization', '1', {packages: ['corechart']}); </script> diff --git a/sourcecodes/network_layout_inv_2.php b/sourcecodes/network_layout_inv_2.php index c851f018..e6e9b128 100644 --- a/sourcecodes/network_layout_inv_2.php +++ b/sourcecodes/network_layout_inv_2.php @@ -27,8 +27,7 @@ foreach($leve_l as $l) $keyval=valid_keyval($_GET["My_key"]); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $lfile=$dir.$keyval."nlevels.txt"; $levelmap=file_get_contents($lfile); @@ -528,7 +527,7 @@ $nedges=$ii; <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=utf-8"/> -<script type="text/javascript" src="https://www.google.com/jsapi"></script> +<script type="text/javascript" src="http://www.google.com/jsapi"></script> <script type="text/javascript"> google.load('visualization', '1', {packages: ['corechart']}); </script> diff --git a/sourcecodes/parameter_display.php b/sourcecodes/parameter_display.php index df85468c..0eff882c 100644 --- a/sourcecodes/parameter_display.php +++ b/sourcecodes/parameter_display.php @@ -5,12 +5,11 @@ include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; +$dir="./data/"; //$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; -$param_file = $keyval."parameters.txt"; -$param_ev_file = $keyval."parameters_ev.txt"; +$param_file = $dir.$keyval."parameters.txt"; +$param_ev_file = $dir.$keyval."parameters_ev.txt"; ?> @@ -27,14 +26,9 @@ $param_ev_file = $keyval."parameters_ev.txt"; <body> <div class='table_div' id='parameter_div'> - <?php - $table_text = json_encode(file("file://".$dir.$param_file)); - ?> <script type="text/javascript"> - d3.text("", function(error, raw){ - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data = data2.split("\n\n"); + d3.text("<?php print($param_file);?>", function(error, raw){ + var data = raw.split("\n\n"); var dsv = d3.dsvFormat("\t"); var i; for (i = 0; i < data.length; i++) { @@ -55,15 +49,12 @@ $param_ev_file = $keyval."parameters_ev.txt"; }); </script> <?php -if(file_exists($dir.$param_ev_file)) -{ -$table_text = json_encode(file("file://".$dir.$param_ev_file)); -?> +$filename="/tmp/bnw/".$keyval."parameters_ev.txt"; +if(file_exists($filename)) +{?> <script type="text/javascript"> - d3.text("", function(error, raw){ - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data = data2.split("\n\n"); + d3.text("<?php print($param_ev_file);?>", function(error, raw){ + var data = raw.split("\n\n"); var dsv = d3.dsvFormat("\t"); var i; for (i = 1000; i < data.length + 1000; i++) { @@ -91,9 +82,10 @@ $table_text = json_encode(file("file://".$dir.$param_ev_file)); <h3 id="header">Original network parameters</h3> </div> <div id="download"> - <a class=button2 target="_blank" href="<?php print("reroute.php?".$param_file);?>">Download original parameters</a><br><br> + <a class=button2 href="<?php print($param_file);?>">Download original parameters</a><br><br> <?php -if(file_exists($dir.$param_ev_file)) +$filename="/tmp/bnw/".$keyval."parameters_ev.txt"; +if(file_exists($filename)) {?> <h3> Network parameters considering evidence/intervention</h3> <?php @@ -111,10 +103,11 @@ if(file_exists($dir.$param_ev_file)) } </script> <?php -if(file_exists($dir.$param_ev_file)) +$filename="/tmp/bnw/".$keyval."parameters_ev.txt"; +if(file_exists($filename)) {?> <div id="download2"> - <a class=button2 href="<?php print("reroute.php?".$param_ev_file);?>">Download parameters considering evidence/intervention</a><br><br> + <a class=button2 href="<?php print($param_ev_file);?>">Download parameters considering evidence/intervention</a><br><br> </div> <?php } diff --git a/sourcecodes/parameter_display.php.bk b/sourcecodes/parameter_display.php.bk deleted file mode 100644 index dedfa3cb..00000000 --- a/sourcecodes/parameter_display.php.bk +++ /dev/null @@ -1,19 +0,0 @@ -<?php -include("input_validate.php"); -$keyval=valid_keyval($_GET["My_key"]); -?> - -<h3> <a href=<?php $d="./data/".$keyval."parameters.txt"; print($d);?>>View original parameters</a></h3> -<br> - -<br> - -<?php -$filename="/tmp/bnw/".$keyval."parameters_ev.txt"; -if(file_exists($filename)) -{?> -<h3> <a href=<?php $d="./data/".$keyval."parameters_ev.txt"; print($d);?>>View parameters after added evidence or intervention</a></h3> -<br> -<?php -} -?> diff --git a/sourcecodes/parameter_learning/createJSON.m b/sourcecodes/parameter_learning/createJSON.m index e6fd7ea2..59a3aec4 100644 --- a/sourcecodes/parameter_learning/createJSON.m +++ b/sourcecodes/parameter_learning/createJSON.m @@ -12,10 +12,6 @@ function [ ] = createJSON( pre ) % -nnodefile=strcat(pre,'nnode.txt'); -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - % open file for input, include error handling dfile=strcat(pre,'structure_input.txt'); @@ -26,6 +22,7 @@ end % Read in first line to get the number of nodes and the node labels. buffer = strtrim(fgetl(fin)); %get header line as a string +nnodes = numel(strfind(buffer,"\t"))+1; labels = cell(1,nnodes); for j=1:nnodes [next,buffer] = strtok(buffer); diff --git a/sourcecodes/parameter_learning/createSVG.m b/sourcecodes/parameter_learning/createSVG.m index 2d190b68..47894c1b 100644 --- a/sourcecodes/parameter_learning/createSVG.m +++ b/sourcecodes/parameter_learning/createSVG.m @@ -16,10 +16,6 @@ function [ ] = createSVG( pre ) % -nnodefile=strcat(pre,'nnode.txt'); -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - % open file for input, include error handling dfile=strcat(pre,'structure_input.txt'); @@ -30,20 +26,19 @@ end % Read in first line to get the number of nodes and the node labels. buffer = fgetl(fin); %get header line as a string - +nnodes = numel(strfind(buffer,"\t")) + 1; labels = cell(1,nnodes); for j=1:nnodes - j, buffer [next,buffer] = strtok(buffer); labels{j} = next; end + % Read in the edges edges = cell(nnodes,nnodes); for i = 1:nnodes buffer = fgetl(fin); for j = 1:nnodes - i, j, buffer [next,buffer] = strtok(buffer); edges{i,j} = next; end diff --git a/sourcecodes/parameter_learning/kfoldCrossValid.m b/sourcecodes/parameter_learning/kfoldCrossValid.m index 40b72c61..2af690d7 100644 --- a/sourcecodes/parameter_learning/kfoldCrossValid.m +++ b/sourcecodes/parameter_learning/kfoldCrossValid.m @@ -4,7 +4,7 @@ function kfoldCrossValid(pre,predict_label,nfolds) % that you want to predict and the number of folds that the % data should be divided into. -nfolds = uint8(str2num(nfolds)); +nfolds = uint16(str2num(nfolds)); sfile=strcat(pre,'structure_input.txt'); dfile=strcat(pre,'continuous_input.txt'); diff --git a/sourcecodes/parameter_learning/modifyEdges.m b/sourcecodes/parameter_learning/modifyEdges.m index 6542d9fb..c435806a 100644 --- a/sourcecodes/parameter_learning/modifyEdges.m +++ b/sourcecodes/parameter_learning/modifyEdges.m @@ -58,7 +58,6 @@ for j=1:nedges sources{j} = str2num(next); end - buffer = fgetl(fin2); buffer = buffer(2:end-1); buffer = strrep(buffer,"\"",""); @@ -76,7 +75,6 @@ for j=1:nedges weights{j} = next; end - %label_map is the index in "labels" that corresponds to each label in "labels2" label_map = cell(1,nnodes); for i = 1:nnodes @@ -99,6 +97,8 @@ for i = 1:nedges edges_out(source_i,target_i) = "1"; end +%scores_out + tf = cellfun('isempty',edges_out); edges_out(tf) = {"0"}; @@ -113,28 +113,25 @@ for i=1:nnodes end end - if test_score == 1 outfile = strcat(pre_new,'structure_input_temp.txt'); fout = fopen(outfile,'w'); fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\t\n',labels{end}); +fprintf(fout,'%s\n',labels{end}); for i = 1:nnodes fprintf(fout,'%s\t',scores_out{i,1:end-1}); - fprintf(fout,'%s\t\n',scores_out{i,end}); + fprintf(fout,'%s\n',scores_out{i,end}); end fclose(fout); end - - outfile2 = strcat(pre_new,'structure_input.txt'); fout2 = fopen(outfile2,'w'); fprintf(fout2,'%s\t',labels{1:end-1}); -fprintf(fout2,'%s\t\n',labels{end}); +fprintf(fout2,'%s\n',labels{end}); for i = 1:nnodes fprintf(fout2,'%s\t',edges_out{i,1:end-1}); - fprintf(fout2,'%s\t\n',edges_out{i,end}); + fprintf(fout2,'%s\n',edges_out{i,end}); end fclose(fout2); diff --git