[Jalview-discuss] Jalview Not saving visible columns

[rquiroga at fcq.unc.edu.ar]

Greetings to everyone,

This is actually a head´s up and not a question. The Java Webstart  
version of Jalview no longer displays this "save visible columns" bug,  
but the installanywhere version still does.

Best regards!

Rodrigo Quiroga


>    1. Re: Problem with saving visible columns (James Procter)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 14 Apr 2009 14:02:43 +0100
> From: James Procter <jimp at compbio.dundee.ac.uk>
> Subject: Re: [Jalview-discuss] Problem with saving visible columns
> To: rquiroga at fcq.unc.edu.ar
> Cc: jalview-discuss at jalview.org
> Message-ID: <49E48973.2070501 at compbio.dundee.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>> _______________________________________________
>> Jalview-discuss mailing list
>> Jalview-discuss at jalview.org
>> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>
>
> --
> -------------------------------------------------------------------
> 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.
>
>
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>
> End of Jalview-discuss Digest, Vol 17, Issue 6
> **********************************************
>



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