Bio::Search::HSP::PSLHSP - A HSP for PSL output

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Search::HSP::PSLHSP - A HSP for PSL output

SYNOPSIS

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  # get a PSLHSP somehow (SearchIO::psl)

DESCRIPTION

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This is a HSP for PSL output so we can handle seq_inds differently.

FEEDBACK

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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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl-dot-org

APPENDIX

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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::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

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

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)
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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



# 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);


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;
}


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;
    }
}


sub mismatches{
    my $self = shift;
    return $self->{'mismatches'} = shift if @_;
    return $self->{'mismatches'};
}

1;