hi seth- you are right - the fix for null titles was put in BioSQLRichObjectBuilder on 7.19 - i guess there must be a bug in the fix - i offered to check the fix - so i'll have to hang my head in shame. i'm looking at the code now - not the 1st time for me and i don't see the problem. i'll try one of your test cases - but i can't get to it until tomorrow.
don't tell anyone i messed up- david Seth Johnson wrote: > 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] > <mailto:[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] http://lists.open-bio.org/mailman/listinfo/biojava-l
