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

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

Name
       SWISS::OXs

Description
       SWISS::OXs represents the OX lines within an SWISS-PROT + TrEMBL entry as specified in the user manual
	http://www.expasy.org/sprot/userman.html . The OXs object is a container object which holds a list of SWISS::OX objects for each currently
       permitted taxonomic resource.

Inherits from
       SWISS::BaseClass.pm

Attributes
       "NCBI_TaxID"
	     A ListBase object which holds a list of tax ids.

   Standard methods
       new
       fromText
       toText

Example
	 $taxid = new SWISS::OX;
	 $taxid->text('1234');
	 $entry->OXs->NCBI_TaxID()->add($taxid);

	 foreach my $taxid ($entry->OXs->NCBI_TaxID()->elements()) {
	   print $taxid->text, "
";
	 }

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 131:
	   =back doesn't take any parameters, but you said =back  =head1 Methods

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