rbvi / clustermaker2 Goto Github PK

Got this after running Fuzzifier a few times (clusterMaker2 0.9.5)...

java.lang.ClassCastException: Cannot cast org.cytoscape.model.internal.CyListImpl to java.lang.Integer
at java.lang.Class.cast(Class.java:3369)
at org.cytoscape.model.internal.CyTableImpl.getX(CyTableImpl.java:833)
at org.cytoscape.model.internal.CyTableImpl.access$200(CyTableImpl.java:64)
at org.cytoscape.model.internal.CyTableImpl$InternalRow.get(CyTableImpl.java:1161)
at org.cytoscape.model.internal.AbstractTableFacade$RowFacade.get(AbstractTableFacade.java:259)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.Fuzzifier.Fuzzifier.getClusters(Fuzzifier.java:208)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.Fuzzifier.Fuzzifier.(Fuzzifier.java:99)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.Fuzzifier.FuzzifierTaskFactory.createTaskIterator(FuzzifierTaskFactory.java:47)
at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:78)
at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:180)
at org.cytoscape.command.internal.CommandExecutorImpl.handleCommand(CommandExecutorImpl.java:221)
at org.cytoscape.command.internal.CommandExecutorImpl.executeList(CommandExecutorImpl.java:158)
at org.cytoscape.command.internal.CommandStringsExecutorTask.run(CommandStringsExecutorTask.java:50)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:92)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:108)
at org.cytoscape.work.SynchronousTaskManager$pbryglu.execute(Unknown Source)
at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.runClusterMaker(CreateAnnotationSetTask.java:152)
at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.run(CreateAnnotationSetTask.java:65)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:342)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

I triggered this with an EnrichmentMap network...
I went to the edge table, selected column of type double, and set the entire column to the same value (in this case 1.0).
Then open the MCL Cluster settings dialog, and selected that coumn for Array Source.
The following exception appears in the log...

java.lang.IllegalArgumentException: Upper value is less than or equal to lower value
	at org.cytoscape.work.util.AbstractBounded.setBounds(AbstractBounded.java:180) ~[classes/:?]
	at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.edgeConverters.EdgeAttributeHandler.updateBounds(EdgeAttributeHandler.java:239) ~[?:?]
	at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.edgeConverters.EdgeAttributeHandler.getedgeCutOff(EdgeAttributeHandler.java:100) ~[?:?]
	... 91 more

The BoundedDouble tunable does not accept the upper and lower bound to be the same value.

Create 2 networks - network1 and network2
Run on first network
cluster mcl attribute="EM1_similarity_coeffecients" clusterAttribute="test1"
and clustermake works fine

Run on second network
cluster mcl attribute="EM2_similarity_coeffecients" clusterAttribute="test2"

crashes with below error:

Error in command tool output:
Error executing task: unrecognized (table entry): Node suid: 99 (table name): LOCAL_ATTRS

Stack:
AWT-EventQueue-0 ERROR [TaskMonitor.org.cytoscape.command.internal.CommandExecutorTask] - Error executing task: unrecognized (table entry): Node suid: 99 (table name): LOCAL_ATTRS
java.lang.IllegalArgumentException: unrecognized (table entry): Node suid: 99 (table name): LOCAL_ATTRS
at org.cytoscape.model.internal.DefaultTablesNetwork.getRow(DefaultTablesNetwork.java:118)
at org.cytoscape.model.internal.CySubNetworkImpl.getRow(CySubNetworkImpl.java:60)
at edu.ucsf.rbvi.clusterMaker2.internal.utils.ModelUtils.createAndSet(ModelUtils.java:120)
at edu.ucsf.rbvi.clusterMaker2.internal.utils.ModelUtils.createAndSetLocal(ModelUtils.java:110)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.AbstractNetworkClusterer.createGroups(AbstractNetworkClusterer.java:79)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.MCLCluster.run(MCLCluster.java:97)
at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:90)
at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:180)
at org.cytoscape.command.internal.CommandExecutorTask.run(CommandExecutorTask.java:54)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:92)
at org.cytoscape.commandDialog.internal.handlers.CommandHandler.handleCommand(CommandHandler.java:167)
at org.cytoscape.commandDialog.internal.handlers.CommandHandler.handleCommand(CommandHandler.java:94)
at org.cytoscape.commandDialog.internal.ui.CommandToolDialog.actionPerformed(CommandToolDialog.java:177)
at javax.swing.JTextField.fireActionPerformed(JTextField.java:508)
at javax.swing.JTextField.postActionEvent(JTextField.java:721)
at javax.swing.JTextField$NotifyAction.actionPerformed(JTextField.java:836)
at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1664)
at javax.swing.JComponent.processKeyBinding(JComponent.java:2879)
at javax.swing.JComponent.processKeyBindings(JComponent.java:2926)
at javax.swing.JComponent.processKeyEvent(JComponent.java:2842)
at java.awt.Component.processEvent(Component.java:6282)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1895)
at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:762)
at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1027)
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:899)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:727)
at java.awt.Component.dispatchEventImpl(Component.java:4731)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:694)
at java.awt.EventQueue$3.run(EventQueue.java:692)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:708)
at java.awt.EventQueue$4.run(EventQueue.java:706)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

