NAME

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

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

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');
 }

DESCRIPTION

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

METHODS

new()

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

get_alignment()

 Name:       get_alignment()
 Purpose:    return the sequence alignment of the Prospect::Thread objects
 Arguments:  
             -format => one of: 'clustalw', 'bl2seq','clustalw',
                        'emboss','fasta','mase','mega','meme','msf','nexus',
            'pfam','phylip','prodom','psi','selex','stockholm'
            (default: clustalw)
             -show_ss => output secondard structure (default: off)
       -show_seq => output target sequence (default: on)
 Returns:    scalar containing the alignment

get_threads()

 Name:       get_threads()
 Purpose:    return the Prospect::Thread object list associated with this object
 Arguments:  none
 Returns:    list of Prospect::Thread objects

INTERNAL METHODS & ROUTINES

The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.

_align()

 Name:       _align()
 Purpose:    private method that does the alignment work - called by new().
             Builds a clustalw alignment internally.  use get_alignment() to
             retrieve the alignment in other formats.
 Arguments:  
             -show_ss => 0 | 1 output secondard structure (default: off)
       -show_seq => 0 | 1  output target sequence (default: on)
 Returns:    nothing