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PathwayCommons / chibe

Pathway visualization and analysis tool for Pathway Commons and other BioPAX data
Eclipse Public License 1.0
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Layout is not performed while running from jar #40

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
With certain models, layout is not performed while running the project from jar 
file. Layout is initialized but cannot go further. It throws the following 
exception if you load Interferon Gamma Signaling pathway from samples but works 
normal if you load Extracellular Matrix Organization. 

java.lang.NoSuchMethodError: org.ivis.layout.LEdge.setTarget(Lorg/ivis/layout/LN
ode;)V
        at org.gvt.layout.BiPaLayout.clearComplexes(BiPaLayout.java:87)
        at org.gvt.layout.BiPaLayout.layout(BiPaLayout.java:118)
        at org.ivis.layout.Layout.runLayout(Layout.java:243)
        at org.gvt.LayoutManager.runLayout(LayoutManager.java:266)
        at org.gvt.command.LayoutCommand.execute(LayoutCommand.java:39)
        at org.gvt.action.CoSELayoutAction.run(CoSELayoutAction.java:61)
        at org.gvt.action.OpenPathwaysAction.openPathwayInTab(OpenPathwaysAction
.java:177)
        at org.gvt.action.OpenPathwaysAction.run(OpenPathwaysAction.java:148)
        at org.gvt.action.LoadBioPaxModelAction.run(LoadBioPaxModelAction.java:2
53)
        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(ActionContri
butionItem.java:488)
        at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionC
ontributionItem.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.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)

I did not observe this exception while working in idea.

Original issue reported on code.google.com by mervecak...@gmail.com on 2 Oct 2012 at 8:08

GoogleCodeExporter commented 9 years ago 
This method now moved into chilay jar. My ChiBE jar can run layout. Please 
check if the bug is fixed.

Original comment by ozgunba...@gmail.com on 5 Oct 2012 at 9:38

GoogleCodeExporter commented 9 years ago

Original comment by mervecak...@gmail.com on 8 Oct 2012 at 9:44