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# $Id: asciitree.pm,v 1.4.4.1 2006/10/02 23:10:28 sendu Exp $
#
# BioPerl module for Bio::SeqIO::asciitree
#
# Cared for by Chris Mungall <cjm@fruitfly.org>
#
# Copyright Chris Mungall
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 55 lines of Pod
=head1 NAME
Bio::SeqIO::asciitree - asciitree sequence input/output stream
=head1 SYNOPSIS
  # It is probably best not to use this object directly, but
  # rather go through the SeqIO handler system. Go:
    $instream  = Bio::SeqIO->new(-file => $filename,
                                 -format => 'chadoxml');
    $outstream = Bio::SeqIO->new(-file => $filename,
                                 -format => 'asciitree');
    while ( my $seq = $instream->next_seq() ) {
            $outstream->write_seq();
    }
=head1 DESCRIPTION
This is a WRITE-ONLY SeqIO module. It writes a Bio::SeqI object
containing nested SeqFeature objects in such a way that the SeqFeature
containment hierarchy is visible as a tree structure
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Chris Mungall
Email cjm@fruitfly.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::asciitree;
use strict;
use base qw(Bio::SeqIO);
sub _initialize {
    my($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    # hash for functions for decoding keys.
}
HideShow 12 lines of Pod
=head2 show_detail
 Title   : show_detail
 Usage   : $obj->show_detail($newval)
 Function:
 Example :
 Returns : value of show_detail (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub show_detail{
    my $self = shift;
    return $self->{'show_detail'} = shift if @_;
    return $self->{'show_detail'};
}
HideShow 10 lines of Pod
=head2 next_seq
 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :
=cut
sub next_seq {
    my ($self,@args) = @_;
    $self->throw("This is a WRITE-ONLY adapter");
}
HideShow 10 lines of Pod
=head2 write_seq
 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and 0 for error
 Args    : array of 1 to n Bio::SeqI objects
=cut
sub write_seq {
    my ($self,@seqs) = @_;
    foreach my $seq ( @seqs ) {
        $self->throw("Attempting to write with no seq!") unless defined $seq;
        if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
            $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
        }
        $self->_print("Seq: ".$seq->accession_number);
        $self->_print("\n");
        my @top_sfs = $seq->get_SeqFeatures;
        $self->write_indented_sf(1, @top_sfs);
    }
}
sub write_indented_sf {
    my $self = shift;
    my $indent = shift;
    my @sfs = @_;
    foreach my $sf (@sfs) {
        my $label = '';
        if ($sf->has_tag('standard_name')) {
            ($label) = $sf->get_tag_values('standard_name');
        }
        if ($sf->has_tag('product')) {
            ($label) = $sf->get_tag_values('product');
        }
        my $COLS = 60;
        my $tab = ' ' x 10;
        my @lines = ();
        if ($self->show_detail) {
            my @tags = $sf->all_tags;
            foreach my $tag (@tags) {
                my @vals = $sf->get_tag_values($tag);
                foreach my $val (@vals) {
                    $val = "\"$val\"";
                    push(@lines,
                         "$tab/$tag=");
                    while (my $cut =
                           substr($val, 0, $COLS - length($lines[-1]), '')) {
                        $lines[-1] .= "$cut";
                        if ($val) {
                            push(@lines, $tab);
                        }
                    }
                }
            }
        }
        my $detail = join("\n", @lines);
        my @sub_sfs = $sf->get_SeqFeatures;
        my $locstr = '';
        if (!@sub_sfs) {
            $locstr = $self->_locstr($sf);
        }
        my $col1 = sprintf("%s%s $label",
                           '  ' x $indent, $sf->primary_tag);
        my $line = sprintf("%-50s %s\n",
                           substr($col1, 0, 50), $locstr);
        $self->_print($line);
        if ($detail) {
            $self->_print($detail."\n");
        }
        $self->write_indented_sf($indent+1, @sub_sfs);
    }
    return;
}
sub _locstr {
    my $self = shift;
    my $sf = shift;
    my $strand = $sf->strand || 0;
    my $ss = '.';
    $ss = '+' if $strand > 0;
    $ss = '-' if $strand < 0;
    my $splitlocstr = '';
    if ($sf->isa("Bio::SeqFeatureI")) {
        my @locs = ($sf->location);
        if ($sf->location->isa("Bio::Location::SplitLocationI")) {
            @locs = $sf->location->each_Location;
            $splitlocstr = "; SPLIT: ".join(" ",
                                          map {$self->_locstr($_)} @locs);
        }
    }
    return
      sprintf("%d..%d[%s] $splitlocstr", $sf->start, $sf->end, $ss);
}
1;