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

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

Name
       SWISS::ACs

Description
       SWISS::ACs represents the AC (accession) lines within an SWISS-PROT + TrEMBL entry as specified in the user manual
       http://www.expasy.org/sprot/userman.html .

       The SWISS-PROT format has recently been changed to multiple AC lines.  This module will read

	Ordinary AC lines
	   AC	P10585;

	The old temporary format (for internal use only)
	   AC	Q57333; O08291; O08202; O08292; O08203; O08293; O08204; O08294;
	   **	O08205; O08295; O08206; O08296; O08207; O08297; O08208; O08298;
	   **	O08213;

	and the new format.
	   AC	Q57333; O08291; O08202; O08292; O08203; O08293; O08204; O08294;
	   AC	O08205; O08295; O08206; O08296; O08207; O08297; O08208; O08298;
	   AC	O08213;

       But, SWISS::ACs will DROP funny ** comment lines that are sometimes found following an AC line:

	   AC	Q48558; P71434;
	   **	MERGED 2 TREMBL ENTRIES.

       This module will always write the new format with multiple AC lines.

Inherits from
       SWISS::ListBase.pm

Attributes
       "list"
	   This is an array containing a list of all the accession numbers associated with this entry.	The first member will be the primary
	   accession number, and any following are the secondary accession numbers.

Methods
   Standard methods
       new
       fromText
       toText
       sort
	   This method sorts the secondary AC numbers alphanumerically, i.e.  all but the first. The primary AC number must never be sorted.

perl v5.10.1							    2006-01-26							   SWISS::ACs(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)