a/sourcecodes/parameter_learning/normpdf.m b/sourcecodes/parameter_learning/normpdf.m deleted file mode 100644 index 2b154f02..00000000 --- a/sourcecodes/parameter_learning/normpdf.m +++ /dev/null @@ -1,50 +0,0 @@ -function p = normpdf(x,m,s); -% Normal probability density function -% -% pdf = normpdf(x,m,s); -% -% Computes the PDF of a the normal distribution -% with mean m and standard deviation s -% default: m=0; s=1; -% x,m,s must be matrices of same size, or any one can be a scalar. -% -% see also: NORMCDF, NORMINV - -% Reference(s): - -% Version 1.28 Date: 23.Sep.2002 -% Copyright (c) 2000-2002 by Alois Schloegl <a.schloegl@ieee.org> - -% This program is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published by -% the Free Software Foundation; either version 2 of the License, or -% (at your option) any later version. -% -% This program is distributed in the hope that it will be useful, -% but WITHOUT ANY WARRANTY; without even the implied warranty of -% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License for more details. -% -% You should have received a copy of the GNU General Public License -% along with this program; if not, write to the Free Software -% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - -if nargin==1, - m=0;s=1; -elseif nargin==2, - s=1; -end; - -% allocate output memory and check size of argument -z = (x-m)./s; % if this line causes an error, input arguments do not fit. - -%p = ((2*pi)^(-1/2))*exp(-z.^2/2)./s; -SQ2PI = 2.5066282746310005024157652848110; -p = exp(-z.^2/2)./(s*SQ2PI); - -p((x==m) & (s==0)) = inf; - -p(isinf(z)~=0) = 0; - -p(isnan(x) | isnan(m) | isnan(s) | (s<0)) = nan; - diff --git a/sourcecodes/parameter_learning/normrnd.m b/sourcecodes/parameter_learning/normrnd.m deleted file mode 100644 index 0267ddf6..00000000 --- a/sourcecodes/parameter_learning/normrnd.m +++ /dev/null @@ -1,130 +0,0 @@ -## Copyright (C) 2012 Rik Wehbring -## Copyright (C) 1995-2012 Kurt Hornik -## -## This file is part of Octave. -## -## Octave is free software; you can redistribute it and/or modify it -## under the terms of the GNU General Public License as published by -## the Free Software Foundation; either version 3 of the License, or (at -## your option) any later version. -## -## Octave is distributed in the hope that it will be useful, but -## WITHOUT ANY WARRANTY; without even the implied warranty of -## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -## General Public License for more details. -## -## You should have received a copy of the GNU General Public License -## along with Octave; see the file COPYING. If not, see -## <http://www.gnu.org/licenses/>. - -## -*- texinfo -*- -## @deftypefn {Function File} {} normrnd (@var{mu}, @var{sigma}) -## @deftypefnx {Function File} {} normrnd (@var{mu}, @var{sigma}, @var{r}) -## @deftypefnx {Function File} {} normrnd (@var{mu}, @var{sigma}, @var{r}, @var{c}, @dots{}) -## @deftypefnx {Function File} {} normrnd (@var{mu}, @var{sigma}, [@var{sz}]) -## Return a matrix of random samples from the normal distribution with -## parameters mean @var{mu} and standard deviation @var{sigma}. -## -## When called with a single size argument, return a square matrix with -## the dimension specified. When called with more than one scalar argument the -## first two arguments are taken as the number of rows and columns and any -## further arguments specify additional matrix dimensions. The size may also -## be specified with a vector of dimensions @var{sz}. -## -## If no size arguments are given then the result matrix is the common size of -## @var{mu} and @var{sigma}. -## @end deftypefn - -## Author: KH <Kurt.Hornik@wu-wien.ac.at> -## Description: Random deviates from the normal distribution - -function rnd = normrnd (mu, sigma, varargin) - - if (nargin < 2) - print_usage (); - endif - - if (!isscalar (mu) || !isscalar (sigma)) - [retval, mu, sigma] = common_size (mu, sigma); - if (retval > 0) - error ("normrnd: mu and sigma must be of common size or scalars"); - endif - endif - - if (iscomplex (mu) || iscomplex (sigma)) - error ("normrnd: MU and SIGMA must not be complex"); - endif - - if (nargin == 2) - sz = size (mu); - elseif (nargin == 3) - if (isscalar (varargin{1}) && varargin{1} >= 0) - sz = [varargin{1}, varargin{1}]; - elseif (isrow (varargin{1}) && all (varargin{1} >= 0)) - sz = varargin{1}; - else - error ("normrnd: dimension vector must be row vector of non-negative integers"); - endif - elseif (nargin > 3) - if (any (cellfun (@(x) (!isscalar (x) || x < 0), varargin))) - error ("normrnd: dimensions must be non-negative integers"); - endif - sz = [varargin{:}]; - endif - - if (!isscalar (mu) && !isequal (size (mu), sz)) - error ("normrnd: mu and sigma must be scalar or of size SZ"); - endif - - if (isa (mu, "single") || isa (sigma, "single")) - cls = "single"; - else - cls = "double"; - endif - - if (isscalar (mu) && isscalar (sigma)) - if (!isnan (mu) && !isinf (mu) && (sigma > 0) && (sigma < Inf)) - rnd = mu + sigma * randn (sz); - else - rnd = NaN (sz, cls); - endif - else - rnd = mu + sigma .* randn (sz); - k = isnan (mu) | isinf (mu) | !(sigma > 0) | !(sigma < Inf); - rnd(k) = NaN; - endif - -endfunction - - -%!assert(size (normrnd (1,2)), [1, 1]); -%!assert(size (normrnd (ones(2,1), 2)), [2, 1]); -%!assert(size (normrnd (ones(2,2), 2)), [2, 2]); -%!assert(size (normrnd (1, 2*ones(2,1))), [2, 1]); -%!assert(size (normrnd (1, 2*ones(2,2))), [2, 2]); -%!assert(size (normrnd (1, 2, 3)), [3, 3]); -%!assert(size (normrnd (1, 2, [4 1])), [4, 1]); -%!assert(size (normrnd (1, 2, 4, 1)), [4, 1]); - -%% Test class of input preserved -%!assert(class (normrnd (1, 2)), "double"); -%!assert(class (normrnd (single(1), 2)), "single"); -%!assert(class (normrnd (single([1 1]), 2)), "single"); -%!assert(class (normrnd (1, single(2))), "single"); -%!assert(class (normrnd (1, single([2 2]))), "single"); - -%% Test input validation -%!error normrnd () -%!error normrnd (1) -%!error normrnd (ones(3),ones(2)) -%!error normrnd (ones(2),ones(3)) -%!error normrnd (i, 2) -%!error normrnd (2, i) -%!error normrnd (1,2, -1) -%!error normrnd (1,2, ones(2)) -%!error normrnd (1, 2, [2 -1 2]) -%!error normrnd (1,2, 1, ones(2)) -%!error normrnd (1,2, 1, -1) -%!error normrnd (ones(2,2), 2, 3) -%!error normrnd (ones(2,2), 2, [3, 2]) -%!error normrnd (ones(2,2), 2, 2, 3) diff --git a/sourcecodes/remove_variables.php b/sourcecodes/remove_variables.php index 1373bcae..5069904f 100644 --- a/sourcecodes/remove_variables.php +++ b/sourcecodes/remove_variables.php @@ -8,8 +8,7 @@ include("input_validate.php"); $keyval=$_GET["My_key"]; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $type_n=array(); @@ -101,14 +100,14 @@ $runtime=exe_time($keyval,$parent_number,$k_number); <?php -if(isset($_POST["bantext"])) +if(isset($HTTP_POST_VARS["bantext"])) { - $ban_search=$_POST["searchkey"]; + $ban_search=$HTTP_POST_VARS["searchkey"]; } -if(isset($_POST["whitetext"])) +if(isset($HTTP_POST_VARS["whitetext"])) { - $white_search=$_POST["searchkey"]; + $white_search=$HTTP_POST_VARS["searchkey"]; } ?> @@ -834,7 +833,7 @@ function getcombineDescription(ntiers,ban_from,ban_to,white_from,white_to,keyv) ntiers = 1; var tier=getNodesInTiers(ntiers); // var txtFile="./data/"+keyv+"del_var.txt"; - var txtFile="/var/lib/genene/bnw/"+keyv+"del_var.txt"; + var txtFile="/tmp/bnw/"+keyv+"del_var.txt"; //var file = new File(txtFile); //file.open("w"); //file.write(tier); diff --git a/sourcecodes/remove_variables_processing.php b/sourcecodes/remove_variables_processing.php index 0a147595..1d3aba2c 100644 --- a/sourcecodes/remove_variables_processing.php +++ b/sourcecodes/remove_variables_processing.php @@ -7,8 +7,7 @@ function get_tier($keyval) $tier=trim($_GET['tier']); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."del_var.txt"; $fpvar = fopen("$tf","w"); @@ -50,8 +49,7 @@ function describe_tier($fpvar,$keyval) $tierdesc=trim($_GET['tierdesc']); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."tier.txt"; $tier=file_get_contents("$tf"); @@ -195,8 +193,7 @@ if($d1!