[Jalview-discuss] Problem with saving visible columns

[James Procter]

Hello Rodrigo.

Thanks for your email - the error you posted unveiled a tiny but
annoying bug in jalview 2.4 that most often emerges when you have
sequence associated annotation in the alignment (say from a secondary
structure prediction). There are two solutions here:

 1. Enable 'Pad Gaps' in the edit menu of the alignment window - this
should avoid the situation where the bug occurs.
 2. Use the newly patched versions available from from the
(http://www.jalview.org/versions.html) web site.

happy jalviewing!
Jim.

rquiroga at fcq.unc.edu.ar wrote:
> Greetings,
> 
> I am having trouble saving only the visible columns of an alignment,  
> since no file is actually created (if I try output to textbox, and  
> select to only save visible columns I get an empty textbox).
> 
> If I save all columns, everything works.
> 
> The weird thing is that I have used Jalview to save only visible  
> columns before, and it used to work. I am sure it isn´t a problem with  
> my alignment file (an aligned FASTA file), have tried multiple inputs  
> with no success.
> 
> The only thing I can think of that has changed is my installing of  
> TOPALI, which also uses Java.
> 
> I am not sure if this started happening after installing Java 6 update  
> 13 or not, but it may be a possibility.
> 
> I have tried reinstalling Jalview, both the non-JavaVM and the JavaVM  
> versions with no success.
> 
> I am running Windows XP Pro. I tried incresing available memory as it  
> says here:
> 
> http://www.jalview.org/jvmmemoryparams.html
> 
> But when I include the lines
> lax.nl.java.option.java.heap.size.max=1000m
> lax.nl.java.option.java.heap.size.initial=500m
> 
> in Jalview.lax, Jalview will not start, regardless of how small value  
> I set (tried 50m and it doesn´t work). My PC has 2GB of RAM.
> 
> This is my output.txt file dump:
> 
> Java version: 1.6.0_13
> x86 Windows XP 5.1
> Jalview Version: 2.4
> # INFO: Setting default net timeout to 30 seconds.
> log4j:WARN No appenders could be found for logger  
> (org.exolab.castor.xml.ValidationContext).
> log4j:WARN Please initialize the log4j system properly.
> Exception in thread "AWT-EventQueue-0"  
> java.lang.ArrayIndexOutOfBoundsException
> 	at java.lang.System.arraycopy(Native Method)
> 	at  
> jalview.datamodel.ColumnSelection.makeVisibleAnnotation(ColumnSelection.java:1003)
> 	at  
> jalview.datamodel.ColumnSelection.makeVisibleAnnotation(ColumnSelection.java:935)
> 	at jalview.io.FormatAdapter.formatSequences(FormatAdapter.java:207)
> 	at jalview.io.FormatAdapter.formatSequences(FormatAdapter.java:156)
> 	at jalview.gui.AlignFrame.outputText_actionPerformed(AlignFrame.java:883)
> 	at jalview.jbgui.GAlignFrame$1.actionPerformed(GAlignFrame.java:290)
> 	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> 	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> 	at javax.swing.AbstractButton.doClick(Unknown Source)
> 	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> 	at  
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown  
> Source)
> 	at java.awt.Component.processMouseEvent(Unknown Source)
> 	at javax.swing.JComponent.processMouseEvent(Unknown Source)
> 	at java.awt.Component.processEvent(Unknown Source)
> 	at java.awt.Container.processEvent(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)
> 
> 
> I would appreciate any help you can give me.
> 
> Thanks, best regards!
> 
> Rodrigo Quiroga
> 
> ----------------------------------------------------------------
> Webmail de la Facultad de Ciencias Quimicas
> Universidad Nacional de Cordoba
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-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.