Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data


         # get a FastaHSP from a SearchIO stream
         my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');

         while( my $r = $in->next_result) {
             while( my $hit = $r->next_result ) {
                  while( my $hsp = $hit->next_hsp ) {
                     print "smith-waterman score (if available): ",


       Describe the object here


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AUTHOR - Jason Stajich



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::Search::HSP::FastaHSP->new();
        Function: Builds a new Bio::Search::HSP::FastaHSP object
        Returns : Bio::Search::HSP::FastaHSP
        Args    : -swscore => smith-waterman score

        Title   : sw_score
        Usage   : $obj->sw_score($newval)
        Function: Get/Set Smith-Waterman score
        Returns : value of sw_score
        Args    : newvalue (optional)

        Title   : evalue2
        Usage   : $obj->evalue2($newval)
        Function: Get/Set E2() expectation value
        Returns : value of evalue2
        Args    : newvalue (optional)