="" && $d2!="") //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; //$sid1=$dir.$keyval."ban"; //$sid2=$dir.$keyval."white"; @@ -235,4 +232,4 @@ shell_exec('./run_scripts/run_del_var '.$oldkey.' '.$keyval); ?> <script> window.open("create_tiers_gom_part1.php?My_key=<?php print($keyval);?>",'_self',false); -</script> +</script> \ No newline at end of file diff --git a/sourcecodes/remove_variables_processing_default.php b/sourcecodes/remove_variables_processing_default.php index 90258420..3c5ffb68 100644 --- a/sourcecodes/remove_variables_processing_default.php +++ b/sourcecodes/remove_variables_processing_default.php @@ -7,8 +7,7 @@ function get_tier($keyval) $tier=trim($_GET['tier']); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."del_var.txt"; $fpvar = fopen("$tf","w"); @@ -50,8 +49,7 @@ function describe_tier($fpvar,$keyval) $tierdesc=trim($_GET['tierdesc']); //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."tier.txt"; $tier=file_get_contents("$tf"); @@ -195,8 +193,7 @@ if($d1!="" && $d2!="") //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; //$sid1=$dir.$keyval."ban"; //$sid2=$dir.$keyval."white"; @@ -235,4 +232,4 @@ shell_exec('./run_scripts/run_del_var '.$oldkey.' '.$keyval); ?> <script> window.open("executionprogress.php?My_key=<?php print($keyval);?>",'_self',false); -</script> +</script> \ No newline at end of file diff --git a/sourcecodes/reroute.php b/sourcecodes/reroute.php deleted file mode 100644 index da1152dd..00000000 --- a/sourcecodes/reroute.php +++ /dev/null @@ -1,21 +0,0 @@ -<?php -## -## Retrieve the file passed in the URL and send it to the browser. -## Set the $WORKDIR variable to point to the directory containing -## the files to be displayed. - -$FILENAME = $_SERVER['QUERY_STRING']; -$WORKDIR = '/var/lib/genenet/bnw/'; - -if ( file_exists( $WORKDIR . $FILENAME ) ) -{ - header("Content-type: text/plain"); - ##readfile($WORKDIR.$FILENAME); - print file_get_contents( "file://" . $WORKDIR . $FILENAME, FALSE ); -} -else -{ - echo " File " . $FILENAME . " not found in " . $WORKDIR . "\n"; -} -?> - diff --git a/sourcecodes/review_settings.php b/sourcecodes/review_settings.php index d945ce00..0a2d93d8 100644 --- a/sourcecodes/review_settings.php +++ b/sourcecodes/review_settings.php @@ -5,11 +5,10 @@ include("header_new.inc"); include("input_validate.php"); $keyval=valid_keyval($_GET["My_key"]); -//$dir="./data/"; +$dir="./data/"; //$dir="/tmp/bnw/"; -$dir = "/var/lib/genenet/bnw/"; -$settings_file = $keyval."slsettings.txt"; +$settings_file = $dir.$keyval."slsettings.txt"; ?> @@ -25,24 +24,10 @@ $settings_file = $keyval."slsettings.txt"; </ul> <body> - -<?php -if(!file_exists($dir.$settings_file)) - { -?> - <div class='table_div'> - <h3> No structure learning settings file found. </h3> - </div> -<?php -} else { -$table_text = json_encode(file("file://".$dir.$settings_file)); -?> <div class='table_div' id='parameter_div'> <script type="text/javascript"> - d3.text("", function(error, raw){ - var data1 = <?php echo $table_text;?>; - var data2 = data1.join("") - var data = data2.split("\n\n"); + d3.text("<?php print($settings_file);?>", function(error, raw){ + var data = raw.split("\n\n"); var dsv = d3.dsvFormat("\t"); var i; for (i = 0; i < data.length; i++) { @@ -66,15 +51,13 @@ $table_text = json_encode(file("file://".$dir.$settings_file)); <div id="table_header"> </div> <div id="download"> - <a class=button2 href="<?php print("reroute.php?".$settings_file);?>">Download structure learning settings file</a><br><br> + <a class=button2 href="<?php print($settings_file);?>">Download structure learning settings file</a><br><br> </div> -<?php -} -?> <script type="text/javascript"> function add_header() { var element = document.getElementById("table_header"); var parentNode = document.getElementById("parameter_div"); + console.log(parentNode); parentNode.insertBefore(element,parentNode.firstChild); var element = document.getElementById("download"); parentNode.appendChild(element); diff --git a/sourcecodes/run.sh b/sourcecodes/run.sh index 344b7591..12bab53f 100644 --- a/sourcecodes/run.sh +++ b/sourcecodes/run.sh @@ -3,24 +3,24 @@ #ess=1 #DIR="$d/data/$1" #DIR_1="$d/data/$1/" -cd /var/lib/genenet/bnw +cd /tmp/bnw -mkdir -p /var/lib/genenet/bnw/$1 +mkdir -p /tmp/bnw/$1 maxparent=$2 k=$3 THR=$4 -./network_score /var/lib/genenet/bnw/$1continuous_input.txt /var/lib/genenet/bnw/$1ban.txt /var/lib/genenet/bnw/$1white.txt $maxparent /var/lib/genenet/bnw/$1 +./network_score /tmp/bnw/$1continuous_input.txt /tmp/bnw/$1ban.txt /tmp/bnw/$1white.txt $maxparent /tmp/bnw/$1 -./k-best/src/data2netk_poster.sh /var/lib/genenet/bnw/$1continuous_input.txt /var/lib/genenet/bnw/$1 $k $maxparent +./k-best/src/data2netk_poster.sh /tmp/bnw/$1continuous_input.txt /tmp/bnw/$1 $k $maxparent -./structure /var/lib/genenet/bnw/$1continuous_input.txt /var/lib/genenet/bnw/$1/postProbEachEdge.txt /var/lib/genenet/bnw/$1structure_input_temp.txt /var/lib/genenet/bnw/$1structure_input.txt $THR +./structure /tmp/bnw/$1continuous_input.txt /tmp/bnw/$1/postProbEachEdge.txt /tmp/bnw/$1structure_input_temp.txt /tmp/bnw/$1structure_input.txt $THR -rm -r /var/lib/genenet/bnw/$1 +rm -r /tmp/bnw/$1 if [ $k = 1 ] then - rm -r /var/lib/genenet/bnw/$1structure_input_temp.txt + rm -r /tmp/bnw/$1structure_input_temp.txt fi diff --git a/sourcecodes/run_scripts/BNW_workflow_sci.htm b/sourcecodes/run_scripts/BNW_workflow_sci.htm deleted file mode 100644 index 3911d400..00000000 --- a/sourcecodes/run_scripts/BNW_workflow_sci.htm +++ /dev/null @@ -1,381 +0,0 @@ -<html xmlns:v="urn:schemas-microsoft-com:vml" -xmlns:o="urn:schemas-microsoft-com:office:office" -xmlns:w="urn:schemas-microsoft-com:office:word" -xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" -xmlns="http://www.w3.org/TR/REC-html40"> - -<head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> -<meta name=ProgId content=Word.Document> -<meta name=Generator content="Microsoft Word 12"> -<meta name=Originator content="Microsoft Word 12"> -<link rel=File-List href="BNW_workflow_test_files/filelist.xml"> -<link rel=Edit-Time-Data href="BNW_workflow_test_files/editdata.mso"> -<style> -<!-- - /* Font Definitions */ - @font-face - {font-family:"Cambria Math"; - panose-1:2 4 5 3 5 4 6 3 2 4; - mso-font-charset:1; - mso-generic-font-family:roman; - mso-font-format:other; - mso-font-pitch:variable; - mso-font-signature:0 0 0 0 0 0;} -@font-face - {font-family:Calibri; - panose-1:2 15 5 2 2 2 4 3 2 4; - mso-font-charset:0; - mso-generic-font-family:swiss; - mso-font-pitch:variable; - mso-font-signature:-1610611985 1073750139 0 0 159 0;} -@font-face - {font-family:Tahoma; - panose-1:2 11 6 4 3 5 4 4 2 4; - mso-font-charset:0; - mso-generic-font-family:swiss; - mso-font-pitch:variable; - mso-font-signature:-520081665 -1073717157 41 0 66047 0;} - /* Style Definitions */ - p.MsoNormal, li.MsoNormal, div.MsoNormal - {mso-style-unhide:no; 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- mso-style-noshow:yes; - mso-style-priority:99; - mso-style-qformat:yes; - mso-style-parent:""; - mso-padding-alt:0in 5.4pt 0in 5.4pt; - mso-para-margin:0in; - mso-para-margin-bottom:.0001pt; - mso-pagination:widow-orphan; - font-size:10.0pt; - font-family:"Calibri","sans-serif"; - mso-ascii-font-family:Calibri; - mso-ascii-theme-font:minor-latin; - mso-hansi-font-family:Calibri; - mso-hansi-theme-font:minor-latin;} -</style> -<![endif]--><!--[if gte mso 9]><xml> - <o:shapedefaults v:ext="edit" spidmax="4098"/> -</xml><![endif]--><!