Bio::Search::HSP PSLHSP
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Summary
Bio::Search::HSP::PSLHSP - A HSP for PSL output
Package variables
No package variables defined.
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
newDescriptionCode
gap_blocksDescriptionCode
mismatchesDescriptionCode
Methods description
newcode    nextTop
 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_blockscodeprevnextTop
 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
mismatchescodeprevnextTop
 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
newdescriptionprevnextTop
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 $self;
}
gap_blocksdescriptionprevnextTop
sub gap_blocks {
    my ($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;
    }
}
mismatchesdescriptionprevnextTop
sub mismatches {
    my $self = shift;
    return $self->{'mismatches'} = shift if @_;
    return $self->{'mismatches'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _