Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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

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://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, obtained from ENV variable.
  Returns:  string
  Args    :
 
 

new

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