[Biojava-l] Question about BioJava DASClient classes

[Patrick McConnell]

I am getting a NullPointerException running Fasta2XML in
demos/eventbasedparsing on a test fasta run using -m 10 output.  I have
pasted the output/stack trace at the end.

Any ideas?

Thanks,

-Patrick

<?xml version="1.0"?>

<biojava:BlastLikeDataSetCollection xmlns=""
                                    xmlns:biojava="http://www.biojava.org">
  <biojava:BlastLikeDataSet program="FASTA"
                            version="v2.0u63 Dec, 1996">
    <biojava:Header>
      <biojava:DatabaseId id="test.lib"
                          metaData="none"></biojava:DatabaseId>
      <biojava:RawOutput xml:space="preserve">
pg_cgap: 46
pg_gap-pen: -16 -4
pg_ktup: 6
pg_matrix: DNA
pg_name: FASTA
pg_optcut: 31
pg_ver: v2.0u63 Dec, 1996
</biojava:RawOutput>
    </biojava:Header>
    <biojava:Detail>
      <biojava:Hit sequenceLength="112">
        <biojava:HitId id=">test.lib"
                       metaData="none"></biojava:HitId>
        <biojava:QueryId id="seq1"
                         metaData="none"></biojava:QueryId>
        <biojava:HitDescription>No description</biojava:HitDescription>
        <biojava:HSPCollection>
          <biojava:HSP>Exception in thread "main" java.lang.NullPointerException

        at org.biojava.bio.program.sax.FastaSearchSAXParser.endSubHit(FastaSearc
hSAXParser.java:541)
        at org.biojava.bio.program.search.FastaSearchParser.parseSearch(FastaSea
rchParser.java:320)
        at org.biojava.bio.program.sax.FastaSearchSAXParser.parse(FastaSearchSAX
Parser.java:145)
        at Fasta2XML.main(Fasta2XML.java:34)