Summary

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

Package variables

Included modules

Inherit

Bio::Search::HSP::GenericHSP

Synopsis

  # get a FastaHSP from a SearchIO stream
  my $in = new Bio::SearchIO(-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

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Search::HSP::FastaHSP();
 Function: Builds a new Bio::Search::HSP::FastaHSP object 
 Returns : Bio::Search::HSP::FastaHSP
 Args    :

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

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  
  my ($swscore) = $self->_rearrange([qw(SWSCORE)], @args);

  defined $swscore && $self->sw_score($swscore);

  return $self;

}

sub sw_score {

    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_sw_score'} ) {
	$value = 0 unless defined $value; # default value
	$self->{'_sw_score'} = $value;
    }
    return $self->{'_sw_score'};

}

General documentation

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Email jason@bioperl.org
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Additional contributors names and emails here

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