Provided by: libbio-perl-run-perl_1.6.9-2_all bug


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


         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


       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



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

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


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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


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

        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

        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

        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

        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.

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

        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

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

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

        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

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