bio::treeio::nexus(3pm) [debian man page]

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

NAME

       Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

SYNOPSIS

	 use Bio::TreeIO;
	 my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
	 while( my $tree = $in->next_tree ) {
	 }

DESCRIPTION

       This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees.

   Comments
       The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are used
       to give a name for an internal node or record the bootstap value, but other uses are possible.

       The FigTree program by Andrew Rambaut adds various rendering parameters inside comments and flags these comments by starting them with
       '&!'. The parameters implemented here are 'label' and 'color'.

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-open-bio-dot-org

APPENDIX

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

   new
	Title	: new
	Args	: -header    => boolean  default is true
				print/do not print #NEXUS header
		  -translate => boolean default is true
				print/do not print Node Id translation to a number

   next_tree
	Title	: next_tree
	Usage	: my $tree = $treeio->next_tree
	Function: Gets the next tree in the stream
	Returns : 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	: Bio::Tree::TreeI

   header
	Title	: header
	Usage	: $obj->header($newval)
	Function:
	Example :
	Returns : value of header (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   translate_node
	Title	: translate_node
	Usage	: $obj->translate_node($newval)
	Function:
	Example :
	Returns : value of translate_node (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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

Check Out this Related Man Page

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)

Linux and UNIX Man Pages

bio::treeio::nexus(3pm) [debian man page]

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