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  1. Jalview
  2. JAL-1032

PCA calculation fails when sequence has been selected and then deselected

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.7
    • Fix Version/s: 2.8
    • Component/s: analysis, gui
    • Labels:
      None
    • Environment:
      Jalview Desktop 2.7
      Build Date: 27 September 2011
      Java version: 1.6.0_29

      Description

      If a selection is made and then toggled to deselect the selection (rather then clearing the selection), and then the PCA calculation option selected, no window is displayed, but the following exception is generated:

      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at jalview.datamodel.CigarArray.getSeqCigarArray(CigarArray.java:372)
      at jalview.datamodel.AlignmentView.<init>(AlignmentView.java:234)
      at jalview.datamodel.AlignmentView.<init>(AlignmentView.java:247)
      at jalview.datamodel.AlignmentView.<init>(AlignmentView.java:95)
      at jalview.gui.AlignViewport.getAlignmentView(AlignViewport.java:1595)
      at jalview.gui.AlignViewport.getAlignmentView(AlignViewport.java:1580)
      at jalview.gui.PCAPanel.<init>(PCAPanel.java:69)
      at jalview.gui.AlignFrame.PCAMenuItem_actionPerformed(AlignFrame.java:3414)
      at jalview.jbgui.GAlignFrame$25.actionPerformed(GAlignFrame.java:734)
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
      at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
      at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
      at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
      at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
      at java.awt.Component.processMouseEvent(Component.java:6373)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      at java.awt.EventQueue.access$000(EventQueue.java:85)
      at java.awt.EventQueue$1.run(EventQueue.java:638)
      at java.awt.EventQueue$1.run(EventQueue.java:636)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

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              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
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                Dates

                Created:
                Updated:
                Resolved: