Summary

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

Package variables

Included modules

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 = new Bio::Search::HSP::PSLHSP();
 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'};

}

General documentation

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