NAME

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

SYNOPSIS

# 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): ", 
                  $hsp->sw_score(),"\n";
         }
    }
}

DESCRIPTION

Describe the object here

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

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

new

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

sw_score

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

evalue2

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