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.
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']);