Hi David, I compiled my biojava.jar on 7/28 and, just to make sure, I've updated my biojava-live cvs just now and it doesn't look like there were any changes made since that date. The SimpleDocRef.java was last updated on 7/18 and the version that I have does include the second constructor with 2 parameters. It seems to be related to null TITLE since all of the entries are missing it, but I was also under the impression that null TITLE issue was fixed. That's what is so puzzling about this. Below is the list of the problem accession IDs if you'd like to replicate the exception:
NM_006145 NM_000602 NM_006226 NM_000371 NM_019072 NM_017884 NM_022107 NM_031418 NM_030809 NM_032731 NM_001029888 NM_001029869 NM_182572 On 8/4/06, David Scott <[EMAIL PROTECTED]> wrote: > > hi seth- > > the 3rd argument to SimpleDocRef constructor is the REFERENCE title - > which appears to be null in the trace - which happens, but rarely. i had > the exact same problem recently - and richard put in code to check for a > null title and then call a special 2 argument constructor for > SimpleDocRef - any chance you don't have that code checked out? > > best- > david > > Seth Johnson wrote: > > Hi Richard, > > > > > > I'm back for more help. I've just completed getting and parsing the > entire > > human genome RefSeq list from NCBI. I'm not going to post my source > code > > since the invoking code has been described by the gentlemen who started > the > > original thread last month. The result of the parsing is such that out > of > > ~28K sequences, 13 produced the exceptions below. I've used the latest > > biojava code from CVS, not quite sure what the problem is on these 13. > > > > > > > > Trying to get: NM_006145 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > > -------------------------------------------------------------------------------- > > > > Trying to get: NM_000602 > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ------------------------------------------------------------------------------- > > > > Trying to get: NM_006226 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ---------------------------------------------------------------------------------- > > > > Trying to get: NM_000371 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > -------------------------------------------------------------------------------- > > > > Trying to get: NM_019072 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > -------------------------------------------------------------------------------- > > > > Trying to get: NM_017884 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > -------------------------------------------------------------------------------- > > > > Trying to get: NM_022107 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > --------------------------------------------------------------------------------- > > > > Trying to get: NM_031418 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > --------------------------------------------------------------------------------------- > > > > Trying to get: NM_030809 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ------------------------------------------------------------------------------------- > > > > Trying to get: NM_032731 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ------------------------------------------------------------------------------------ > > > > Trying to get: NM_001029888 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ------------------------------------------------------------------------------------ > > > > Trying to get: NM_001029869 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > ------------------------------------------------------------------------------------ > > > > Trying to get: NM_182572 > > > > org.biojava.bio.BioException: Failed to read Genbank sequence > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:157) > > > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java > :162) > > > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > > > Caused by: org.biojava.bio.BioException: Could not read sequence > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:112) > > > > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > > GenbankRichSequenceDB.java:153) > > > > ... 3 more > > > > Caused by: java.lang.IllegalArgumentException: Could not find > constructor > > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > > java.lang.String,null) > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:78) > > > > at org.biojavax.RichObjectFactory.getObject( > RichObjectFactory.java > > :104) > > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > > GenbankFormat.java:387) > > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > > RichStreamReader.java:109) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > > SimpleRichObjectBuilder.java:59) > > > > ... 7 more > > > > > > > > > > > > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 _______________________________________________ Biojava-l mailing list - [email protected] 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