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Bio::Tools::Run::Phylo::Phylip::DrawTree(3) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Phylip::DrawTree(3)

Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees

  use Bio::Tools::Run::Phylo::Phylip::DrawTree;

  my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
  my $treeimagefile = $drawfact->run($tree);

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.

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

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.

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/

Email jason-at-bioperl.org

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 Title   : program_name
 Usage   : $obj->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

 Title   : program_dir
 Usage   : $drawfact->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns :  string
 Args    :

 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

 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

 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

 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

 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

 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)

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

 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

 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

 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

2022-04-13 perl v5.32.1

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