# 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

=head1 NAME

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


  # get a PSLHSP somehow (SearchIO::psl)


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


=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:


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:


=head1 AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org


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


# Let the code begin...

package Bio::Search::HSP::PSLHSP;
$Bio::Search::HSP::PSLHSP::VERSION = '1.7.7';
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


sub new { 
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($qgaplocs,
	$mismatches) = $self->_rearrange([qw(QUERY_GAPBLOCKS
    $self->gap_blocks('query',$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


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)


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