view release on metacpan or  search on metacpan

Prospect/Align.pm  view on Meta::CPAN

# $Id: Align.pm,v 1.14 2003/11/07 00:46:09 cavs Exp $
# @@banner@@

=head1 NAME

Prospect::Align -- Package for overlaying multiple Prospect alignments

S<$Id: Align.pm,v 1.14 2003/11/07 00:46:09 cavs Exp $>

=head1 SYNOPSIS

 use Prospect::Options;
 use Prospect::LocalClient;
 use Prospect::Align;
 use Bio::SeqIO;

 my $in = new Bio::SeqIO( -format=> 'Fasta', '-file' => $ARGV[0] );
 my $po = new Prospect::Options( seq=>1, svm=>1, global_local=>1,
                 templates=>[qw(1bgc 1alu 1rcb 1eera)] );
 my $pf = new Prospect::LocalClient( {options=>$po} );

 while ( my $s = $in->next_seq() ) {
   my @threads = $pf->thread( $s );
   my $pa = new Prospect::Align( -debug=>0,-threads => \@threads );
   print $pa->getAlignment(-format=>'html');
 }

=head1 DESCRIPTION

B<Prospect::Align> represents an alignment of one or more
Prospect structural alignments.

=cut


package Prospect::Align;
use vars qw( $VERSION );
$VERSION = sprintf( "%d.%02d", q$Revision: 1.14 $ =~ /(\d+)\.(\d+)/ );

use strict;
use fields qw( debug threads alignment );
use Carp qw(cluck);
use IO::Scalar;
use Bio::AlignIO;
use Prospect::Init;


=head1 METHODS

=cut


#-------------------------------------------------------------------------------
# new()
#-------------------------------------------------------------------------------

=head2 new()

 Name:       new()
 Purpose:    return Prospect::Align object
 Arguments: 
            -threads => [ Prospect::Thread objects ],
 Returns:   Prospect::Align object

=cut