Name

       SWISS::DRs

Description

       SWISS::DRs represents the DR (database crossreference) lines within an SWISS-PROT + TrEMBL
       entry as specified in the user manual http://www.expasy.org/sprot/userman.html .

Inherits from

       SWISS::ListBase.pm

Attributes

       "list"
           An array of arrays. Each element is an array (Database_identifier, primary_key,
           secondary_key[,further elements]).

Methods

   Standard methods
       new
       fromText
       toText
       sort

   Reading methods
       emblacs
           Returns a list of all EMBL accession numbers. These are the primary keys of EMBL
           crossreferences.

       pids [$dropVersion]
           Returns a list of all PIDs. These are the secondary keys of EMBL crossreferences.

           ATTENTION: The EMBL protein identifiers introduced in 1999 are of the form xxxxx.yy,
           e.g. CAA33128.1 If $dropVersion is set, the version number (.yy) will be dropped from
           each PID.

           Example:

           If the EMBL DR line is

           DR   EMBL; L37685; AAC41668.1; -.

           pids(1) will only return AAC41668, NOT AAC41668.1

   Writing methods
       deleteUnlessEvidenceCategories $evidenceCategories, @patterns
           Like del, but deletes an item only if the item has no evidence tags, or if the
           evidence tags are not in one of the categories given in $evidenceCategories.

           Example:

           $entry->DRs->deleteUnlessEvidenceCategories('CA', 'FlyBase')

           will only delete Flybase DR lines which do not have the evidence category 'A' or 'C'.

   Filter functions
       dbName($dbTargetName)
           True if the first element of a DR line (the DB name) matches $dbTargetName.
           $dbTargetName has to match in full, not only a partial match.

       notDbName($dbTargetName)
           True if the first element of a DR line (the DB name) does NOT macht $dbTargetName.

   ** lines (SWISS-PROT internal format)
       Each DR line may be followed by a ** line like

        **   DR   PROSITE; PS12345; XXX_PAT; FALSE_POS_1

        These will be stored internally as DR lines with the DB identifier
        '_HIDDEN_'. Therefore adding a ** PROSITE line is done as:

        $entry->DRs->add(['_HIDDEN_', 'PS12345', 'XXX_PAT', 'FALSE_POS_1']);