--[if gte mso 9]><xml> - <o:shapelayout v:ext="edit"> - <o:idmap v:ext="edit" data="1"/> - </o:shapelayout></xml><![endif]--> -</head> - -<body lang=EN-US style='tab-interval:.5in'> - -<div class=WordSection1> - -<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: -normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'>1. -A genetic network linking genotype and phenotype<o:p></o:p></span></b></p> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif"'>In this example, we will use the structural constraint interface to create a genetic network linking a genotype with gene expression traits and a higher-order phenotype. There are 5 nodes in the network: Genotype, Gene1, Gene2, Gene3, and Phenotype. The input data file is available <a href="example_datasets/sci_5node_input_data2.txt">here</a>. To begin, select <u>Learn a network model from data</u> on the BNW homepage and load the data file, displaying what is shown below:<br><br><o:p></o:p></span></p> - - -<img width=776 height=322 src="BNW_workflow_test_files/sci_5node_upload.png" v:shapes="Picture_x0020_2"></img> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif"'><br>We now have the option of either learning performing structure learning using the default BNW settings or we can modify settings and add structural constraints. Here, we will select <u>Go to structure learning settings and the BNW structural constraint interface</u> to select the latter option. The BNW structural constraint interface is described in our <a href="help.php#constraint_interface">Help page</a>. At shown in the figure below, the first page has several settings for global features of the structure search. We have kept the default settings, except we have changed the <u>Number of networks to include in model averaging</u> to 1000. As this is a small network with only 5 nodes, including many high scoring networks had little effect on the estimated time required to perform structure learning, and the estimated run time increased from 12 to 13 seconds. We also could increase the <u>Maximum number of parents for any node</u> to any value without significantly changing the run time for a network of this size. For larger networks with more than approximately 10 nodes, changing these settings can have a major impact on estimated run times.<br><br><o:p></o:p></span></p> - -<img width=508 height=175 src="BNW_workflow_test_files/sci_5node_part1.png" v:shapes="Picture_x0020_2"></img> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif"'><br>Clicking the <u>Continue to assign variables to tiers</u> button allows the assignment of nodes to tiers which can focus network searches on biologically meaningful networks. Our dataset contains a genotype, three gene expression traits, and a higher order phenotype. Instead of considering all possible network models for this dataset, we may want to focus on models relevant to a questions such as: How does variation in genotype and gene expression explain the variation observed in the phenotype? To address this question, we assign the network nodes to three tiers: Tier1 contains the genotype, Tier2 contains the gene expression traits, and Tier3 contains the phenotype.<br><br><o:p></o:p></span></p> - -<img width=671 height=320 src="BNW_workflow_test_files/sci_5node_part2.png" v:shapes="Picture_x0020_2"></img> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif"'><br>The third section of the BNW structural constraint interface allows users to specify the interactions that are allowed within and between tiers. By default, within tier interactions (i.e., nodes in TierX can be parents or children of other nodes in TierX) are allowed, but users may want to prevent within tier interactions for some cases. For example, it may be advantageous to prevent interactions between a tier that contained a set of some demographic variables (e.g., age, sex, and race), as these variables are not likely to be causal factor that influence other factors in the tier. In this case, within tier interactions only apply to Tier2, and we do not have any prior knowledge that indicates that between gene interactions should not be allowed, so we will keep the default setting and allow within tier interactions.<br><br> The default settings for between tier interactions allow nodes within a tier to be the parents of all nodes in lower ranking tiers. Here, the Genotype node in Tier1 can be parents of the gene nodes in Tier2 and the Phenotype node in Tier3, the gene nodes in Tier2 can be the parents of the Tier3 Phenotype node, and the Tier3 Phenotype node cannot be the parents of nodes in any other tier. Therefore, by default, the Genotype node can be the direct parent of the Phenotype node. We may want to allow this interaction, as the genotype may influence genotype through genes or other factors that are not explicitly included as variables in the network. If users do not want to allow this direct Genotype-Phenotype interaction, they can unclick the Tier3 box in the <u>Which tiers contain nodes that can be the children of this tier?</u> for Tier1. In this case, we have maintained the default settings which are shown below. The final section of this menu allows for listing specific edges that should be banned or required in the network structures. We will not ban or require any specific edges in this network.<br><br><o:p></o:p></span></p> - -<img width=886 height=443 src="BNW_workflow_test_files/sci_5node_part3.png" v:shapes="Picture_x0020_2"></img> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif"'><br>In this example, we will not specify any additional constraints in the fourth section of the structural constraint interface, and we can click <u>Click here to perform Bayesian network modeling</u> on the top of the page. The figure below shows the network with the model average network of the 1000 highest scoring networks and this network is available <a href="example.php?My_key=example_sci|Llu" target="_blank">here</a>. Genotype directly influences two of the genes (Gene1 and Gene3), and two of the genes (Gene2 and Gene3) directly influence the Phenotype. In this case, although we did not prevent the Genotype from directly influencing the Phenotype, the highest scoring networks did not include this directed edge. The right side of the figure shows the predictions of the network with Genotype=1 used as evidence. If Genotype is known to be in state 1, the values of all other variables in the network are expected to decrease compared to the distributions learned using all phenotypes. A more complete description of using BNW to make predictions with network models can be found in a <a href="BNW_workflow_net1.htm">separate tutorial</a>.<br><br><o:p></o:p></span></p> - -<img width=587 height=561 src="BNW_workflow_test_files/sci_5node_network1.png" v:shapes="Picture_x0020_2"></img> - - -<p class=MsoNormal style='margin-right:307.5pt'><b style='mso-bidi-font-weight: -normal'><span style='font-size:14.0pt;line-height:115%;font-family:"Arial","sans-serif"'><br>2. -A genetic network with multiple genotypes and cis- and trans-regulated genes.<o:p></o:p></span></b></p> - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> In this example, we will add restrictions to a network containing 8 nodes: 2 genotype nodes (Geno1 and Geno2), 3 cis-regulated gene expression traits (cisGene1, cisGene2, and cisGene3), 2 trans-regulated gene expression traits (transGene1 and transGene2), and a phenotype (Pheno). We have four tiers of nodes (genotypes, cis-regulated genes, trans-regulated genes, and phenotype), so we have selected 4 from the dropdown menu at the top of the page and assigned the nodes to the correct tiers. We could make a more complex system of tiers that would allow us to specify which genes are regulated by which genotypes (for example, Geno1 regulates cisGene1 and transGene1, while Geno2 regulates cisGene2, cisGene3, and transGene2), but, for this example, we will use a simpler system of 4 tiers.<br><br><o:p></o:p></span></p> - -<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> -<![if !vml]><img width=863 height=419 -src="BNW_workflow_test_files/image2_4.png" v:shapes="Picture_x0020_14"><![endif]><o:p></o:p></span></p> - - -<p class=MsoNormal style='margin-top:0in;margin-right:307.5pt;margin-bottom: -0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> We have made one change to the default setting in the <u>Define interactions allowed between tiers</u> section. For Tier1, which contains the genotypes, we have selected "No" for the "Are within tier interactions allowed?", as it does not make biological sense for one genotype variation to cause the variation in another genotype in this example.