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
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
Title : _load_format_module
Usage : *INTERNAL TreeIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :