Bio::Tools::Run::EMBOSSacd(3pm) 			User Contributed Perl Documentation			   Bio::Tools::Run::EMBOSSacd(3pm)

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 . "
";

	 $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

perl v5.12.3							    2011-06-18					   Bio::Tools::Run::EMBOSSacd(3pm)