Bio::TreeIO newick
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::TreeIO::newick
Package variables
No package variables defined.
Included modules
Bio::Event::EventGeneratorI
Inherit
Bio::TreeIO Bio::TreeIO::NewickParser
Synopsis
  # do not use this module directly
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 't/data/LOAD_Ccd1.dnd'); my $tree = $treeio->next_tree;
Description
This module handles parsing and writing of Newick/PHYLIP/New Hampshire format.
Methods
_initialize
No description
Code
next_treeDescriptionCode
get_default_params
No description
Code
write_treeDescriptionCode
_write_tree_Helper
No description
Code
_node_as_string
No description
Code
print_tree_countDescriptionCode
bootstrap_styleDescriptionCode
order_byDescriptionCode
Methods description
next_treecode    nextTop
Title : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args : none
write_treecodeprevnextTop
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Write a tree out to data stream in newick/phylip format
Returns : none
Args : Bio::Tree::TreeI object
print_tree_countcodeprevnextTop
Title : print_tree_count
Usage : $obj->print_tree_count($newval)
Function: Get/Set flag for printing out the tree count (paml,protml way)
Returns : value of print_tree_count (a scalar)
Args : on set, new value (a scalar or undef, optional)
bootstrap_stylecodeprevnextTop
Title : bootstrap_style
Usage : $obj->bootstrap_style($newval)
Function: A description of how bootstraps and branch lengths are
written, as the ID part of the internal node or else in []
in the branch length (Molphy-like; I am sure there is a
better name for this but am not sure where to go for some
sort of format documentation)
           If no branch lengths are requested then no bootstraps are usually
written (unless someone REALLY wants this functionality...)
Can take on strings which contain the possible values of 'nobranchlength' --> don't draw any branch lengths - this is helpful if you don't want to have to go through and delete branch len on all nodes 'molphy' --> draw bootstraps (100) like (A:0.11,B:0.22):0.33[100]; 'traditional' --> draw bootstraps (100) like (A:0.11,B:0.22)100:0.33; Returns : value of bootstrap_style (a scalar) Args : on set, new value (a scalar or undef, optional)
order_bycodeprevnextTop
Title : order_by
Usage : $obj->order_by($newval)
Function: Allow node order to be specified (typically "alpha")
See Bio::Node::Node::each_Descendent()
Returns : value of order_by (a scalar)
Args : on set, new value (a scalar or undef, optional)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my $self = shift;
    $self->SUPER::_initialize(@_);
    my ( $print_count ) = $self->_rearrange(
        [
            qw(PRINT_COUNT)
        ],
        @_
    );
    $self->print_tree_count( $print_count || 0 );
    return;
}
next_treedescriptionprevnextTop
sub next_tree {
    my ($self) = @_;
    local $/ = ";\n";
    return unless $_ = $self->_readline;

    s/[\r\n]//gs;
    my $score;
    my $despace = sub { my $dirty = shift; $dirty =~ s/\s+//gs; return $dirty };
    my $dequote = sub {
        my $dirty = shift;
        $dirty =~ s/^"?\s*(.+?)\s*"?$/$1/;
        return $dirty;
    };
s/([^"]*)(".+?")([^"]*)/$despace->($1) . $dequote->($2) . $despace->($3)/egsx;

    if (s/^\s*\[([^\]]+)\]//) {
        my $match = $1;
        $match =~ s/\s//g;
        $match =~ s/lh\=//;
        if ( $match =~ /([-\d\.+]+)/ ) {
            $score = $1;
        }
    }

    $self->_eventHandler->start_document;

