NAME

       Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes
         in a given protein seequence.

SYNOPSIS

         # Build a Tmhmm  factory

         # $paramfile is the full path to the seg binary file

         my @params = ('PROGRAM',$paramfile);
         my $factory = Bio::Tools::Run::Tmhmm->new($param);

         # Pass the factory a Bio::Seq object
         # @feats is an array of Bio::SeqFeature::Generic objects

         my @feats = $factory->run($seq);

DESCRIPTION

       Tmhmm is a program for identifying transmembrane helices in proteins.

       You must have the environmental variable TMHMMDIR set to the base directory where tmhmm
       and it's associated data/option files reside (NOT the bin directory where the actual
       executable resides)

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

       head2 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 - Bala

        Email savikalpa@fugu-sg.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   : $factory>program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

   program_dir
        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable, in this
                  case it is the tmhmm installation directory, not the location of
                  the executable.
        Returns:  string
        Args    :

   program_path
        Title   : program_path
        Usage   : my $path = $factory->program_path();
        Function: Builds path for executable
        Returns : string representing the full path to the exe
        Args    : none

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

   predict_protein_features
        Title   :   predict_protein_features()
        Usage   :   DEPRECATED Use $obj->run($seq) instead
        Function:   Runs Tmhmm and creates an array of featrues
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :   A Bio::PrimarySeqI

   executable
        Title   : executable
        Usage   : my $exe = $tmhmm->executable('tmhmm');
        Function: Finds the full path to the 'tmhmm' executable
        Returns : string representing the full path to the exe
        Args    : [optional] name of executable to set path to
                  [optional] boolean flag whether or not warn when exe is not found

   run
        Title   :   run()
        Usage   :   $obj->run($seq)
        Function:   Runs Tmhmm and creates an array of featrues
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :   A Bio::PrimarySeqI

   _input
        Title   :   _input
        Usage   :   obj->_input($seqFile)
        Function:   Internal(not to be used directly)
        Returns :
        Args    :

   _run
        Title   :   _run
        Usage   :   $obj->_run()
        Function:   Internal(not to be used directly)
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :

   _writeSeqFile
        Title   :   _writeSeqFile
        Usage   :   obj->_writeSeqFile($seq)
        Function:   Internal(not to be used directly)
        Returns :
        Args    :