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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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)