NAME

       Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers

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
                            # (could be just 1)
         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 EMBOSSacd represents all the possible command line arguments that can be given to an
       EMBOSS application.

       Do not create this object directly. It will be created and attached to its corresponding
       Bio::Tools::Run::EMBOSSApplication if you set

         $application->verbose > 0

       Call

         $application->acd

       to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object.

       See also Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS.

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 Address:

            EMBL Outstation, European Bioinformatics Institute
            Wellcome Trust Genome Campus, Hinxton
            Cambs. CB10 1SD, United Kingdom

APPENDIX

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

   new
        Title   : new
        Usage   : $emboss_prog->acd($prog_name);
        Function: Constructor for the class.
                  Calls EMBOSS program 'acdc', converts the
                  HTML output into XML and uses XML::Twig XML
                  parser to write out a hash of qualifiers which is
                  then blessed.
        Throws  : without program name
        Returns : new object
        Args    : EMBOSS program name

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

   print
        Title   : print
        Usage   : $embossacd->print; $embossacd->print('-word');
        Function: Print out the qualifiers.
                  Uses Data::Dumper to print the qualifiers into STDOUT.
                  A valid qualifier name given as an argment limits the output.
        Throws  :
        Returns : print string
        Args    : optional qualifier name

   mandatory
        Title   : mandatory
        Usage   : $acd->mandatory
        Function: gets a  mandatory subset of qualifiers
        Throws  :
        Returns : Bio::Tools::Run::EMBOSSacd object
        Args    : none

   Qualifier queries
       These methods can be used test qualifier names and read values.

   qualifier
        Title   : qualifier
        Usage   : $acd->qualifier($string)
        Function: tests for the existence of the qualifier
        Throws  :
        Returns : boolean
        Args    : string, name of the qualifier

   category
        Title   : category
        Usage   : $acd->category($qual_name)
        Function: Return the category of the qualifier
        Throws  :
        Returns : 'mandatory' or 'optional' or 'advanced' or
                   'associated' or 'general'
        Args    : string, name of the qualifier

   values
        Title   : values
        Usage   : $acd->values($qual_name)
        Function: Return the possible values for the qualifier
        Throws  :
        Returns : string
        Args    : string, name of the qualifier

   descr
        Title   : descr
        Usage   : $acd->descr($qual_name)
        Function: Return the description of the qualifier
        Throws  :
        Returns : boolean
        Args    : string, name of the qualifier

   unnamed
        Title   : unnamed
        Usage   : $acd->unnamed($qual_name)
        Function: Find if the qualifier can be left unnamed
        Throws  :
        Returns : 0 if needs to be named, order number otherwise
        Args    : string, name of the qualifier

   default
        Title   : default
        Usage   : $acd->default($qual_name)
        Function: Return the default value for the qualifier
        Throws  :
        Returns : scalar
        Args    : string, name of the qualifier