bio::tree::nodenhx(3pm) [debian man page]

Bio::Tree::NodeNHX(3pm) 				User Contributed Perl Documentation				   Bio::Tree::NodeNHX(3pm)

NAME

       Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags

SYNOPSIS

	   use Bio::Tree::NodeNHX;
	   my $nodeA = Bio::Tree::NodeNHX->new();
	   my $nodeL = Bio::Tree::NodeNHX->new();
	   my $nodeR = Bio::Tree::NodeNHX->new();

	   my $node = Bio::Tree::NodeNHX->new();
	   $node->add_Descendents($nodeL);
	   $node->add_Descendents($nodeR);

	   print "node is not a leaf 
" if( $node->is_leaf);

DESCRIPTION

       Makes a Tree Node with NHX tags, suitable for building a Tree.  See Bio::Tree::Node for a full list of functionality.

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 - Aaron Mackey
       Email amackey@virginia.edu

CONTRIBUTORS

       The NHX (New Hampshire eXtended) format was created by Chris Zmasek, and is described at:

	 http://sourceforge.net/projects/forester-atv/

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::Tree::NodeNHX->new();
	Function: Builds a new Bio::Tree::NodeNHX object
	Returns : Bio::Tree::NodeNHX
	Args	: -left 	 => pointer to Left descendent (optional)
		  -right	 => pointer to Right descenent (optional)
		  -branch_length => branch length [integer] (optional)
		  -bootstrap	 => bootstrap value (string)
		  -description	 => description of node
		  -id		 => unique id for node
		  -nhx		 => hashref of NHX tags and values

   nhx_tag
	Title	: nhx_tag
	Usage	: my $tag = $nodenhx->nhx_tag(%tags);
	Function: Set tag-value pairs for NHX nodes
	Returns : none
	Args	: hashref to update the tags/value pairs
		  OR
		  with a scalar value update the bootstrap value by default

perl v5.14.2							    2012-03-02						   Bio::Tree::NodeNHX(3pm)

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

NAME

       Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and
	 Bio::Tree::Node's from Events

SYNOPSIS

       # internal use only

DESCRIPTION

       This object will take events and build a Bio::Tree::TreeI compliant object makde up of Bio::Tree::NodeI 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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.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::TreeEventBuilder->new();
	Function: Builds a new Bio::TreeIO::TreeEventBuilder object
	Returns : Bio::TreeIO::TreeEventBuilder
	Args	:

   treetype
	Title	: treetype
	Usage	: $obj->treetype($newval)
	Function:
	Returns : value of treetype
	Args	: newvalue (optional)

   nodetype
	Title	: nodetype
	Usage	: $obj->nodetype($newval)
	Function:
	Returns : value of nodetype
	Args	: newvalue (optional)

   SAX methods
   start_document
	Title	: start_document
	Usage	: $handler->start_document
	Function: Begins a Tree event cycle
	Returns : none
	Args	: none

   end_document
	Title	: end_document
	Usage	: my @trees = $parser->end_document
	Function: Finishes a Phylogeny cycle
	Returns : An array  Bio::Tree::TreeI
	Args	: none

   start_element
	Title	: start_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	: $data => hashref with key 'Name'

   end_element
	Title	: end_element
	Usage	:
	Function:
	Returns : none
	Args	: $data => hashref with key 'Name'

   in_element
	Title	: in_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   within_element
	Title	: within_element
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   characters
	Title	: characters
	Usage	: $handler->characters($text);
	Function: Processes characters
	Returns : none
	Args	: text string

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