Christopher Fields > BioPerl > Bio::Factory::TreeFactoryI

Download:
BioPerl-1.6.923.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Source  

NAME ^

Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream

SYNOPSIS ^

  # get a $factory from somewhere Bio::TreeIO likely
  my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
                               -file   => 'file.tre');
  my $treeout = Bio::TreeIO->new(-format => 'nexus',
                                -file   => ">file.nexus");

  # convert tree formats from newick/phylip to nexus
  while(my $tree = $treeio->next_tree) {
      $treeout->write_tree($tree);
  }

DESCRIPTION ^

This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO factory.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich ^

Email jason@bioperl.org

APPENDIX ^

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_tree

 Title   : next_tree
 Usage   : my $tree = $factory->next_tree;
 Function: Get a tree from the factory
 Returns : L<Bio::Tree::TreeI>
 Args    : none

write_tree

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