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kiyoko / eurocarb

Automatically exported from code.google.com/p/eurocarb
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Crash #57

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
while creating structures in 66%, compact with linkage orientation I could 
not place the galactose residue in postion 2.

java.lang.Exception: Cannot place residue Gal in position(s) -90
    at 
org.eurocarbdb.application.glycanbuilder.BookingManager.add(BookingManager.
java:58)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.assignPosition(Glyc
anRenderer.java:634)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.assignPosition(Glyc
anRenderer.java:650)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.assignPosition(Glyc
anRenderer.java:650)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:546)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:494)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:464)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.paintComponent(Glycan
Canvas.java:1193)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JViewport.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintToOffscreen(Unknown Source)
    at 
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown Source)
    at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
    at javax.swing.RepaintManager.paint(Unknown Source)
    at javax.swing.JComponent._paintImmediately(Unknown Source)
    at javax.swing.JComponent.paintImmediately(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)
    at 
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown 
Source)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown 
Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.Dialog$1.run(Unknown Source)
    at java.awt.Dialog$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at 
org.eurocarbdb.application.glycanbuilder.LogUtils.report(LogUtils.java:125)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:576)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:494)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanRenderer.computeBoundingBoxe
s(GlycanRenderer.java:464)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.showSelection(GlycanC
anvas.java:2642)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.fireUpdatedSelection(
GlycanCanvas.java:2631)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.resetSelection(Glycan
Canvas.java:1338)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.documentChanged(Glyca
nCanvas.java:2594)
    at 
org.eurocarbdb.application.glycanbuilder.BaseDocument.fireDocumentChanged(B
aseDocument.java:435)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.onSetProperties(Glyca
nCanvas.java:2431)
    at 
org.eurocarbdb.application.glycanbuilder.GlycanCanvas.actionPerformed(Glyca
nCanvas.java:2560)
    at 
org.eurocarbdb.application.glycanbuilder.DropDownList.fireActionEvent(DropD
ownList.java:138)
    at 
org.eurocarbdb.application.glycanbuilder.DropDownList.popupMenuWillBecomeIn
visible(DropDownList.java:186)
    at javax.swing.JPopupMenu.firePopupMenuWillBecomeInvisible(Unknown 
Source)
    at javax.swing.JPopupMenu.setVisible(Unknown Source)
    at 
org.eurocarbdb.application.glycanbuilder.DropDownList$MyPopupMenu.setVisibl
e(DropDownList.java:28)
    at javax.swing.JPopupMenu.menuSelectionChanged(Unknown Source)
    at javax.swing.MenuSelectionManager.setSelectedPath(Unknown Source)
    at javax.swing.MenuSelectionManager.clearSelectedPath(Unknown 
Source)
    at 
javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.cancelPopupMenu(Unknow
n Source)
    at 
javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(Unknow
n Source)
    at 
java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Unknown Source)
    at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Unknown 
Source)
    at java.awt.Toolkit.notifyAWTEventListeners(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown 
Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown 
Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown 
Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

What is the expected output? What do you see instead?

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Original issue reported on code.google.com by a.ara...@gmail.com on 28 May 2010 at 10:14