Bio::TreeIO nexml
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Summary
Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files
Package variables
No package variables defined.
Included modules
Bio::Event::EventGeneratorI
Bio::Nexml::Factory
Bio::Phylo::IO qw ( parse unparse )
IO::String
Inherit
Bio::TreeIO
Synopsis
  use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 'data.nexml' -format => 'Nexml');
while( my $tree = $in->next_tree ) {
}
Description
This is a driver module for parsing tree data in a NeXML format. For
more information on NeXML, visit http://www.nexml.org.
Methods
_initialize
No description
Code
next_treeDescriptionCode
docDescriptionCode
rewindDescriptionCode
_parse
No description
Code
write_treeDescriptionCode
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
doccodeprevnextTop
 Title   : doc
Usage : $treeio->doc
Function: Returns the biophylo nexml document object
Returns : Bio::Phylo::Project
Args : none or Bio::Phylo::Project object
rewindcodeprevnextTop
 Title   : rewind
Usage : $treeio->rewind
Function: Resets the stream
Returns : none
Args : none
write_treecodeprevnextTop
 Title   : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my $self = shift;
    $self->SUPER::_initialize(@_);
    $self->{_doc} = undef;
}
next_treedescriptionprevnextTop
sub next_tree {
    my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
        $self->_parse;
    }
    return $self->{'_trees'}->[ $self->{'_treeiter'}++ ];
}
docdescriptionprevnextTop
sub doc {
	my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_doc'} = $value;
	}
	return $obj->{'_doc'};
}
rewinddescriptionprevnextTop
sub rewind {
    my $self = shift;
    $self->{'_treeiter'} = 0;
}
_parsedescriptionprevnextTop
sub _parse {
    my ($self) = @_;
    
    $self->{'_parsed'}   = 1;
    $self->{'_treeiter'} = 0;
    my $fac = Bio::Nexml::Factory->new();
    
    
    $self->doc(parse(
 	'-file'       => $self->{'_file'},
 	'-format'     => 'nexml',
 	'-as_project' => '1'
 	));
 	
 	$self->{'_trees'} = $fac->create_bperl_tree($self);
}
write_treedescriptionprevnextTop
sub write_tree {
	my ($self, $bp_tree) = @_;
	
	my $fac = Bio::Nexml::Factory->new();
	my $taxa = $fac->create_bphylo_taxa($bp_tree);
	my ($tree) = $fac->create_bphylo_tree($bp_tree, $taxa);
	
	my $forest = Bio::Phylo::Factory->create_forest();
	$self->doc(Bio::Phylo::Factory->create_project());
	
	$forest->set_taxa($taxa);
	$forest->insert($tree);
	
	$self->doc->insert($forest);
	
	my $ret = $self->_print($self->doc->to_xml());
	$self->flush;
	return $ret;
}


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 - Chase MillerTop
Email chmille4@gmail.com
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _