Bio::Tools::Run::Phylo::Phylip::DrawGram(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Phylip::DrawGram(3pm)
NAME
Bio::Tools::Run::Phylo::Phylip::DrawGram - use Phylip DrawTree program to draw phylograms or phenograms
SYNOPSIS
use Bio::Tools::Run::Phylo::Phylip::DrawGram;
my $drawfact = Bio::Tools::Run::Phylo::Phylip::DrawGram->new();
my $treeimage = $drawfact->run($tree);
DESCRIPTION
This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite.
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 : >program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : ->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::DrawGram->new();
Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawGram object
Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawGram
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 instead.
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 DrawGram run
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Phylip::DrawGram(3pm)