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Bio::Tools::Run::Phylo::Phylip::DrawTree

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 AT bioperl DOT 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 AT bioperl DOT 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

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