/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ Bio::TreeIO

NAME

Bio::TreeIO - Parser for Tree files

SYNOPSIS

  {
      use Bio::TreeIO;
      my $treeio = Bio::TreeIO->new(-format => 'newick',
                                    -file   => 'globin.dnd');
      while( my $tree = $treeio->next_tree ) {
		print "Tree is ", $tree->number_nodes, "\n";
      }
  }

DESCRIPTION

This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects.

FEEDBACK

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Allen Day <allenday@ucla.edu>

APPENDIX

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->new();
Function: Builds a new Bio::TreeIO object 
Returns : Bio::TreeIO
Args    : a hash.  useful keys:
  -format : Specify the format of the file.  Supported formats:

    newick             Newick tree format
    nexus              Nexus tree format
    nhx                NHX tree format
    svggraph           SVG graphical representation of tree
    tabtree            ASCII text representation of tree
    lintree            lintree output format

format

Title   : format
Usage   : $format = $obj->format()
Function: Get the tree format
Returns : tree format
Args    : none

next_tree

Title   : next_tree
Usage   : my $tree = $treeio->next_tree;
Function: Gets the next tree off the stream
Returns : Bio::Tree::TreeI or undef if no more trees
Args    : none

write_tree

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

attach_EventHandler

Title   : attach_EventHandler
Usage   : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args    : Bio::Event::EventHandlerI

_eventHandler

Title   : _eventHandler
Usage   : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args    : none

_load_format_module

Title   : _load_format_module
Usage   : *INTERNAL TreeIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args    :

_guess_format

Title   : _guess_format
Usage   : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args    :