swiss::genegroup(3pm) [debian man page]

SWISS::GeneGroup(3pm)					User Contributed Perl Documentation				     SWISS::GeneGroup(3pm)

Name
       SWISS::GeneGroup.pm

Description
       A SWISS::GeneGroup object contain all synonyms for a given gene name. See SWISS::GNs for a description of the gene name format.

Inherits from
       SWISS::BaseClass.pm

       (also implements many methods from SWISS::ListBase.pm)

Attributes
       "Names"
	     Each list element is a SWISS::GN object, describing a primary name
	     or synonym. Concatenation of Name and Synonyms lists.

       "OLN"
	     Each list element is a SWISS::GN object, describing an
	     OrderedLocusName.

       "ORFNames"
	     Each list element is a SWISS::GN object, describing an ORFName.

Methods
   Standard methods
       new
       fromText
       toText

   Specific methods
       Name
	   Returns the Name (primary name).

       Synonyms
	   Returns the Synonyms.

       elements
	     Concatenates all elements from Names, OLN and ORFNames in
	     a single array.

   List manipulation methods
       Since GeneGroup was a previous implementation of SWISS::ListBase, the list manipulation methods below are provided to facilitate
       compatibility.

       size
       isEmpty
       elements
       filter
       get (deprecated)
       head (deprecated)
       tail (deprecated)
       item (deprecated)
       push (deprecated)
       pop (deprecated)
       shift (deprecated)
       splice (deprecated)
       unshift (deprecated)
       set (deprecated)
       add (deprecated)

perl v5.10.1							    2006-01-26						     SWISS::GeneGroup(3pm)

SWISS::CCs(3pm) 					User Contributed Perl Documentation					   SWISS::CCs(3pm)

Name
       SWISS::CCs

Description
       SWISS::CCs represents the CC lines within a Swiss-Prot or TrEMBL entry as specified in the user manual
	http://www.expasy.org/sprot/userman.html . The CCs object is a container object which holds a list comprised of object of the type
       SWISS::CC or derived classes (see below).

       Code example

       local $/="
//
";

       while (<>) {

	 my $entry = SWISS::Entry-> fromText($_);
	 my @CCs = $entry -> CCs -> elements();

	 for my $CC (@CCs) {

	   if ($CC -> topic eq 'ALTERNATIVE PRODUCTS') {

	     # now can call methods of CCalt_prod

	   } elsif ($CC -> topic eq 'Copyright') {

	     # now can call methods of CCcopyright

	   } else {

	     # now can call methods of CC
	   }
	 }
       }

Inherits from
       SWISS::ListBase.pm

Attributes
       "list"
	   Each list element is an object of one of the following classes, depending of the type of comment:

	    topic			    object
	    --------------------	    --------------------
	    ALTERNATIVE PRODUCTS	    SWISS::CCalt_prod
	    RNA EDITING 		    SWISS::CCrna_editing
	    BIOPHYSICOCHEMICAL PROPERTIES   SWISS::CCbpc_properties
	    INTERACTION 		    SWISS::CCinteraction
	    Copyright			    SWISS::CCcopyright
	    (all other topics)		    SWISS::CC

Methods
   Standard methods
       new
       fromText
       sort
	   Sort the CC block according to the order given in Swiss-Prot annotation note ANN017.

       toText
       update

   Reading/Writing methods
       ccTopic ($topic)
	   Returns true if entry contains a comment block with the specified topic.

       copyright
	   Returns a string representation of the copyright text.

       del (@patternList)
	   Deletes all comment elements whose topic matches the first element of the pattern list.  The second element is the used to specify a
	   requirement for the comment to match as well.

       get (@patternList)
	   An array is returned consisting of all comment elements elements whose topic matches any elements of the pattern list.

       getObject (@patternList)
	   Same as get, but returns the results wrapped in a new ListBase object.

       toString
	   Returns a string representation of the CCs object.

perl v5.10.1							    2008-07-16							   SWISS::CCs(3pm)