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']);

perl v5.10.0                                       2006-01-26                                    SWISS::DRs(3pm)