Hello,
I am having problems with the graphical interface to Mauve.
It takes a couple of minutes to launch and then the following message is
printed at the console:
Error checking for updates.
Once it has started, if I try to open a sequence file using the menu
options, the following error messages apear at the console:
Exception in thread "Thread-1"
java.lang.StringIndexOutOfBoundsException: String index out of range: -2
at java.lang.String.substring(String.java:1768)
at org.gel.mauve.XMFAAlignment.<init>(Unknown Source)
at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
at java.lang.Thread.run(Thread.java:595)
Assuming that the second problem is related with first, and because we
work behind a proxy, I have tried to use TransConnect which is a library
that "allow users behind a HTTP proxy like squid to use applications
like telnet,ssh, irc, fetchmail etc as if they were directly connected
to the internet".
Using transconnect has worked for me with other applications that
require a connection to internet to download patches, for example, but
not with Mauve.
I have tested j2sdk1.4.2_12, jdk1.5.0_14 and jdk1.6.0_04, both in Suse
(running on a Compaq with a 32 bit processor) and Ubuntu (running on a
Dell with four 64 bit processors).
Running mauveAligner or progressiveMauve by command line works perfectly
well.
Any hint regarding what is happening?
Best regards and thanks a lot.
--
Manuel J. Gómez
Laboratorio de Bioinformática
Centro de Astrobiología, INTA-CSIC.
Ctra. Torrejón - Ajalvir, Km 4. Torrejón de Ardoz, 28850 Madrid.
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