bio::factory::treefactoryi(3pm) [debian man page]

Bio::Factory::TreeFactoryI(3pm) 			User Contributed Perl Documentation			   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:

	 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>

perl v5.14.2							    2012-03-02					   Bio::Factory::TreeFactoryI(3pm)

Bio::TreeIO::pag(3pm)					User Contributed Perl Documentation				     Bio::TreeIO::pag(3pm)

NAME

       Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format

SYNOPSIS

	 use Bio::TreeIO;
	 my $in = Bio::TreeIO->new(-format => 'nexus',
				   -file   => 't/data/adh.mb_tree.nexus');

	 my $out = Bio::TreeIO->new(-format => 'pag');
	 while( my $tree = $in->next_tree ) {
	   $out->write_tree($tree);
	 }

DESCRIPTION

       Convert a Bio::TreeIO to Pagel format.  More information here http://www.evolution.reading.ac.uk/index.html

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-at-bioperl-dot-org

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::pag->new();
	Function: Builds a new Bio::TreeIO::pag object
	Returns : an instance of Bio::TreeIO::pag
	Args	: -file/-fh for filename or filehandles
		  -name_length for minimum name length (default = 10)

   write_tree
	Title	: write_tree
	Usage	:
	Function: Write a tree out in Pagel format
		  Some options are only appropriate for bayesianmultistate and
		  the simpler output is only proper for discrete
	Returns : none
	Args	: -no_outgroups => (number)
		  -print_header => 0/1 (leave 0 for discrete, 1 for bayesianms)
		  -special_node => special node - not sure what they wanted to do here
		  -keep_outgroup => 0/1 (keep the outgroup node in the output)
		  -outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on)
		  -tree_no	 => a tree number label - only useful for BayesianMultistate

   next_tree
	Title	: next_tree
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   name_length
	Title	: name_length
	Usage	: $self->name_length(20);
	Function: set mininum taxon name length
	Returns : integer (length of name)
	Args	: integer

perl v5.14.2							    2012-03-02						     Bio::TreeIO::pag(3pm)