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

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)