NAME

       Bio::Factory::EMBOSS - EMBOSS application factory class

SYNOPSIS

         # get an EMBOSS factory
         use Bio::Factory::EMBOSS;
         $f = Bio::Factory::EMBOSS -> new();
         # get an EMBOSS application  object from the factory
         $water = $f->program('water') || die "Program not found!\n";

         # here is an example of running the application -
         # water can compare 1 sequence against 1 or more sequences
         # in a database using Smith-Waterman
         my $seq_to_test; # this would have a seq here
         my @seqs_to_check; # this would be a list of seqs to compare
                              # (could be just 1)
         my $wateroutfile = 'out.water';
         $water->run({-sequences => $seq_to_test,
                      -seqall    => \@seqs_to_check,
                      -gapopen   => '10.0',
                      -gapextend => '0.5',
                      -outfile   => $wateroutfile});
         # now you might want to get the alignment
         use Bio::AlignIO;
         my $alnin = Bio::AlignIO->new(-format => 'emboss',
                                       -file   => $wateroutfile);

         while ( my $aln = $alnin->next_aln ) {
             # process the alignment -- these will be Bio::SimpleAlign objects
         }

DESCRIPTION

       The EMBOSS factory class encapsulates access to EMBOSS programs.  A factory object allows
       creation of only known applications.

       If you want to check command line options before sending them to the program set
       $prog->verbose to positive integer. The value is passed on to programs objects and the ADC
       description of the available command line options is parsed and compared to input.

       See also Bio::Tools::Run::EMBOSSApplication and Bio::Tools::Run::EMBOSSacd.

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 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 - Heikki Lehvaslaiho

       Email heikki-at-bioperl-dot-org

APPENDIX

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

   location
        Title   : location
        Usage   : $embossfactory->location
        Function: get/set the location of EMBOSS programs.
                  Valid values are 'local' and 'novella'.
        Returns : string, defaults to 'local'
        Args    : string

   program
        Title   : program
        Usage   : $embossfactory->program('program_name')
        Function: Creates a representation of a single EMBOSS program and issues a
                  warning if the program was not found.
        Returns : Bio::Tools::Run::EMBOSSApplication object or undef
        Args    : string, program name

   version
        Title   : $self->version
        Usage   : $embossfactory->version()
        Function: gets the version of EMBOSS programs
        Throws  : if EMBOSS suite is not accessible
        Returns : version value
        Args    : None

   Programs
       These methods allow the programmer to query the EMBOSS suite and find out which program
       names can be used and what arguments can be used.

   program_info
        Title   : program_info
        Usage   : $embossfactory->program_info('emma')
        Function: Finds out if the program is available.
        Returns : definition string of the program, undef if program name not known
        Args    : string, prgramname

   Internal methods
       Do not call these methods directly

   _program_list
        Title   : _program_list
        Usage   : $embossfactory->_program_list()
        Function: Finds out what programs are available.
                  Writes the names into an internal hash.
        Returns : true if successful
        Args    : None