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)
--
Morgan Langille
PhD Student, Brinkman Laboratory
Department of Molecular Biology and Biochemistry
Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6
Phone: 778-782-5414 Fax: 778-782-5583
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