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.

         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   : $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

perl v5.36.0                                2023-01-Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)