[Biojava-dev] bioperl like blastparser

[Michael Gang]

Hi All,

I used the interface of the java blast parser.
I had mainly two problems with it:
1) The blast parser does not parse all the information (for example
query length)
2) The blast parser parses the whole blast report into a list which
eats a lot of memory.

I would be interested to write and contribute a blast parser which
parses all the information of the blast and parses the blast
iteratively.
Something like the following code in bioperl (just in Java).
  use Bio::SearchIO;
    # format can be 'fasta', 'blast'
    my $searchio = new Bio::SearchIO( -format => 'blastxml',
                                      -file   => 'blastout.xml' );
    while ( my $result = $searchio->next_result() ) {
       while( my $hit = $result->next_hit ) {
        # process the Bio::Search::Hit::HitI object
           while( my $hsp = $hit->next_hsp ) {
            # process the Bio::Search::HSP::HSPI object
        }
    }

Would you be interested in such a contribution ?

Best regards,
Michael