# $Id: PSLHSP.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Search::HSP::PSLHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # 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 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: http://bugzilla.open-bio.org/ =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;