    # Call the parse_newick method as defined in NewickParser.pm
$self->parse_newick($_); my $tree = $self->_eventHandler->end_document; # Add the tree score afterwards if it exists.
if (defined $tree) { $tree->score($score); return $tree; } } # Returns the default set of parsing & writing parameters for the Newick format.
}
get_default_paramsdescriptionprevnextTop
sub get_default_params {
  my $self = shift;

  return {
    newline_each_node => 0,
    order_by => '', # ???
bootstrap_style => 'traditional', # Can be 'traditional', 'molphy', 'nobranchlength'
internal_node_id => 'id', # Can be 'id' or 'bootstrap'
no_branch_lengths => 0, no_bootstrap_values => 0, no_internal_node_labels => 0 };
}
write_treedescriptionprevnextTop
sub write_tree {
    my ( $self, @trees ) = @_;
    if ( $self->print_tree_count ) {
        $self->_print( sprintf( " %d\n", scalar @trees ) );
    }

    my $params = $self->get_params;

    foreach my $tree (@trees) {
      if (  !defined $tree
            || ref($tree) =~ /ARRAY/i
            || !$tree->isa('Bio::Tree::TreeI') )
      {
        $self->throw(
                     "Calling write_tree with non Bio::Tree::TreeI object\n");
      }
      my @data = $self->_write_tree_Helper( $tree->get_root_node, $params);
      $self->_print( join( ',', @data ).";" );
    }
    
    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return;
}
_write_tree_HelperdescriptionprevnextTop
sub _write_tree_Helper {
  my $self = shift;
    my ( $node, $params ) = @_;
    my @data;

    foreach my $n ( $node->each_Descendent($params->{order_by}) ) {
        push @data, $self->_write_tree_Helper( $n, $params );
    }

    my $label = $self->_node_as_string($node,$params);

    if ( scalar(@data) >= 1) {
      $data[0] = "(" . $data[0];
      $data[-1] .= ")";
      $data[-1] .= $label;
    } else {
      push @data, $label;
    }

    return @data;
}
_node_as_stringdescriptionprevnextTop
sub _node_as_string {
  my $self = shift;
  my $node = shift;
  my $params = shift;

  my $label_stringbuffer = '';

  if ($params->{no_bootstrap_values} != 1 &&
      !$node->is_Leaf && 
      defined $node->bootstrap &&
      $params->{bootstrap_style} eq 'traditional' &&
      $params->{internal_node_id} eq 'bootstrap') {
    # If we're an internal node and we're using 'traditional' bootstrap style,
# we output the bootstrap instead of any label.
my $bootstrap = $node->bootstrap; $label_stringbuffer .= $bootstrap if (defined $bootstrap); } elsif ($params->{no_internal_node_labels} != 1) { my $id = $node->id; $label_stringbuffer .= $id if( defined $id ); } if ($params->{no_branch_lengths} != 1) { my $blen = $node->branch_length; $label_stringbuffer .= ":". $blen if (defined $blen); } if ($params->{bootstrap_style} eq 'molphy') { my $bootstrap = $node->bootstrap; $label_stringbuffer .= "[$bootstrap]" if (defined $bootstrap); } if ($params->{newline_each_node} == 1) { $label_stringbuffer .= "\n"; } return $label_stringbuffer;
}
print_tree_countdescriptionprevnextTop
sub print_tree_count {
    my $self = shift;
    return $self->{'_print_tree_count'} = shift if @_;
    return $self->{'_print_tree_count'} || 0;
}
bootstrap_styledescriptionprevnextTop
sub bootstrap_style {
    my $self = shift;
    my $val  = shift;
    if ( defined $val ) {

        if ( $val !~ /^nobranchlength|molphy|traditional/i ) {
            $self->warn(
"requested an unknown bootstrap style $val, expect one of nobranchlength,molphy,traditional, not updating value.\n"
            );
        }
        else {
            $self->{'_bootstrap_style'} = $val;
        }
    }
    return $self->{'_bootstrap_style'} || 'traditional';
}
order_bydescriptionprevnextTop
sub order_by {
    my $self = shift;

    return $self->{'order_by'} = shift if @_;
    return $self->{'order_by'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
Title : new
Args : -print_count => boolean default is false
-bootstrap_style => set the bootstrap style (one of nobranchlength,
molphy, traditional)
-order_by => set the order by sort method
See Bio::Node::Node::each_Descendent()