Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)		User Contributed Perl Documentation	     Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)

NAME

       Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees

SYNOPSIS

	 use Bio::Tools::Run::Phylo::Phylip::DrawTree;

	 my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
	 my $treeimagefile = $drawfact->run($tree);

DESCRIPTION

       This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite.

       To set parameters with option you need to pass in an array reference or a string, depending on the parameter. For example:

	 $treedraw->HORIZMARGINS(['2.00','2.5']);
	 $treedraw->ANCESTRALNODES('C');
	 $treedraw->TREESTYLE('PHEN');
	 $treedraw->USEBRANCHLENS('N');

       This can be a brittle module as the menus change in PHYLIP.  It should support phylip 3.6 but no guarantees.

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://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 _

   program_name
	Title	: program_name
	Usage	: $obj->program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $drawfact->program_dir()
	Function: returns the program directory, obtained from ENV variable.
	Returns :  string
	Args	:

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
	Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawTree object
	Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawTree
	Args	: The available DrawGram parameters

   run
	Title	: run
	Usage	: my $file = $app->run($treefile);
	Function: Draw a tree
	Returns : File containing the rendered tree
	Args	: either a Bio::Tree::TreeI
		   OR
		  filename of a tree in newick format

   draw_tree
	Title	: draw_tree
	Usage	: my $file = $app->draw_tree($treefile);
	Function: This method is deprecated. Please use run method.
	Returns : File containing the rendered tree
	Args	: either a Bio::Tree::TreeI
		   OR
		  filename of a tree in newick format

   _run
	Title	:  _run
	Usage	:  Internal function, not to be called directly
	Function:  makes actual system call to drawgram program
	Example :
	Returns : Bio::Tree object
	Args	: Name of a file the tree to draw in newick format
		  and a parameter string to be passed to drawgram

   _setinput()
	Title	:  _setinput
	Usage	:  Internal function, not to be called directly
	Function:  Create input file for drawing program
	Example :
	Returns : filename containing tree in newick format
	Args	: Bio::Tree::TreeI object

   _setparams()
	Title	:  _setparams
	Usage	:  Internal function, not to be called directly
	Function:   Create parameter inputs for drawgram program
	Example :
	Returns : parameter string to be passed to drawgram
	Args	: name of calling object

Bio::Tools::Run::Wrapper methods
   no_param_checks
	Title	: no_param_checks
	Usage	: $obj->no_param_checks($newval)
	Function: Boolean flag as to whether or not we should
		  trust the sanity checks for parameter values
	Returns : value of no_param_checks
	Args	: newvalue (optional)

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

   outfile_name
	Title	: outfile_name
	Usage	: my $outfile = $dragram->outfile_name();
	Function: Get/Set the name of the output file for this run
		  (if you wanted to do something special)
	Returns : string
	Args	: [optional] string to set value to

   tempdir
	Title	: tempdir
	Usage	: my $tmpdir = $self->tempdir();
	Function: Retrieve a temporary directory name (which is created)
	Returns : string which is the name of the temporary directory
	Args	: none

   cleanup
	Title	: cleanup
	Usage	: $codeml->cleanup();
	Function: Will cleanup the tempdir directory after a DrawTree run
	Returns : none
	Args	: none

   io
	Title	: io
	Usage	: $obj->io($newval)
	Function: Gets a Bio::Root::IO object
	Returns : Bio::Root::IO object
	Args	: none

       See Bio::Root::IO

perl v5.12.3							    2011-06-18			     Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)