"Find GoI on SIF file" does not work

[GoogleCodeExporter]

rev a47d3fc39f1c:

1. Select SIF > Find GoI on SIF file
2. Select sample.sif as your network, genes.txt as your gene set; select all 
SIF rules
3. Click on "OK"

You get:

SIF view contains 55 nodes and 50 edges.
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
    at java.lang.String.substring(String.java:1937)
    at org.patika.mada.util.XRef.<init>(XRef.java:72)
    at org.gvt.action.GOIofSIFAction.run(GOIofSIFAction.java:108)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.notifyListeners(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:207)

Original issue reported on code.google.com by arm...@gmail.com on 21 Sep 2012 at 8:42

Attachments:

• genes.txt
• sample.sif

[GoogleCodeExporter]

Should be fixed now. Please verify.

Original comment by ozgunba...@gmail.com on 2 Oct 2012 at 9:14

[GoogleCodeExporter]

verified; closing this one.

Thanks!

Original comment by arm...@gmail.com on 3 Oct 2012 at 12:37

• Changed state: Verified