Bio::Search::HSP::FastaHSP(3) 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)