NAME

       Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

SYNOPSIS

         use Bio::Factory::EMBOSS;
         # get an EMBOSS application object from the EMBOSS factory
         $factory = Bio::Factory::EMBOSS->new();
         $application = $factory->program('embossversion');
         # run the application with an optional hash containing parameters
         $result = $application->run(); # returns a string or creates a file
         print $result . "\n";

         $water = $factory->program('water');

         # here is an example of running the application
         # water can compare 1 seq against 1->many 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

         my $wateroutfile = 'out.water';
         $water->run({-sequencea => $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 EMBOSSApplication class can represent EMBOSS any program. It is created by a
       Bio::Factory::EMBOSS object.

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

       See also Bio::Factory::EMBOSS 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

   CONTRIBUTORS
       Email: jason-AT-bioperl_DOT_org

APPENDIX

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

   run
        Title   : run
        Usage   : $embossapplication->run($attribute_hash)
        Function: Runs the EMBOSS program.
        Returns : string or creates files for now; will return objects!
        Args    : hash of input to the program

   acd
        Title   : acd
        Usage   : $embossprogram->acd
        Function: finds out all the possible qualifiers for this
                  EMBOSS application. They can be used to debug the
                  options given.
        Throws  :
        Returns : boolean
        Args    :

   name
        Title   : name
        Usage   : $embossprogram->name
        Function: sets/gets the name of the EMBOSS program
                  Setting is done by the EMBOSSFactory object,
                  you should only get it.
        Throws  :
        Returns : name string
        Args    : None

   descr
        Title   : descr
        Usage   : $embossprogram->descr
        Function: sets/gets the descr of the EMBOSS program
                  Setting is done by the EMBOSSFactory object,
                  you should only get it.
        Throws  :
        Returns : description string
        Args    : None

   group
        Title   : group
        Usage   : $embossprogram->group
        Function: sets/gets the group of the EMBOSS program
                  Setting is done by the EMBOSSFactory object,
                  you should only get it.

                  If the application is assigned into a subgroup
                  use l<subgroup> to get it.
        Throws  :
        Returns : string, group name
        Args    : group string

   subgroup
        Title   : subgroup
        Usage   : $embossprogram->subgroup
        Function: sets/gets the subgroup of the EMBOSS program
                  Setting is done by the EMBOSSFactory object,
                  you should only get it.
        Throws  :
        Returns : string, subgroup name; undef if not defined
        Args    : None

   program_dir
        Title   : program_dir
        Usage   :
        Function: Required by WrapperBase
        Throws  :
        Returns : Name of directory with EMBOSS programs
        Args    :

   program_path
        Title   : program_path
        Usage   :
        Function: Required by WrapperBase
        Throws  :
        Returns : Full path of program
        Args    :

   executable
        Title   : executable
        Usage   :
        Function: Required by WrapperBase
        Throws  :
        Returns : Name of program
        Args    :