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  1. Jalview
  2. JAL-476

commandline png output not generated if das features are retrieved

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    • Mantis ID:
      59977

      Description

      Reported via jalview-discuss.

      It looks like the Jalview.main does not continue processing the command line after retrieving the features. Debugging is in progress to check this. A dialog box deadlock was also noticed when trying to construct a command line.


      ---------
      First email from Ali (ffenics at googlemail):

      Jalview -open /my_dir/myfile..fa -dasserver das1=http://mydas1url -dasserver das2=http://mydas2url -png myalignment.png

      But the .png file s not being created. The alignment itself opens up fine as do the DAS connections.

      And Second followon:

      Hi there

      I've been having fun with jalview again and I'd much appreciate any advice you could give.

      In order to try and fix the problem I mentioned in a thread in the jalview discussion forum today (see http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2010-February/000295.html) I downloaded the Nov 2009 release if the InstallAnywhere Jalview application. However.. this now freezes every time I try to connect to a das server on the command line.

      I get the following message in the output.txt file

      Java version: 1.6.0_02
      i386 Linux 2.6.18-128.1.6.el5
      Jalview Version: 2.4.0.b2
      # INFO: Setting default net timeout to 30 seconds.
      Opening file: /cath/data/release/v3.3.0/supplementary/fsg5_gemma_nr40_tcoffee.fasta_aln
      INFO - Not enabling Google Tracking.
      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
          at com.sun.java.swing.plaf.gtk.Metacity.parseColor2(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.parseColor(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.drawGradient(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.draw(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.drawInclude(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.draw(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.drawPiece(Unknown Source)
          at com.sun.java.swing.plaf.gtk.Metacity.paintFrameBorder(Unknown Source)
          at com.sun.java.swing.plaf.gtk.GTKPainter.paintInternalFrameBorder(Unknown Source)
          at javax.swing.plaf.synth.SynthInternalFrameUI.paintBorder(Unknown Source)
          at javax.swing.plaf.synth..SynthBorder.paintBorder(Unknown Source)
          at javax.swing.JComponent.paintBorder(Unknown Source)
          at javax.swing.JComponent.paint(Unknown Source)
          at javax.swing.JComponent.paintToOffscreen(Unknown Source)
          at javax.swing.BufferStrategyPaintManager.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.pumpEventsForHierarchy(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)
      NOTE! dasserver parameter not yet really supported (got args of csa|http://cathdb.info:9000/das/domain_catalytic_residues
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=344f39eb28b035f87bcdd8acfa959cc4
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=1o6bA00
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=e1a6e0c1fd1e2b404c639d931d23ca0d
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=f68289e309553cf574dbc8f1a0fb39c7
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=fc8f5bb7e2fa534615844f283a5716f8
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=2ec0b957055d645a3171b488db661871
      Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1 >= 1
          at java.util.Vector.elementAt(Unknown Source)
          at javax.swing.table.DefaultTableColumnModel.getColumn(Unknown Source)
          at javax.swing.plaf.synth.SynthTableUI.paintCells(Unknown Source)
          at javax.swing.plaf.synth.SynthTableUI.paint(Unknown Source)
          at javax.swing.plaf.synth.SynthTableUI..update(Unknown Source)
          at javax.swing.JComponent.paintComponent(Unknown Source)
          at javax.swing.JComponent.paint(Unknown Source)
          at javax.swing.JComponent.paintToOffscreen(Unknown Source)
          at javax.swing.BufferStrategyPaintManager.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.pumpEventsForHierarchy(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
          at java.awt.EventDispatchThread.run(Unknown Source)
      Feb 9, 2010 5:50:53 PM org.biojava.dasobert.das.FeatureThread run
      INFO: requesting features from http://cathdb.info:9000/das/domain_catalytic_residues/features?segment=6db2544d1a24d7f0e4a9682f6d29b426

      Any pointers in the right direction much appreciated!!!!

      Ali ;)



      ****** ADDITIONAL INFORMATION ******

      das registry appears to be down at the moment - there may be compatibility issues. See related bug

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Updated:
              Resolved: