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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 $/=``\n//\n'';

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.