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#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy

=head1 SYNOPSIS

  use Bio::Tools::Run::Phylo::Semphy;

  # Make a Semphy factory
  $factory = Bio::Tools::Run::Phylo::Semphy->new();

  # Run Semphy with an alignment
  my $tree = $factory->run($alignfilename);

  # or with alignment object
  $tree = $factory->run($bio_simplalign);

  # you can supply an initial tree as well, which can be a newick tree file,
  # Bio::Tree::Tree object...
  $tree = $factory->run($bio_simplalign, $tree_obj);

  # ... or Bio::DB::Taxonomy object
  $tree = $factory->run($bio_simplalign, $bio_db_taxonomy);

  # (mixtures of all the above are possible)

  # $tree isa Bio::Tree::Tree

=head1 DESCRIPTION

This is a wrapper for running the Semphy application by N. Friedman et a.. You
can get details here: http://compbio.cs.huji.ac.il/semphy/. Semphy is used for
phylogenetic reconstruction (making a tree with branch lengths from an aligned
set of input sequences).

You can try supplying normal Semphy command-line arguments to new(), eg.
new(-hky => 1) or calling arg-named methods (excluding the initial hyphen(s),
eg. $factory->hky(1) to set the --hky switch to true).
Note that Semphy args are case-sensitive. To distinguish between Bioperl's
-verbose and the Semphy's --verbose, you must set Semphy's verbosity with
-semphy_verbose or the semphy_verbose() method.


You will need to enable this Semphy wrapper to find the Semphy program.
This can be done in (at least) three ways:

 1. Make sure the Semphy executable is in your path.
 2. Define an environmental variable SEMPHYDIR which is a 
    directory which contains the Semphy application:
    In bash:

    export SEMPHYDIR=/home/username/semphy/

    In csh/tcsh:

    setenv SEMPHYDIR /home/username/semphy

 3. Include a definition of an environmental variable SEMPHYDIR in
    every script that will use this Semphy wrapper module, e.g.:

    BEGIN { $ENV{SEMPHYDIR} = '/home/username/semphy/' }
    use Bio::Tools::Run::Phylo::Semphy;

=head1 FEEDBACK

=head2 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

=head2 Support 

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

I<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.

=head2 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/

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=head1 APPENDIX

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

=cut

package Bio::Tools::Run::Phylo::Semphy;
use strict;

use File::Spec;
use Bio::AlignIO;
use Bio::TreeIO;

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

our $PROGRAM_NAME = 'semphy';
our $PROGRAM_DIR = $ENV{'SEMPHYDIR'};