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