commandline png output not generated if das features are retrieved

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.


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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