<br><br>Also, assume that a known regulatory relationship between cisGene1 and transGene1 has been established from previous experiments. We can require that this relationship is included in the network by adding the edge list of required edges in the <u>Specify additional constraints</u> section.<br><br><o:p></o:p></span></p> - -<p class=MsoNormal style='margin-right:307.5pt'><span style='font-size:12.0pt; -line-height:115%;font-family:"Arial","sans-serif";mso-no-proof:yes'> -<![if !vml]><img width=1006 height=631 -src="BNW_workflow_test_files/image2_5.png" v:shapes="Picture_x0020_14"><![endif]><o:p></o:p></span></p> - -</div> - -</body> - -</html> diff --git a/sourcecodes/run_scripts/path_cd.m b/sourcecodes/run_scripts/path_cd.m index d45098d0..4c5c04ad 100644 --- a/sourcecodes/run_scripts/path_cd.m +++ b/sourcecodes/run_scripts/path_cd.m @@ -2,4 +2,4 @@ base_dir = pwd(); addpath(strcat(base_dir,"/bnt-master")); addpath(genpathKPM(strcat(base_dir,"/bnt-master"))); addpath(strcat(base_dir,"/parameter_learning")); -cd /var/lib/genenet/bnw/; +cd /tmp/bnw; diff --git a/sourcecodes/run_scripts/run_kfold b/sourcecodes/run_scripts/run_kfold index 371649e4..02d70da1 100644 --- a/sourcecodes/run_scripts/run_kfold +++ b/sourcecodes/run_scripts/run_kfold @@ -10,6 +10,8 @@ fout_temp=fopen(filename,'w'); fprintf(fout_temp,arg_list{2}); kfoldCrossValid(arg_list{1},arg_list{2},arg_list{3}); fclose(fout_temp); -command=cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/kfold_plotly.py ",arg_list{1}); -test=system(command); delete(filename); + + +command=cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/kfold_plotly.py ",arg_list{1}); +test=system(command); diff --git a/sourcecodes/run_scripts/run_loo b/sourcecodes/run_scripts/run_loo index 4fbc0b28..c73bf1a6 100644 --- a/sourcecodes/run_scripts/run_loo +++ b/sourcecodes/run_scripts/run_loo @@ -11,5 +11,6 @@ fprintf(fout_temp,arg_list{2}); fclose(fout_temp); looCrossValid(arg_list{1},arg_list{2}); delete(filename); -command=cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/cv_plotly.py ",arg_list{1}); + +command=cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/cv_plotly.py ",arg_list{1}); test=system(command); diff --git a/sourcecodes/run_scripts/run_octave b/sourcecodes/run_scripts/run_octave index 5bc782ef..92971614 100644 --- a/sourcecodes/run_scripts/run_octave +++ b/sourcecodes/run_scripts/run_octave @@ -10,5 +10,5 @@ system(command); output2 = strcat(arg_list{1},"network_no_edge.svg"); command2 = cstrcat("/usr/bin/dot -Tsvg -o",output2," ",arg_list{1},"graphviz_svg_no_edge.txt > ",output2); system(command2); -command= cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/violin_plotly.py ",arg_list{1}); +command= cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/violin_plotly.py ",arg_list{1}); test=system(command); diff --git a/sourcecodes/run_scripts/run_octave_evd b/sourcecodes/run_scripts/run_octave_evd index ae072fdd..dfcac1f3 100644 --- a/sourcecodes/run_scripts/run_octave_evd +++ b/sourcecodes/run_scripts/run_octave_evd @@ -2,5 +2,5 @@ source("./run_scripts/path_cd.m") arg_list = argv(); Predictmultiple(arg_list{1}); -command=cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/violin_ev_plotly.py ",arg_list{1}); +command=cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/violin_ev_plotly.py ",arg_list{1}); test=system(command); diff --git a/sourcecodes/run_scripts/run_octave_inv b/sourcecodes/run_scripts/run_octave_inv index 12c1d204..fc9d0636 100644 --- a/sourcecodes/run_scripts/run_octave_inv +++ b/sourcecodes/run_scripts/run_octave_inv @@ -2,5 +2,5 @@ source("./run_scripts/path_cd.m") arg_list = argv(); Predictmultipleintervention(arg_list{1}); -command=cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/violin_int_plotly.py ",arg_list{1}); +command=cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/violin_int_plotly.py ",arg_list{1}); test=system(command); diff --git a/sourcecodes/run_scripts/run_test_set b/sourcecodes/run_scripts/run_test_set index 67ae66cd..aef01887 100644 --- a/sourcecodes/run_scripts/run_test_set +++ b/sourcecodes/run_scripts/run_test_set @@ -9,5 +9,6 @@ testSetPredictions(arg_list{1}); #fclose(filename); filename=strcat(arg_list{1},"ts_upload.txt"); delete(filename); -command=cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"/ts_plotly.py ",arg_list{1}); + +command=cstrcat("/home/jziebart/python/Python-2.7.15/python ",base_dir,"/ts_plotly.py ",arg_list{1}); test=system(command); diff --git a/sourcecodes/run_scripts/run_violin b/sourcecodes/run_scripts/run_violin index d7605671..c5ce7737 100644 --- a/sourcecodes/run_scripts/run_violin +++ b/sourcecodes/run_scripts/run_violin @@ -1,8 +1,7 @@ #!/usr/bin/octave -qf source("./run_scripts/path_cd.m"); arg_list = argv(); -command(cstrcat("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 ",base_dir,"violin.py ",arg_list{1}); -test=system(command); + #command=strcat({"/home/jziebart/python/Python-2.7.15/python ../violin_plotly.py "},arg_list{1}); #test=system(command); #command=strcat({"/home/jziebart/python/Python-2.7.15/python ../violin_ev_plotly.py "},arg_list{1}); diff --git a/sourcecodes/runtime_check.php b/sourcecodes/runtime_check.php index d8c30bb7..300a197f 100644 --- a/sourcecodes/runtime_check.php +++ b/sourcecodes/runtime_check.php @@ -4,8 +4,8 @@ function exe_time($keyval,$parent_number,$k_number) { //$dir="./data/"; - //$dir="/tmp/bnw/"; - $dir="/var/lib/genenet/bnw/"; + $dir="/tmp/bnw/"; + $nrf = $dir.$keyval."nrows.txt"; $nrows=trim(file_get_contents("$nrf")); @@ -62,4 +62,4 @@ $totaltime=$local*($nrows/100)+$k_time+12; //return $max_parent_row[$node]; return $totaltime; -} +} \ No newline at end of file diff --git a/sourcecodes/scripts/accordion.js b/sourcecodes/scripts/accordion.js index 513bde84..f2d83076 100644 --- a/sourcecodes/scripts/accordion.js +++ b/sourcecodes/scripts/accordion.js @@ -28,4 +28,4 @@ $('button').click(function() { $(this).find('i').toggleClass('fa-angle-down fa-angle-up') }); } - ) + ) \ No newline at end of file diff --git a/sourcecodes/test_set_predictions.php b/sourcecodes/test_set_predictions.php index ca76927b..66400a66 100644 --- a/sourcecodes/test_set_predictions.php +++ b/sourcecodes/test_set_predictions.php @@ -5,7 +5,7 @@ <script src="./scripts/d3.v4.min.js"></script> <script src="./scripts/create_table.js"></script> -<?php +<?php include("header_new.inc"); include("header_batchsearch.inc"); include("input_validate.php"); @@ -13,50 +13,49 @@ if($_GET["My_key"]!="") $keyval=valid_keyval($_GET["My_key"]); if($_POST["My_key"]!="") $keyval=valid_keyval($_POST["My_key"]); -?> -</head> - -<?php $searchID=""; $UploadValue="NO"; -$TextFile=$_FILES["MyFile"]["name"]; +$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; //$TextinFile="./data/".$keyval."ts_upload.txt"; -$TextinFile="/var/lib/genenet/bnw/".$keyval."ts_upload.txt"; +$TextinFile="/tmp/bnw/".$keyval."ts_upload.txt"; +?> +</header> -if(isset($_POST["searchkey"])) +<?php +if(isset($HTTP_POST_VARS["searchkey"])) { - $searchID=$_POST["searchkey"]; + $searchID=$HTTP_POST_VARS["searchkey"]; } -if(isset($_POST["MyUpload"])) +if(isset($HTTP_POST_VARS["MyUpload"])) { - $UploadValue=$_POST["MyUpload"]; + $UploadValue=$HTTP_POST_VARS["MyUpload"]; if ($UploadValue=="YES") { if($TextFile!="") - { - $sta=move_uploaded_file($_FILES['MyFile']['tmp_name'],$TextinFile); + { + $sta=move_uploaded_file($HTTP_POST_FILES['MyFile']['tmp_name'],$TextinFile); if(!$sta) - { + { echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>\ "; flush(); exit(); - } + } else - { + { $searchID=file_get_contents("$TextinFile"); //unlink($TextinFile); - } + } - } + } else - { + { echo "<script type='text/javascript'> window.alert ('Sorry, please select upload file.')