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Summary

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

Package variables

Inherit

Bio::Search::HSP::GenericHSP

Synopsis

  # get a PSLHSP somehow (SearchIO::psl)

Description

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

Methods

Methods description

 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

 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

 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)

Methods code

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;

}

General documentation

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
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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.

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/

Email jason-at-bioperl-dot-org

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