Hi -
I have used the GenBankToGFF demo to generate GFF files for some genbank
genome files (U00096) and (AB001339). When reading these files back in I
get the following exception
java.lang.StringIndexOutOfBoundsException: String index out of range: -2
at java.lang.String.substring(String.java:1503) at
org.biojava.bio.program.gff.GFFParser.parseAttribute(GFFParser.java:275)
at
org.biojava.bio.program.gff.GFFParser.createRecord(GFFParser.java:230)
at org.biojava.bio.program.gff.GFFParser.parse(GFFParser.java:128)
at org.biojava.bio.program.gff.GFFParser.parse(GFFParser.java:76)
The offending line of code seems to be in the following, some how the
quote index has become -2.
} while(quoteIndx != -1 && attValList.charAt(quoteIndx-1) == '\\');
valList.add(attValList.substring(1, quoteIndx));
Perhaps the while statement should begin
while(quoteInx > -1 && ...
But I might be wrong.
The same error occurs for both gbk files
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
