Reference

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
 COFACTOR                        SWISS::CCcofactor
 DISEASE                         SWISS::CCdisease
 SEQUENCE CAUTION                SWISS::CCseq_caution
 SUBCELLULAR LOCATION            SWISS::CCsubcell_location
 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.

History