Bio::Tools::Run::Phylo::Phylip::DrawGram(3)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich
Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS
Additional contributors names and emails here

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 PAML 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