Hi Manuel, A short answer to your question is that it is not possible to open a sequence file with the menu. A longer answer is that the two problems are unrelated. Mauve fails the update check, which does cause it to launch slowly, but that is not a problem. If you don't mind waiting then it's not necessary to configure the proxy. The File->Open menu option can be used to open XMFA alignment files, but not sequence files. Instead, sequence files should be added in the "Align sequences..." window. More detailed instructions can be found in the Mauve User's Guide on our web site or in the included PDF manual. Unfortunately the documentation is only available in English at the moment, but if somebody were to volunteer a translation we would happily accept!
-Aaron Manuel J Gomez wrote: > 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. > > > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
