Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output

SYNOPSIS

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  # do not use this module directly
  use Bio::TreeIO;
  use Algorithm::Cluster;
  my ($result, $linkdist) = Algorithm::Cluster::treecluster(
    distances => $matrix
  );
  my $treeio = Bio::TreeIO->new(
    -format   => 'cluster',
    -result   =>  $result,
    -linkdist =>  $linkdist,
    -labels   =>  $labels
  );
  my $tree = $treeio->next_tree;

DESCRIPTION

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This is a driver module for parsing Algorithm::Cluster::treecluster() output.

FEEDBACK

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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

Support

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 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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Guillaume Rousse

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Email Guillaume-dot-Rousse-at-inria-dot-fr

CONTRIBUTORS

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Jason Stajich - jason-at-bioperl-dot-org

APPENDIX

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

new

 Title   : new
 Usage   : my $obj = Bio::TreeIO::cluster->new();
 Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output
 Returns : Bio::TreeIO::cluster
 Args    :-result   => Algorithm::Cluster result
          -linkdist => distance between links
          -labels   => node labels

next_tree

 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree
 Function: Gets the next tree in the stream
 Returns : Bio::Tree::TreeI
 Args    : none

write_tree

 Title   : write_tree
 Usage   :
 Function: Sorry not possible with this format
 Returns : none
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::TreeIO::cluster
#
# Contributed by Guillaume Rousse <Guillaume-dot-Rousse-at-inria-dot-fr>
#
# Copyright INRIA
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::TreeIO::cluster;
use strict;

use Bio::Event::EventGeneratorI;
use IO::String;

use base qw(Bio::TreeIO);


sub _initialize {
  my $self = shift;
  ($self->{_result},$self->{_linkdist},
   $self->{_labels}) = $self->_rearrange([qw
					  (RESULT LINKDIST LABELS)],
					 @_);
  $self->SUPER::_initialize(@_);
}


sub next_tree {
    my ($self) = @_;
    if( ! $self->{_result} ){
	$self->warn("Must provide value 'result' and 'linkdist' and 'labels' when initializing a TreeIO::cluster object");
	return;
    }
    $self->_eventHandler->start_document();

    # build tree from the root
    $self->_eventHandler->start_element({Name => 'tree'});
    $self->_recurse(-1, 0);
    $self->_recurse(-1, 1);
    $self->_eventHandler->end_element({Name => 'tree'});

    return $self->_eventHandler->end_document;
}

sub _recurse {
    my ($self, $line, $column) = @_;

    my $id  = $self->{_result}->[$line]->[$column];
    if ($id >= 0) {
	# leaf
	$self->debug("leaf $id\n");
	$self->debug("distance $self->{_linkdist}->[$line]\n");
	$self->debug("label $self->{_labels}->[$id]\n");
	$self->_eventHandler->start_element({Name => 'node'});
	$self->_eventHandler->start_element({Name => 'branch_length'});
	$self->_eventHandler->characters($self->{_linkdist}->[$line]);
	$self->_eventHandler->end_element({Name => 'branch_length'});
	$self->_eventHandler->start_element({Name => 'id'});
	$self->_eventHandler->characters($self->{_labels}->[$id]);
	$self->_eventHandler->end_element({Name => 'id'});
	$self->_eventHandler->start_element({Name => 'leaf'});
	$self->_eventHandler->characters(1);
	$self->_eventHandler->end_element({Name => 'leaf'});
	$self->_eventHandler->end_element({Name => 'node'});
    } else {
	# internal node
	$self->debug("internal node $id\n");
	$self->debug("distance $self->{_linkdist}->[$line]\n");
	$self->_eventHandler->start_element({Name => 'node'});
	$self->_eventHandler->start_element({Name => 'branch_length'});
	$self->_eventHandler->characters($self->{_linkdist}->[$line]);
	$self->_eventHandler->end_element({Name => 'branch_length'});
	$self->_eventHandler->start_element({Name => 'leaf'});
	$self->_eventHandler->characters(0);
	$self->_eventHandler->end_element({Name => 'leaf'});
	$self->_eventHandler->start_element({Name => 'tree'});
	my $child_id = - ($id + 1);
	$self->_recurse($child_id, 0);
	$self->_recurse($child_id, 1);
	$self->_eventHandler->end_element({Name => 'tree'});
	$self->_eventHandler->end_element({Name => 'node'});

    }
}


sub write_tree{
    $_[0]->throw("Sorry the format 'cluster' can only be used as an input format");
}

1;