Summary

Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

Package variables

Included modules

Inherit

Bio::TreeIO

Synopsis

  use Bio::TreeIO;
  my $in = new Bio::TreeIO(-file => 't/data/cat_tre.tre');
  while( my $tree = $in->next_tree ) {
  }

Description

This is a driver module for parsing PAUP Nexus tree format which
basically is just a remapping of trees.

Methods

Methods description

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

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI

Methods code

sub next_tree {

    my ($self) = @_;
    unless ( $self->{'_parsed'} ) { 
	$self->_parse;
    }
    return $self->{'_trees'}->[$self->{'_treeiter'}++];

}

sub rewind {

     shift->{'_treeiter'} = 0;

}

sub _parse {

   my ($self) = @_;

   $self->{'_parsed'} = 1;
   $self->{'_treeiter'} = 0;

   while( defined ( $_ = $self->_readline ) ) {
       next if /^\s+$/;
       last;
   }
   return unless( defined $_ );
   
   unless( /^\#NEXUS/i ) {
       $self->warn("File does not start with #NEXUS"); #'
	   return;
   }
   my $state = 0;
   my %translate;
   while( defined ( $_ = $self->_readline ) ) {
       if( $state > 0 ) {	   
	   if( /^\[/ ) {
	       $state++;
	   } elsif( /^\]/ ) {
	       $state--;
	   } elsif( /^\s*Translate/ ) { 
	       $state = 3;
	   } elsif( $state == 3) {
	       if( /^\s+(\S+)\s+(\S+)\,\s*$/ ) {
		   $translate{$1} = $2;
	       } elsif( /^\s+;/) {
		   $state = 1;
	       }
	   } elsif( /^tree\s+(\S+)\s+\=\s+(?:\[\S+\])?\s+(.+\;)\s*$/ ) {
	       my $buf = new IO::String($2);
	       my $treeio = new Bio::TreeIO(-format => 'newick',
					    -fh     => $buf);
	       my $tree = $treeio->next_tree;
	       foreach my $node ( grep { $_->is_Leaf } $tree->get_nodes ) {
		   my $id = $node->id;
		   my $lookup = $translate{$id};
		   $node->id($lookup || $id);
	       }
	       push @{$self->{'_trees'}},$tree;
	   }
       } elsif( /^\s*Begin\s+trees;/i ) {
	   $state = 1;
       } elsif( /^\s*End(\s+trees);/i ) {
	   $state = 0;
	   return;
       }
   }

}

sub write_tree {

   my ($self,$tree) = @_;
   $self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");

}

General documentation

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
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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:

  http://bugzilla.bioperl.org/

Email jason-at-open-bio-dot-org
Describe contact details here

Additional contributors names and emails here

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