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

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)

Check Out this Related Man Page

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

NAME

       SWISS::Stars.pm

DESCRIPTION

       SWISS::Stars represents the ** lines within an SWISS-PROT + TrEMBL entry. These are the lines with the line tag ** which are normally not
       publicly visible.

       SWISS::Stars is a master object like SWISS::Entry. It contains subobjects which represent the different line types in the ** section. Each
       line type has a two letter tag in addition to the ** line tag. This module has been written to allow easy addition of new ** line types. To
       use a new ** line tag, just use the tag as an object dereference. Example:

	$entry->Stars->XX->add("New XX tag line.","Second new XX tag line.");

       If there is no class SWISS::Stars::XX, the class of the new object will be SWISS::Stars::default, which handles lines with the
       corresponding tag as an array of lines. If more specific handling is required, a new class SWISS::Stars::XX can be created following the
       template of SWISS::Stars::default. An example is SWISS::Stars::aa.

       Subclass names and new line tags have to be two-letter-tags. No checks are made wheter the dereferenced tag is allowed.

       Access to the (old) unstructured ANNOTATOR'S SECTION is provided by the line tag 'aa'.

	$entry->Stars->aa->add("Testline 1.","Second new test line.");

       will add these two lines to the ANNOTATOR'S SECTION.

Inherits from
       SWISS::BaseClass.pm

Attributes
	   No public attributes apart from the subclasses.

Methods
   Standard methods
       new
       fromText
       toText
       update

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

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

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