The edge cutoff slider on the mcl dialog doesn't move. Even manually setting a value in the text box doesn't work. Providing a value for the edgeCutoff parameter to the mcl command throws an exception.

java.lang.RuntimeException: Error processing arguments: Couldn't parse value from: 2.0 for setting: edgeCutOff
	at org.cytoscape.command.internal.tunables.CommandTunableInterceptorImpl.validateAndWriteBackTunables(CommandTunableInterceptorImpl.java:95)
	at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:82)
	at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:175)
	at org.cytoscape.command.internal.CommandExecutorImpl.handleCommand(CommandExecutorImpl.java:216)
	at org.cytoscape.command.internal.CommandExecutorImpl.executeList(CommandExecutorImpl.java:154)
	at org.cytoscape.command.internal.CommandStringsExecutorTask.run(CommandStringsExecutorTask.java:50)
	at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:92)
	at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:108)
	at org.cytoscape.work.SynchronousTaskManager$pbryglu.execute(Unknown Source)
	at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.runClusterMaker(CreateAnnotationSetTask.java:172)
	at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.run(CreateAnnotationSetTask.java:77)
	at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:342)
	at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Open the tunable dialog for one of the algorithms that has an Array Sources field (such as Fuzzy C-means). Select something in the dropdown list. Cytoscape freezes.

This seems to only happen when the dropdown initially says "--None--". I tried this on two separate computers and was able to reproduce it on both.

Cytoscape 3.4
clusterMaker2 0.9.5.

When I click on the 'tutorial' link from the Cytoscape app store, I am send to this page:

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Cluster_Maker

Hi,

I used ChemViz2 to generate a similarity network of molecules from SMILES strings. The node table contain the SMILES strings and generated properties, the edge table contain the interaction type "similarity" and the Tanimoto similarity score.

Is there anyway cluster the molecules based on the Tanimoto similarity?

Thank you very much, best regards,

Hien

Running clustermaker with only selected nodess selected doesn't work

Clustermaker2 version 0.94
Cytoscape 3.2.1

Stack:
java.lang.ArrayIndexOutOfBoundsException: 0
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.RunMCL.create2DMatrix(RunMCL.java:347)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.RunMCL.multiplyMatrix(RunMCL.java:343)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.RunMCL.run(RunMCL.java:117)
at edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.MCLCluster.run(MCLCluster.java:86)
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$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Steps to reproduce:

• Open a network (eg galFiltered)
• Select a subset of the nodes
• Run mcl with selectedNodes=true
• Result only the selected nodes are clustered, so far so good
• Unselect the nodes
• Run mcl with selectedNodes = false
• Result is that only the nodes that were previously selected are clustered

The behaviour seems to be that whenever you run mcl on some selected nodes, any subsequent call to mcl always runs on the same nodes as the first time.

Trying to run Cluster Fuzzifier results in the following exception...

java.lang.ClassCastException: Cannot cast org.cytoscape.model.internal.CyListImpl to java.lang.Integer
	at java.base/java.lang.Class.cast(Class.java:3889)
	at org.cytoscape.model.internal.CyTableImpl.getX(CyTableImpl.java:873)
	at org.cytoscape.model.internal.CyTableImpl$InternalRow.get(CyTableImpl.java:1219)
	at org.cytoscape.model.internal.AbstractTableFacade$RowFacade.get(AbstractTableFacade.java:280)
	at edu.ucsf.rbvi.clusterMaker2.internal.utils.ClusterUtils.fetchClusters(ClusterUtils.java:172)
	at edu.ucsf.rbvi.clusterMaker2.internal.commands.GetNetworkClusterTask.run(GetNetworkClusterTask.java:78)
	at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:89)
	at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:175)
	at org.cytoscape.command.internal.CommandExecutorImpl.handleCommand(CommandExecutorImpl.java:216)
	at org.cytoscape.command.internal.CommandExecutorImpl.executeList(CommandExecutorImpl.java:154)
	at org.cytoscape.command.internal.CommandStringsExecutorTask.run(CommandStringsExecutorTask.java:50)
	at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:83)
	at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:99)
	at org.cytoscape.work.SynchronousTaskManager$pbryglu.execute(Unknown Source)
	at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.runClusterMaker(CreateAnnotationSetTask.java:219)
	at org.baderlab.autoannotate.internal.task.CreateAnnotationSetTask.run(CreateAnnotationSetTask.java:103)
	at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:337)
	at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)

It seems that the documentation for the Commands is only in a table of contents (and no content).
http://www.rbvi.ucsf.edu/cytoscape/clusterMaker2/
Could you please describe it?