Jalview Not saving visible columns

rquiroga · 14 May 2009 21:00

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)

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Message: 1
Date: Tue, 14 Apr 2009 14:02:43 +0100
From: James Procter <jimp@compbio.dundee.ac.uk>
Subject: Re: [Jalview-discuss] Problem with saving visible columns
To: rquiroga@fcq.unc.edu.ar
Cc: jalview-discuss@jalview.org
Message-ID: <49E48973.2070501@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@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.run(Unknown Source)

I would appreciate any help you can give me.

Thanks, best regards!

Rodrigo Quiroga

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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.

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jimp · 15 May 2009 09:45

Hello Rodrigo.

rquiroga@fcq.unc.edu.ar wrote:

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.

I just checked, and I couldn't reproduce the bug in the installAnywhere
version available from here:
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/InstallAnywhere/Web_Installers/InstData/Windows/NoVM/install.exe

There are two possibilities here:
1. You are somehow running the old version of Jalview - can you
send/post the 'last updated' details found in the 'About' dialog box
(Desktop->Help->About). The latest patch was 14th April 2009.
2. You've found another bug - if so - can you post details to the list?

Jim.

jcohn · 10 June 2009 00:00

Hi,

I have been using Jalview 2.3 for some time now on an Mac Pro running Leopard and it has worked very well. Recently I upgraded to Jalview 2.4 and have experienced some strange behavior with fasta files of multiple sequence alignments produced by the Muscle alignment program.

With Jalview 2.3 (labelled May 2007, version 12.2.0), I have no trouble either opening these files via the menu or by calling a script which executes the jar file with the alignment fasta file plus an automatically generated features file as arguments. When I upgraded to Jalview 2.4 (labelled Sept 16, 2008, version 12.2.0) and tried to run my script from the command line, I get an error message stating:

Couldn’t load xxxxx.fa.muscle
Formats currently supported are Fasta, MSF, Clustal, BLC, PIR, MSP and PFAM

If I tried to manually select this same file from the menu, Jalview just hangs on “loading…”.

I then went back to Jalview 2.3 (I have both 2.3 and 2.4 installed). I could no longer view the files from my script, getting the Couldn’t load error message. But I could load them via the menu option. I kept going back and forth between 2.4 and 2.3 to trouble shoot. Seemingly randomly, 2.3 would work again with the script. I could never get 2.4 to work.

I should mentioned that I uninstalled 2.3 (using the uninstall option), installed 2.4 (using install.app). When 2.4 didn’t work, I used Time Machine to get 2.3 back and rename the 2.4 directory in the Applications folder.

I also have a clean version of 2.4 on my laptop which I installed a few months ago. This version is labelled Aug 27 2008 rather than September. It works fine on the same files - both via the script and by manually loading the files from the menu. The laptop is a Macbook Air running the same version of Leopard (10.5.7).

A colleague did a clean install of 2.4 (I think the same version as on my laptop) and he also cannot use the script but he can manually load the files.

I am completely at a loss to explain this behavior. Has anyone else suffered from similar problems? Any solutions?

Judith Cohn

···

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone: 505-665-0999
email: jcohn@lanl.gov

jcohn · 10 June 2009 00:15

Hi,

I noticed a while back that I cannot open either Jalview 2.3 nor Jalview 2.4 using the icon in the dock on a Mac running Leopard (10.5.7). My default Java version on this computer is 1.6. When I click on the icon in the dock, I get the operating system window stating that the application quite unexpectedly. However, if I run a script which explicitly points to Java 1.6 and the jar file from either Jalview 2.3 or 2.4, the application opens just fine. Is this a known problem?

Judith Cohn

···

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone: 505-665-0999
email: jcohn@lanl.gov

jcohn · 10 June 2009 01:04

p.s. I have a similar problem with a clean install of the latest version of Java 2.4 on Linux. It works similar to my colleague’s copy on Mac with Tiger. I can load fasta files from muscle manually using menu option but cannot open them with my script.

I have been using Jalview 2.3 for some time now on an Mac Pro running Leopard and it has worked very well. Recently I upgraded to Jalview 2.4 and have experienced some strange behavior with fasta files of multiple sequence alignments produced by the Muscle alignment program.

With Jalview 2.3 (labelled May 2007, version 12.2.0), I have no trouble either opening these files via the menu or by calling a script which executes the jar file with the alignment fasta file plus an automatically generated features file as arguments. When I upgraded to Jalview 2.4 (labelled Sept 16, 2008, version 12.2.0) and tried to run my script from the command line, I get an error message stating:

Couldn’t load xxxxx.fa.muscle
Formats currently supported are Fasta, MSF, Clustal, BLC, PIR, MSP and PFAM

If I tried to manually select this same file from the menu, Jalview just hangs on “loading…”.

I then went back to Jalview 2.3 (I have both 2.3 and 2.4 installed). I could no longer view the files from my script, getting the Couldn’t load error message. But I could load them via the menu option. I kept going back and forth between 2.4 and 2.3 to trouble shoot. Seemingly randomly, 2.3 would work again with the script. I could never get 2.4 to work.

I should mentioned that I uninstalled 2.3 (using the uninstall option), installed 2.4 (using install.app). When 2.4 didn’t work, I used Time Machine to get 2.3 back and rename the 2.4 directory in the Applications folder.

I also have a clean version of 2.4 on my laptop which I installed a few months ago. This version is labelled Aug 27 2008 rather than September. It works fine on the same files - both via the script and by manually loading the files from the menu. The laptop is a Macbook Air running the same version of Leopard (10.5.7).

A colleague did a clean install of 2.4 (I think the same version as on my laptop) on a Mac with Tiger and he also cannot use the script but he can manually load the files.

I am completely at a loss to explain this behavior. Has anyone else suffered from similar problems? Any solutions?

Judith Cohn

···

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone: 505-665-0999
email: jcohn@lanl.gov

jimp · 10 June 2009 16:18

Hello Judith.

It sounds like the 2.4 release has caused you a number of problems,which
is a shame. I'm not sure what's going on with your Dock icon - all I can
suggest there is removing and re-pinning the icon. However, as to your
other problem:

Judith Cohn wrote:

p.s. I have a similar problem with a clean install of the latest version
of Java 2.4 on Linux. It works similar to my colleague's copy on Mac
with Tiger. I can load fasta files from muscle manually using menu
option but cannot open them with my script.

The issue is a known one - there seems to be a problem with the jars
generated by InstallAnywhere under the new (well - 6 months old now)
automated build system. I had originally thought it to only really be an
issue on the OSX InstallAnywhere distribution, so its a worry that
you've also noticed it on Linux. On windows, the LaunchAnywhere .exe
file passes command line arguments correctly, so the problem isn't so
serious. However, the workaround for command-line launching on OSX was
to either download the jars for the webstart release
(http://www.jalview.org/webstart/) and use those, or build the jalview
jars using the source distribution.

I'm hoping to put up a bugfix release (2.4.0b2) on www.jalview.org in
the next few weeks. This will use the latest version of InstallAnywhere
to create the local installation distribution, and will - I hope - fix
this particular problem. I'll let you know directly if this really the
case so you can test on your Mac.

until the next email...
Jim Procter.

···

--
-------------------------------------------------------------------
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.