</script>"; - } + } } } @@ -80,43 +79,39 @@ if(isset($_POST["MyUpload"])) <?php // $filename1="./data/".$keyval."ts_upload.txt"; //$filename2="./data/".$keyval."ts_output.txt"; - $dir="/var/lib/genenet/bnw/"; - $filename1=$keyval."ts_upload.txt"; - $filename2=$keyval."ts_output.txt"; -$plotly_file=$keyval."ts_plotly.html"; -//$plotly_file_local="./data/".$keyval."ts_plotly.html"; -//$pred_file_local="./data/".$keyval."ts_output.txt"; + $dir="/tmp/bnw/"; + $filename1=$dir.$keyval."ts_upload.txt"; + $filename2=$dir.$keyval."ts_output.txt"; +$plotly_file=$dir.$keyval."ts_plotly.html"; +$plotly_file_local="./data/".$keyval."ts_plotly.html"; +$pred_file_local="./data/".$keyval."ts_output.txt"; -if(file_exists($dir.$filename1)) +if(file_exists($filename1)) {?> <br> <a class=button3 href="cv_predictions.php?My_key=<?php print($keyval);?>">Calculation submitted. Click here to return to cross-validation and predictions menu.</a> <br> <?php } -else if(file_exists($dir.$plotly_file)) - { - $table_text = json_encode(file("file://".$dir.$filename2)); -?> +else if(file_exists($filename2)) + {?> <div> - <object width="800" height="500" data=<?php include($dir.$plotly_file)?> + <object type="text/html" data=<?php print($plotly_file_local);?> width="800" height="500" > </object> </div> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error,raw) { - var dsv=d3.dsvFormat("\t") - var data1 = <?php echo $table_text;?>; - var data2 = data1.join(""); - var data=dsv.parse(data2) + d3.text("<?php print($pred_file_local);?>", function(error,raw) { + var dsv=d3.dsvFormat("\t") + var data=dsv.parse(raw) var caption_text=data.pop() if (error) throw error; - tabulate_caption("#table_div1",data,caption_text.CaseRow); + tabulate_caption("#table_div1",data,caption_text.CaseRow); }); </script> </div> - <a class=button2 href=<?php print("reroute.php?".$filename2);?>>Download predictions</a> + <a class=button2 href=<?php $d="./data/".$keyval."ts_output.txt"; print($d);?>>View and download predictions</a> <br> <br> diff --git a/sourcecodes/tier_description_processing_gom.php b/sourcecodes/tier_description_processing_gom.php index 9bba8fc9..f6e9eee2 100644 --- a/sourcecodes/tier_description_processing_gom.php +++ b/sourcecodes/tier_description_processing_gom.php @@ -6,9 +6,8 @@ function get_tier($keyval) { $tier=trim($_GET['tier']); -//$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +#$dir="./data/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."tier.txt"; $fpvar = fopen("$tf","w"); fwrite($fpvar,"$tier"); @@ -68,9 +67,8 @@ function describe_tier($fpvar,$keyval) $tierdesc=trim($_GET['tierdesc']); -//$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +#$dir="./data/"; +$dir="/tmp/bnw/"; $tf=$dir.$keyval."tier.txt"; $tier=file_get_contents("$tf"); @@ -216,9 +214,8 @@ $ban=trim($_GET['ban']); get_tier($keyval); shell_exec('./run_scripts/run_settings '.$keyval); -//$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +#$dir="./data/"; +$dir="/tmp/bnw/"; $sid1=$dir.$keyval."ban"; $sid2=$dir.$keyval."white"; @@ -241,4 +238,4 @@ whitelist($fpw,$white); ?> <script> window.open("executionprogress.php?My_key=<?php print($keyval);?>",'_self',false); -</script> +</script> \ No newline at end of file diff --git a/sourcecodes/ts_plotly.py b/sourcecodes/ts_plotly.py index cdd1321a..fa0c2c9a 100644 --- a/sourcecodes/ts_plotly.py +++ b/sourcecodes/ts_plotly.py @@ -1,7 +1,10 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 +#!/home/jziebart/python/Python-2.7.15/python import os import sys +#sys.path.append('/home/jziebart/.local/bin') +#sys.path.append('/home/jziebart/.local/lib') + import plotly import plotly.graph_objs as go import csv @@ -16,10 +19,9 @@ f=open(filename,"r") lines=f.readlines() #Read the last line to get the variable name line=lines.pop() -#line = map(string.strip,line.strip().split(" ")) -line = line.strip().split(" ") +line = map(string.strip,line.strip().split(" ")) varName = line[4][:-1] -plot_title=varName+" Test Set Predictions" +plot_title="<br>"+varName+" Test Set Predictions" #print varName header=lines.pop(0) @@ -27,11 +29,9 @@ header=lines.pop(0) typefile = netID+"type.txt" tf=open(typefile,"r") line=tf.readline() -#varnames = map(string.strip,line.strip().split("\t")) -varnames = line.strip().split("\t") +varnames = map(string.strip,line.strip().split("\t")) line=tf.readline() -#vartypes = map(string.strip,line.strip().split("\t")) -vartypes = line.strip().split("\t") +vartypes = map(string.strip,line.strip().split("\t")) varindex = varnames.index(varName) cd_type = int(vartypes[varindex]) @@ -47,8 +47,7 @@ if cd_type == 1: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) if line[1] != 'NA': x.append(float(line[1])) y.append(float(line[2])) @@ -62,10 +61,6 @@ if cd_type == 1: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", xaxis=dict( autorange=True, title='Actual values', @@ -95,8 +90,7 @@ else: # for i in range(5): # line = f.readline() #Get names of states - #header = map(string.strip,header.strip().split("\t")) - header = header.strip().split("\t") + header = map(string.strip,header.strip().split("\t")) states = header[2:] #Read the data actual = [] @@ -104,8 +98,7 @@ else: # line = f.readline() # while line: for line in lines: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) if line[1] != 'NA': actual.append(line[1]) predict_x = line[2:] @@ -154,10 +147,6 @@ else: size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", xaxis=dict( autorange=True, title='State', diff --git a/sourcecodes/upload_structure_file.php b/sourcecodes/upload_structure_file.php index 35758533..f0c9fc7d 100644 --- a/sourcecodes/upload_structure_file.php +++ b/sourcecodes/upload_structure_file.php @@ -13,7 +13,7 @@ include("input_validate.php"); $searchID=""; $UploadValue="NO"; -$TextFile=$_FILES["MyFile"]["name"]; +$TextFile=$HTTP_POST_FILES["MyFile"]["name"]; /////////////Generate a random key///////////////////// @@ -35,18 +35,17 @@ $keyval=valid_keyval($keyval); $sid=$keyval."continuous_input"; //$dir="./data/"; -//$dir="/tmp/bnw/"; -$dir="/var/lib/genenet/bnw/"; +$dir="/tmp/bnw/"; + +$input_table_file="./data/".$keyval."input_table.txt"; -//$input_table_file="./data/".$keyval."input_table.txt"; -$input_table_file=$dir.$keyval."input_table.txt"; $TextinFile=$dir.$sid."_orig.txt"; -if(isset($_POST["searchkey"])) +if(isset($HTTP_POST_VARS["searchkey"])) { - $searchID=$_POST["searchkey"]; + $searchID=$HTTP_POST_VARS["searchkey"]; } @@ -63,9 +62,9 @@ if($searchID=="") <?php } -if(isset($_POST["MyUpload"])) +if(isset($HTTP_POST_VARS["MyUpload"])) { - $UploadValue=$_POST["MyUpload"]; + $UploadValue=$HTTP_POST_VARS["MyUpload"]; if ($UploadValue=="YES") { if($TextFile!="") @@ -139,16 +138,11 @@ if($searchID!="") <br> <p><h3>The variables in the data file have the following properties: <br></h3> -<?php -$table_text = json_encode(file("file://".$input_table_file)); -?> <div class="d3_table" id="table_div1"> <script type="text/javascript"> - d3.text("", function(error, raw_temp){ - var dsv = d3.dsvFormat("\t"); - var data1 = <?php echo $table_text?>; - var data2 = data1.join(""); - var data = dsv.parse(data2); + d3.text("<?php print($input_table_file);?>", function(error, raw){ + var dsv = d3.dsvFormat("\t") + var data = dsv.parse(raw) var caption_text = data.pop(); if (error) throw error; tabulate_caption("#table_div1",data,caption_text.Variable); diff --git a/sourcecodes/view_distributions.php b/sourcecodes/view_distributions.php deleted file mode 100644 index 811f0c35..00000000 --- a/sourcecodes/view_distributions.php +++ /dev/null @@ -1,94 +0,0 @@ -<?php - -include("header_new.inc"); -include("input_validate.php"); - -$keyval=valid_keyval($_GET["My_key"]); - -?> - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p>Network ID:<br><?php print($keyval);?></p></li> -</ul> -<ul class="navbar"> - <li><a href="javascript:void(0);" - NAME="Network" title="Network" onClick=window.open("layout.php?My_key=<?php print($keyval);?