GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::RUN::PHYLO::PHYLIP::DRAWTREE (3)

.ds Aq ’

NAME

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

CONTENTS

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

Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::RUN::PHYLO::PHYLIP::DRAWTREE (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.