#
# BioPerl module for Bio::Search::HSP::PSLHSP
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::PSLHSP - A HSP for PSL output
=head1 SYNOPSIS
# get a PSLHSP somehow (SearchIO::psl)
=head1 DESCRIPTION
This is a HSP for PSL output so we can handle seq_inds differently.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::HSP::PSLHSP;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Search::HSP::GenericHSP);
=head2 new
Title : new
Usage : my $obj = Bio::Search::HSP::PSLHSP->new();
Function: Builds a new Bio::Search::HSP::PSLHSP object
Returns : an instance of Bio::Search::HSP::PSLHSP
Args : -gapblocks => arrayref of gap locations which are [start,length]
of gaps
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($qgaplocs,
$hgaplocs,
$mismatches) = $self->_rearrange([qw(QUERY_GAPBLOCKS
HIT_GAPBLOCKS
MISMATCHES)],
@args);
$self->gap_blocks('query',$qgaplocs) if defined $qgaplocs;
$self->gap_blocks('hit', $hgaplocs) if defined $hgaplocs;
$self->mismatches($mismatches) if defined $mismatches;
return $self;
}
=head2 gap_blocks
Title : gap_blocks
Usage : $obj->gap_blocks($seqtype,$blocks)
Function: Get/Set the gap blocks
Returns : value of gap_blocks (a scalar)
Args : sequence type - 'query' or 'hit'
blocks - arrayref of block start,length
=cut
sub gap_blocks {
my ($self,$seqtype,$blocks) = @_;
if( ! defined $seqtype ) { $seqtype = 'query' }
$seqtype = lc($seqtype);
$seqtype = 'hit' if $seqtype eq 'sbjct';
if( $seqtype !~ /query|hit/i ) {
$self->warn("Expect either 'query' or 'hit' as argument 1 for gap_blocks");
}
unless( defined $blocks ) {
return $self->{'_gap_blocks'}->{$seqtype};
} else {
return $self->{'_gap_blocks'}->{$seqtype} = $blocks;
}
}
=head2 mismatches
Title : mismatches
Usage : $obj->mismatches($newval)
Function: Get/Set the number of mismatches
Returns : value of mismatches (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub mismatches{
my $self = shift;
return $self->{'mismatches'} = shift if @_;
return $self->{'mismatches'};
}
1;