>","_self");>Return to network</a> - <li><a href="help.php">Help</a> - <li><a href="home.php">Home</a> - - -</ul> - - -<!-- Main content --> -<div id="outer"> -<h1>Cross-validation and predictions</h1> -<br> -<p align="justify"> -<ul class="listbar"> -<?php - $loo_file1="./data/".$keyval."looCV_temp.txt"; - $loo_file2="./data/".$keyval."looCV.txt"; -if(file_exists($loo_file1)) - {?> -<li>1: Leave-one-out cross-validation predictions are being calculated. - <a href="cv_predictions.php?My_key=<?php print($keyval);?>">Refresh and update status</a> -<br> -</li> - <?php - } else if(file_exists($loo_file2)) { - ?> -<li>1: <a href="cross_valid.php?My_key=<?php print($keyval);?>" target='_self'>Leave-one-out cross-validation results are available.</a></li> - <?php - } else { - ?> - <li>1: <a href="cross_valid.php?My_key=<?php print($keyval);?>" target='_self'>Perform leave-one-out cross-validation</a></li> - <?php - } - ?> -<?php - $kfold_file1="./data/".$keyval."kfoldCV_temp.txt"; - $kfold_file2="./data/".$keyval."kfoldCV.txt"; -if(file_exists($kfold_file1)) - {?> -<li>2: k-fold cross-validation predictions are being calculated. - <a href="cv_predictions.php?My_key=<?php print($keyval);?>">Refresh and update status</a> -<br> -</li> - <?php - } else if(file_exists($kfold_file2)) { - ?> -<li>2: <a href="kfold_cv.php?My_key=<?php print($keyval);?>" target='_self'>k-fold cross-validation results are available</a></li> - <?php - } else { - ?> - <li>2: <a href="kfold_cv.php?My_key=<?php print($keyval);?>" target='_self'>Perform k-fold cross-validation</a></li> - <?php - } - ?> -<?php - $ts_file1="./data/".$keyval."ts_upload.txt"; - $ts_file2="./data/".$keyval."ts_output.txt"; -if(file_exists($ts_file1)) - {?> -<li>3: Test set predictions are being calculated. - <a href="cv_predictions.php?My_key=<?php print($keyval);?>">Refresh and update status</a> -<br> -</li> - <?php - } else if(file_exists($ts_file2)) { - ?> -<li>3: <a href="test_set_predictions.php?My_key=<?php print($keyval);?>" target='_self'>Test set predictions are available</a></li> - <?php - } else { - ?> - <li>3: <a href="test_set_predictions.php?My_key=<?php print($keyval);?>" target='_self'>Make predictions using a test data set</a></li> - <?php - } - ?> -</ul> -</p> -</div> -</body> -</html> diff --git a/sourcecodes/view_input_data.php b/sourcecodes/view_input_data.php deleted file mode 100644 index bcf61a3a..00000000 --- a/sourcecodes/view_input_data.php +++ /dev/null @@ -1,203 +0,0 @@ -<head> -<meta charset="utf-8"> -<script src="./scripts/d3.v4.min.js"></script> -<?php -include("header_new.inc"); -include("input_validate.php"); -if($_GET["My_key"]!="") - $keyval=valid_keyval($_GET["My_key"]); -if($_POST["My_key"]!="") - $keyval=valid_keyval($_POST["My_key"]); - -$input_table_file="./data/".$keyval."input_table.txt"; -$input_data_file="./data/".$keyval."continuous_input_orig.txt"; - - -?> - -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - - <!--[if !IE]><!--> - <style> - * { -margin: 0; -padding: 0; -} -/* - Generic Styling, for Desktops/Laptops -*/ -table { -width: 100%; - border-collapse: collapse; -} -/* Zebra striping */ -tr:nth-of-type(odd) { -background: LightGrey; -} -th { -background: #3071a9; -color: white; - font-size: 12pt; -} -td, th { -padding: 6px; -border: 1px solid #ccc; - text-align: left; -} - -th.des:after { -content: "\21E9"; -} - -th.aes:after { -content: "\21E7"; -} - -/* - Max width before this PARTICULAR table gets nasty - This query will take effect for any screen smaller than 760px - and also iPads specifically. -*/ -@media -only screen and (max-width: 760px), - (min-device-width: 768px) and (max-device-width: 1024px) { - - /* Force table to not be like tables anymore */ - table, thead, tbody, th, td, tr { - display: block; - } - - /* Hide table headers (but not display: none;, for accessibility) */ - thead tr { - position: absolute; - top: -9999px; - left: -9999px; - } - - tr { border: 1px solid #ccc; } - - td { - /* Behave like a "row" */ - border: none; - border-bottom: 1px solid #eee; - position: relative; - padding-left: 50%; - } - - td:before { - /* Now like a table header */ - position: absolute; - /* Top/left values mimic padding */ - top: 6px; - left: 6px; - width: 45%; - padding-right: 10px; - white-space: nowrap; - } - - /* - Label the data - */ - td:before { - content: attr(data-th) ": "; - font-weight: bold; - width: 6.5em; - display: inline-block; - } - } - - /* Smartphones (portrait and landscape) ----------- */ - @media only screen - and (min-device-width : 320px) - and (max-device-width : 480px) { - body { - padding: 0; - margin: 0; - width: 320px; } - } - - /* iPads (portrait and landscape) ----------- */ - @media only screen and (min-device-width: 768px) and (max-device-width: 1024px) { - body { - width: 495px; - } - } - - </style> - <!--<![endif]--> - -</head> - - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p>Network ID:<br><?php print($keyval);?></p></li> - <li><a href="help.php">Help</a> - <li><a href="home.php">Home</a> -</ul> - -<body> - <div id="violin_div"> - - <h1>D3.js Sortable & Responsive Table</h1> - - <p>Click the table header to sort data according to that column</p> - - </div> - <script type="text/javascript"> - d3.text("<?php print($input_table_file);?>", function(error, raw){ - var dsv = d3.dsvFormat("\t") - var data = dsv.parse(raw) - var caption_text = data.pop(); - console.log(caption_text.Variable); - if (error) throw error; - var sortAscending = true; - var table = d3.select('#violin_div').append('table'); - var caption = table.append("caption").text(caption_text.Variable); - var titles = d3.keys(data[0]); - var headers = table.append('thead').append('tr') - .selectAll('th') - .data(titles).enter() - .append('th') - .text(function (d) { - return d; - }) - .on('click', function (d) { - headers.attr('class', 'header'); - - if (sortAscending) { - rows.sort(function(a, b) { return b[d] < a[d]; }); - sortAscending = false; - this.className = 'aes'; - } else { - rows.sort(function(a, b) { return b[d] > a[d]; }); - sortAscending = true; - this.className = 'des'; - } - - }); - - var rows = table.append('tbody').selectAll('tr') - .data(data).enter() - .append('tr'); - rows.selectAll('td') - .data(function (d) { - return titles.map(function (k) { - return { 'value': d[k], 'name': k}; - }); - }).enter() - .append('td') - .attr('data-th', function (d) { - return d.name; - }) - .text(function (d) { - return d.value; - }); - }); - - -</script> -</div> -</body> - - diff --git a/sourcecodes/view_input_data_text.php b/sourcecodes/view_input_data_text.php deleted file mode 100644 index 0f5e75c8..00000000 --- a/sourcecodes/view_input_data_text.php +++ /dev/null @@ -1,62 +0,0 @@ -<head> -<meta charset="utf-8"> -<script src="./scripts/d3.v4.min.js"></script> -<script src="./scripts/create_table.js"></script> -<?php -include("header_new.inc"); -include("input_validate.php"); -if($_GET["My_key"]!="") - $keyval=valid_keyval($_GET["My_key"]); -if($_POST["My_key"]!="") - $keyval=valid_keyval($_POST["My_key"]); - -$input_table_file="./data/".$keyval."input_table.txt"; -$input_data_file="./data/".$keyval."continuous_input_orig.txt"; - - -?> - -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -</head> - - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p>Network ID:<br><?php print($keyval);?></p></li> - <li><a href="help.php">Help</a> - <li><a href="home.php">Home</a> -</ul> - -<body> - <div id="table_div"> - <div id="table_div1"> - <script type="text/javascript"> - d3.text("<?php print($input_table_file);?>", function(error, raw){ - var dsv = d3.dsvFormat("\t") - var data = dsv.parse(raw) - var caption_text = data.pop(); - if (error) throw error; - tabulate_caption("#table_div1",data,caption_text.Variable); - }); -</script> -</div> -<br> - <div id="table_div2"> - - <script type="text/javascript"> - - d3.text("<?php print($input_data_file);?