Reference

Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)

use Phylip DrawTree program to draw trees

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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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