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.run(Unknown Source)
I would appreciate any help you can give me.
Thanks, best regards!
Rodrigo Quiroga
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