>", function(error, raw){ - var dsv = d3.dsvFormat("\t") - var data = dsv.parse(raw) - var caption_text = "Input data file:"; - if (error) throw error; - tabulate_caption("#table_div2",data,caption_text); - }); - -</script> - </div> - -</div> -</body> - - diff --git a/sourcecodes/violin.php b/sourcecodes/violin.php index 5733dff3..2e9c6c49 100644 --- a/sourcecodes/violin.php +++ b/sourcecodes/violin.php @@ -1,25 +1,28 @@ <?php include("header_new.inc"); include("input_validate.php"); -include("reroute_image.php"); if($_GET["My_key"]!="") $keyval=valid_keyval($_GET["My_key"]); -//if($_POST["My_key"]!="") -// $keyval=valid_keyval($_POST["My_key"]); +if($_POST["My_key"]!="") + $keyval=valid_keyval($_POST["My_key"]); + +$plotly_file_data="./data/".$keyval."violin_plotly.html"; +$plotly_ev_file_data="./data/".$keyval."violin_plotly_evidence.html"; +$plotly_file_tmp="/tmp/bnw/".$keyval."violin_plotly.html"; +$plotly_ev_file_tmp="/tmp/bnw/".$keyval."violin_plotly_evidence.html"; -$dir="/var/lib/genenet/bnw/"; -$plotly_file=$keyval."violin_plotly.html"; -$plotly_ev_file=$keyval."violin_plotly_evidence.html"; -//$plotly_file_tmp="/tmp/bnw/".$keyval."violin_plotly.html"; -//$plotly_ev_file_tmp="/tmp/bnw/".$keyval."violin_plotly_evidence.html"; ?> + + <!-- Site navigation menu --> <ul class="navbar2"> <li class="noHover"><p>Network ID:<br><?php print($keyval);?></p></li> <li><a href="help.php">Help</a> <li><a href="home.php">Home</a> + + </ul> @@ -28,24 +31,15 @@ $plotly_ev_file=$keyval."violin_plotly_evidence.html"; <div id="violin_div"> <!-- Main content --> <?php - if(file_exists($dir.$plotly_file)) - { - $file_data=file_get_contents($dir.$plotly_file); -?> - - <object width="100%" height="500" data=<?=$file_data?> + if(file_exists($plotly_file_tmp)) + {?> + <object type="text/html" data=<?php print($plotly_file_data);?> width="100%" height="500"> </object> <?php - } else { -?> - <div id="outernew"> - <h3> No violin plot data file found. </h3> -<?php -} - if(file_exists($dir.$plotly_ev_file)) - $ev_file_data=file_get_contents($dir.$plotly_ev_file); + } + if(file_exists($plotly_ev_file_tmp)) {?> - <object width="100%" height="500" data=<?=$ev_file_data?> + <object type="text/html" data=<?php print($plotly_ev_file_data);?> width="100%" height="500"> </object> <?php } diff --git a/sourcecodes/violin_ev_plotly.py b/sourcecodes/violin_ev_plotly.py index 69609d94..8c40740b 100644 --- a/sourcecodes/violin_ev_plotly.py +++ b/sourcecodes/violin_ev_plotly.py @@ -1,4 +1,4 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 +#!/home/jziebart/python/Python-2.7.15/python import os import sys import math @@ -37,12 +37,10 @@ filename=netID+"continuous_input.txt" f=open(filename,"r") #Read the first line to get the variable names line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -varNames = line.strip().split("\t") -#varNames = line +line = map(string.strip,line.strip().split("\t")) +varNames = line line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -line = line.strip().split("\t") +line = map(string.strip,line.strip().split("\t")) for i in range(len(line)): line[i] = int(line[i]) cd_types = line @@ -55,8 +53,7 @@ for i in range(len(varNames)): evfile=netID+"varname.txt" evf=open(evfile,"r") line=evf.readline() -#ev_vars = map(string.strip,line.strip().split("\t")) -ev_vars = line.strip().split("\t") +ev_vars = map(string.strip,line.strip().split("\t")) keepVars = [] for i in cNames: if i not in ev_vars: @@ -66,8 +63,7 @@ for i in cNames: data = [] line = f.readline() while line: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) temp = [] for i in range(len(varNames)): if cd_types[i] == 1: @@ -93,19 +89,16 @@ while line: line = f2.readline() layout = go.Layout( - title="Distributions considering evidence", + title="<br>Distributions considering evidence", titlefont=dict( family='Arial, sans-serif', size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", + yaxis=dict(title="Distributions of standardized data"), legend=dict(orientation='h'), - margin=dict(t=40,l=70,b=40) + margin=dict(t=10,l=70,b=40) ) fig = go.Figure(layout=layout) diff --git a/sourcecodes/violin_int_plotly.py b/sourcecodes/violin_int_plotly.py index 15889500..75d2b3cb 100644 --- a/sourcecodes/violin_int_plotly.py +++ b/sourcecodes/violin_int_plotly.py @@ -1,4 +1,4 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 +#!/home/jziebart/python/Python-2.7.15/python import os import sys import math @@ -37,12 +37,10 @@ filename=netID+"continuous_input.txt" f=open(filename,"r") #Read the first line to get the variable names line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -varNames = line.strip().split("\t") -#varNames = line +line = map(string.strip,line.strip().split("\t")) +varNames = line line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -line = line.strip().split("\t") +line = map(string.strip,line.strip().split("\t")) for i in range(len(line)): line[i] = int(line[i]) cd_types = line @@ -57,8 +55,7 @@ intfile=netID+"parameters_ev.txt" intf=open(intfile,"r") line=intf.readline() while line: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) param_file.append(line) line=intf.readline() keepVars = [] @@ -77,8 +74,7 @@ for i in range(len(param_file)): data = [] line = f.readline() while line: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) temp = [] for i in range(len(varNames)): if cd_types[i] == 1: @@ -105,19 +101,16 @@ while line: layout = go.Layout( - title="Distributions after intervention", + title="<br>Distributions after intervention", titlefont=dict( family='Arial, sans-serif', size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", + yaxis=dict(title="Distributions of standardized data"), legend=dict(orientation='h'), - margin=dict(t=40,l=70,b=40) + margin=dict(t=10,l=70,b=40) ) fig = go.Figure(layout=layout) diff --git a/sourcecodes/violin_plotly.py b/sourcecodes/violin_plotly.py index 8e0f8ea2..b2c9cada 100644 --- a/sourcecodes/violin_plotly.py +++ b/sourcecodes/violin_plotly.py @@ -1,11 +1,10 @@ -#!/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3 +#!/home/jziebart/python/Python-2.7.15/python import os import sys import math #sys.path.append('/home/jziebart/.local/bin') #sys.path.append('/home/jziebart/.local/lib') - import plotly import plotly.graph_objs as go import csv @@ -38,11 +37,10 @@ filename=netID+"continuous_input.txt" f=open(filename,"r") #Read the first line to get the variable names line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -varNames = line.strip().split("\t") +line = map(string.strip,line.strip().split("\t")) +varNames = line line=f.readline() -#line = map(string.strip,line.strip().split("\t")) -line = line.strip().split("\t") +line = map(string.strip,line.strip().split("\t")) for i in range(len(line)): line[i] = int(line[i]) cd_types = line @@ -55,8 +53,7 @@ for i in range(len(varNames)): data = [] line = f.readline() while line: - #line = map(string.strip,line.strip().split("\t")) - line = line.strip().split("\t") + line = map(string.strip,line.strip().split("\t")) temp = [] for i in range(len(varNames)): if cd_types[i] == 1: @@ -87,19 +84,15 @@ for i in range(len(cNames)): del pdf_data layout = go.Layout( - title="Original distributions", + title="<br>Original distributions", titlefont=dict( family='Arial, sans-serif', size=24, color='black' ), - title_xref="paper", - title_x=0.5, - title_xanchor="center", - title_yanchor="middle", yaxis=dict(title="Distributions of standardized data"), legend=dict(orientation='h'), - margin=dict(t=40,l=70,b=40) + margin=dict(t=10,l=70,b=40) ) fig = go.Figure(layout=layout) @@ -117,7 +110,5 @@ for i in range(len(cNames)): fig.add_trace(go.Violin(y=pdf_data2[i],x0=cNames[i],side='positive',legendgroup='Network parameters',name='Network parameters',fillcolor='orange',line=dict(color='orange'),showlegend=False,hoverinfo='none',points=False,scalegroup=cNames[i])) -fig.update_layout(title_xanchor="center") - plotly.offline.plot(fig,filename=outfile) |
