Post_Analysis / defect / source node is not a member of this network #48
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…into EM_Cyto3_port * 'EM_Cyto3_port' of github.com:BaderLab/EnrichmentMapApp: fixed issue #48 - issues creating post analysis (on main cy3 branch)
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fixed in e5cd791 |
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…_port * commit '7c75d9f5ca6e5ad38e8f148102b57b862a129305': (139 commits) fixed issue#56 - load not working for Great. Issue with slider bar creation when the minimum qvalue in the file is greater than the threshold defined. got rid of word cloud print statement. fixed race condition with multiple annotation selections. fixed issue with reloading autoannotated sessions fixed issue with null ranking file returned. fixed issue #48 - issues creating post analysis Added wordcloud selection with no wordcloud node selection (for when the users has manually selected a set of nodes). Also added no wordcloud selection at all when the user has selected more than one cluster. forgot to delete an old file related to fix #47 forgot to delete an old file related to fix #47 fixed issue #47 - changing name of cluster doesn’t work fixed version in the About box and fixed missing About box fix from cyto3_port branch that got over written. Change version to 2.1.0 Fixed extract and merge commands added back version numbers to the jar Action need to be treated separately if they are a selection in the network vs a selection in the table. The observer is only needed if you are selecting from the table. refactored merge, extract and delete. Fixed network action listeners to work more smoothly. fixed issues with constructing annotations on restored sessions that already had annotations. Fixed issue with bounding box around cluster after nodes or cluster is moved. Fixed and refactored Delete cluster action (moved all task specific to a cluster as opposed to the annotation into its own package). fixed issue with combobox in annotation panel (changing annotations didn’t updated the contents of the table) ...
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It is not possible to change the parameters settings to rerun the overlap of the signatures twice on the same session. A "source node is not a member of this network" error appear.
What I'm trying to do is to try different thresholds for example, I try number of common of genes = 1 and then realize that there are too many overlaps and then I try hypergeometric = 0.05, etc,, To do in Cytoscape 2.8 , I delete the signature nodes ( triangle) and related edges and rerun the post-analysis. Here the error (source node is not a member of this network) appears when I hit the "run" button twice.
ERROR LOG AND ENRICHMENT MAP VERSION BELOW:
Cytoscape 3.1.1 EnrichmentMap 2.0.1 build 478 java6
java.lang.IllegalArgumentException: source node is not a member of this network
at org.cytoscape.model.internal.SimpleNetwork.addEdgeInternal(SimpleNetwork.java:265)
at org.cytoscape.model.internal.CyRootNetworkImpl.addEdge(CyRootNetworkImpl.java:254)
at org.cytoscape.model.internal.CySubNetworkImpl.addEdge(CySubNetworkImpl.java:149)
at org.baderlab.csplugins.enrichmentmap.task.BuildDiseaseSignatureTask.buildDiseaseSignature(BuildDiseaseSignatureTask.java:444)
at org.baderlab.csplugins.enrichmentmap.task.BuildDiseaseSignatureTask.run(BuildDiseaseSignatureTask.java:707)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:680)
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