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.IX Title "Bio::Tools::Run::EMBOSSacd 3pm"
.TH Bio::Tools::Run::EMBOSSacd 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Tools::Run::EMBOSSacd \- class for EMBOSS Application qualifiers
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&  # Get an EMBOSS factory
\&  use Bio::Factory::EMBOSS;
\&  $f = Bio::Factory::EMBOSS \-> new();
\&  # Get an EMBOSS application  object from the factory
\&  $water = $f\->program(\*(Aqwater\*(Aq) || die "Program not found!\en";
\&
\&  # Here is an example of running the application \- water can
\&  # compare 1 sequence against 1 or more sequences using Smith\-Waterman.
\&  # Pass a Sequence object and a reference to an array of objects.
\&
\&  my $wateroutfile = \*(Aqout.water\*(Aq;
\&  $water\->run({\-asequence => $seq_object,
\&               \-bsequence => \e@seq_objects,
\&               \-gapopen   => \*(Aq10.0\*(Aq,
\&               \-gapextend => \*(Aq0.5\*(Aq,
\&               \-outfile   => $wateroutfile});
\&
\&  # Now you might want to get the alignment
\&  use Bio::AlignIO;
\&  my $alnin = Bio::AlignIO\->new(\-format => \*(Aqemboss\*(Aq,
\&                                \-file   => $wateroutfile);
\&
\&  while ( my $aln = $alnin\->next_aln ) {
\&      # process the alignment \-\- these will be Bio::SimpleAlign objects
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The EMBOSSacd represents all the possible command line arguments that
can be given to an \s-1EMBOSS\s0 application.
.PP
Do not create this object directly. It will be created and attached to
its corresponding Bio::Tools::Run::EMBOSSApplication if you set
.PP
.Vb 1
\&  $application\->verbose > 0
.Ve
.PP
Call
.PP
.Vb 1
\&  $application\->acd
.Ve
.PP
to retrive the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object.
.PP
See also Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
Address:
.PP
.Vb 3
\&     EMBL Outstation, European Bioinformatics Institute
\&     Wellcome Trust Genome Campus, Hinxton
\&     Cambs. CB10 1SD, United Kingdom
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : $emboss_prog\->acd($prog_name);
\& Function: Constructor for the class.
\&           Calls EMBOSS program \*(Aqacdc\*(Aq, 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
.Ve
.SS "name"
.IX Subsection "name"
.Vb 8
\& 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
.Ve
.SS "print"
.IX Subsection "print"
.Vb 8
\& Title   : print
\& Usage   : $embossacd\->print; $embossacd\->print(\*(Aq\-word\*(Aq);
\& 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
.Ve
.SS "mandatory"
.IX Subsection "mandatory"
.Vb 6
\& Title   : mandatory
\& Usage   : $acd\->mandatory
\& Function: gets a  mandatory subset of qualifiers
\& Throws  :
\& Returns : Bio::Tools::Run::EMBOSSacd object
\& Args    : none
.Ve
.SS "Qualifier queries"
.IX Subsection "Qualifier queries"
These methods can be used test qualifier names and read values.
.SS "qualifier"
.IX Subsection "qualifier"
.Vb 6
\& Title   : qualifier
\& Usage   : $acd\->qualifier($string)
\& Function: tests for the existence of the qualifier
\& Throws  :
\& Returns : boolean
\& Args    : string, name of the qualifier
.Ve
.SS "category"
.IX Subsection "category"
.Vb 7
\& Title   : category
\& Usage   : $acd\->category($qual_name)
\& Function: Return the category of the qualifier
\& Throws  :
\& Returns : \*(Aqmandatory\*(Aq or \*(Aqoptional\*(Aq or \*(Aqadvanced\*(Aq or
\&            \*(Aqassociated\*(Aq or \*(Aqgeneral\*(Aq
\& Args    : string, name of the qualifier
.Ve
.SS "values"
.IX Subsection "values"
.Vb 6
\& Title   : values
\& Usage   : $acd\->values($qual_name)
\& Function: Return the possible values for the qualifier
\& Throws  :
\& Returns : string
\& Args    : string, name of the qualifier
.Ve
.SS "descr"
.IX Subsection "descr"
.Vb 6
\& Title   : descr
\& Usage   : $acd\->descr($qual_name)
\& Function: Return the description of the qualifier
\& Throws  :
\& Returns : boolean
\& Args    : string, name of the qualifier
.Ve
.SS "unnamed"
.IX Subsection "unnamed"
.Vb 6
\& 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
.Ve
.SS "default"
.IX Subsection "default"
.Vb 6
\& Title   : default
\& Usage   : $acd\->default($qual_name)
\& Function: Return the default value for the qualifier
\& Throws  :
\& Returns : scalar
\& Args    : string, name of the qualifier
.Ve