Hi Morgan, I presume this behavior only happens when using Mauve on a Linux machine? There is a known problem with Java 6 for Linux and the Xerces jar which is part of Mauve, documented on Sun's web site here: http://bugs.sun.com/view_bug.do?bug_id=6618386
It seems the problem can be solved by updating the version of Xerces that Mauve uses. I have put the fix in our source code repository and it will be part of the next release! As you discovered, Java 1.5 on Linux can be used to work around the problem in the meantime. Regards, -Aaron Morgan Langille wrote: > When using Mauve with Java 6 (java version "1.6.0_02" ), I get the > error below while loading an alignment. However, if I revert back to an > older version of java (java version "1.5.0_09") it works perfectly. > > Exception in thread "Thread-1" java.lang.AbstractMethodError: > org.apache.xerces.dom.DocumentImpl.getXmlStandalone()Z > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.setDocumentInfo(DOM2TO.java:373) > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.parse(DOM2TO.java:127) > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.parse(DOM2TO.java:94) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transformIdentity(TransformerImpl.java:663) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:709) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:313) > at java.util.prefs.XmlSupport.writeDoc(XmlSupport.java:254) > at java.util.prefs.XmlSupport.exportMap(XmlSupport.java:333) > at > java.util.prefs.FileSystemPreferences$8.run(FileSystemPreferences.java:607) > at java.security.AccessController.doPrivileged(Native Method) > at > java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferences.java:600) > at > java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPreferences.java:784) > at > java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences.java:33) > at > java.util.prefs.FileSystemPreferences$13.run(FileSystemPreferences.java:754) > at java.security.AccessController.doPrivileged(Native Method) > at > java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.java:752) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1317) > at > java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1308) > at > java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:731) > at > java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:807) > at org.gel.mauve.ModelBuilder.saveCachedDirectory(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:619) > Exception in thread "Timer-0" java.lang.AbstractMethodError: > org.apache.xerces.dom.DocumentImpl.getXmlStandalone()Z > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.setDocumentInfo(DOM2TO.java:373) > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.parse(DOM2TO.java:127) > at > com.sun.org.apache.xalan.internal.xsltc.trax.DOM2TO.parse(DOM2TO.java:94) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transformIdentity(TransformerImpl.java:663) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:709) > at > com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:313) > at java.util.prefs.XmlSupport.writeDoc(XmlSupport.java:254) > at java.util.prefs.XmlSupport.exportMap(XmlSupport.java:333) > at > java.util.prefs.FileSystemPreferences$8.run(FileSystemPreferences.java:607) > at java.security.AccessController.doPrivileged(Native Method) > at > java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferences.java:600) > at > java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPreferences.java:784) > at > java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences.java:33) > at > java.util.prefs.FileSystemPreferences$13.run(FileSystemPreferences.java:754) > at java.security.AccessController.doPrivileged(Native Method) > at > java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.java:752) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1317) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1322) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1322) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1322) > at > java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1322) > at > java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1308) > at > java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:731) > at > java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:807) > at > java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:451) > at > java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:33) > at > java.util.prefs.FileSystemPreferences$4.run(FileSystemPreferences.java:419) > at java.util.TimerThread.mainLoop(Timer.java:512) > at java.util.TimerThread.run(Timer.java:462) > > > > ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. 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