Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Factory::TreeFactoryI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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>