Bio::TreeIO(3) User Contributed Perl Documentation Bio::TreeIO(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
-internal_node_id : what is stored in the internal node ids,
bootstrap values or ids, coded as
'bootstrap' or 'id'
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 :
newline_each_node
Title : newline_each_node
Usage : $obj->newline_each_node($newval)
Function: Get/set newline each node flag which is only applicable
for writing tree formats for nhx and newick, will
print a newline after each node or paren
Returns : value of newline_each_node (boolean)
Args : on set, new value (a boolean or undef, optional)
internal_node_id
Title : internal_node_id
Usage : $obj->internal_node_id($newval)
Function: Internal Node Id type, coded as 'bootstrap' or 'id'
Default is 'id'
Returns : value of internal_node_id (a scalar)
Args : on set, new value (a scalar or undef, optional)
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
perl v5.14.1 2011-07-22 Bio::TreeIO(3)
