Sorry for sending another message since this has been so active recently, but I have a genome genbank file that I downloaded from JGI that does not display the annotation in the alignment view. The file is readable by artemis and shows all of the annotation, so I assume that it is in the correct format. I have been able to view the annotations from other genomes that I downloaded from JGI, so I am not sure what the problem is. Below is the error message that I get. Any suggestions on what is wrong would be appreciated.
Sincerely, Jason Flowers Error reading file. org.biojava.bio.BioException: Could not read sequence at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108) at org.gel.mauve.format.BaseFormat$2.nextSequence(BaseFormat.java:113) at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:175) at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:105) at org.gel.mauve.GenomeBuilder.buildGenome(GenomeBuilder.java:59) at org.gel.mauve.XmfaViewerModel.init(XmfaViewerModel.java:151) at org.gel.mauve.XmfaViewerModel.<init>(XmfaViewerModel.java:43) at org.gel.mauve.ModelBuilder.buildModel(ModelBuilder.java:284) at org.gel.mauve.gui.FrameLoader.loadFile(FrameLoader.java:87) at org.gel.mauve.gui.FrameLoader.run(FrameLoader.java:57) at java.lang.Thread.run(Unknown Source) Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 12 at java.lang.String.substring(Unknown Source) at org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:308) at org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129) at org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105) ... 10 more From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" From must be less than To: /function=" Any advice would be appreciated ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users