NAME

       Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer, GlimmerM and
       GlimmerHMM.

SYNOPSIS

         # glimmer2
         my $factory =
             Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
                                           '-model'   => 'model.icm');
         # glimmer3
         my $factory =
             Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
                                           '-model'   => 'model.icm');
         # glimmerm
         my $factory =
             Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');

         # glimmerHMM
         my $factory =
             Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');

         # Pass the factory Bio::Seq objects
         # returns a Bio::Tools::Glimmer object
         my $glimmer = $factory->run($seq);
         or
         my $glimmer = $factor->run(@seq);

DESCRIPTION

       Wrapper module for the Glimmer family of programs.  Should work with all currently
       available flavors: Glimmer, GlimmerM and GlimmerHMM.  However, only Glimmer 2.X and 3.X
       have been tested.

       Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

       GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

       GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

       Note that Glimmer 2.X will only process the first sequence in a fasta file (if you run()
       more than one sequence at a time, only the first will be processed).

       Note that Glimmer 3.X produces two output files.  This module only passes the .predict
       file to Bio::Tools::Glimmer.

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 one of the Bioperl mailing lists.  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark Johnson

        Email: mjohnson-at-watson-dot-wustl-dot-edu

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   : $factory>program_name()
        Function: gets/sets the program name
        Returns:  string
        Args    : string

   program_dir
        Title   : program_dir
        Usage   : $factory->program_dir()
        Function: gets/sets the program dir
        Returns:  string
        Args    : string

   model
        Title   : model
        Usage   : $factory>model()
        Function: gets/sets the name of the model (icm) file
        Returns:  string
        Args    : string

   new
        Title   : new
        Usage   : $glimmer->new(@params)
        Function: creates a new Glimmer factory
        Returns:  Bio::Tools::Run::Glimmer
        Args    :

   run
        Title   :   run
        Usage   :   $obj->run($seq_file)
        Function:   Runs Glimmer/GlimmerM/GlimmerHMM
        Returns :   A Bio::Tools::Glimmer object
        Args    :   An array of Bio::PrimarySeqI objects

   _run
        Title   :   _run
        Usage   :   $obj->_run()
        Function:   Internal(not to be used directly)
        Returns :   An instance of Bio::Tools::Glimmer
        Args    :   file name, sequence identifier (optional)

   _write_seq_file
        Title   :   _write_seq_file
        Usage   :   obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
        Function:   Internal(not to be used directly)
        Returns :   Name of a temp file containing program output
        Args    :   One or more Bio::PrimarySeqI objects