Provided by: libbio-perl-perl_1.7.2-3_all bug

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://github.com/bioperl/bioperl-live/issues

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)