/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phylo::Phylip::DrawGram

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 = new Bio::Tools::Run::Phylo::Phylip::DrawGram();
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

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://bugzilla.open-bio.org/

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, obtiained from ENV variable.
Returns:  string
Args    :

new

Title   : new
Usage   : my $obj = new Bio::Tools::Run::Phylo::Phylip::DrawGram();
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