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

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

Name
       SWISS::DTs

Description
       SWISS::DTs represents the DT lines within an Swiss-Prot + TrEMBL entry as specified in the user manual
       http://www.expasy.org/sprot/userman.html .

Inherits from
       SWISS::BaseClass.pm

Attributes
       "CREATED_date"
	   Creation date

       "ANN_date"
	   Last annotation update

       "SQ_date"
	   Last Sequence update

       "CREATED_rel"
	   Created for release

       "ANN_rel"
	   Last annotation for release

       "SQ_rel"
	   Last sequence update for release

       "ANN_version"
	   Version number for entry annotation

       "SQ_version"
	   Version number for sequence

Methods
   Standard methods
       new
       fromText
       toText
       sort

   Writing methods
       set_Created ($date, $release)
       set_AnnotationUpdate ($date, $release[, $version])
       set_SequenceUpdate ($date, $release[, $version])

TRANSITION

       The format of the DT line will change in early 2004 from:

	DT   01-JUL-1993 (Rel. 26, Created)
	DT   01-JUL-1993 (Rel. 26, Last sequence update)
	DT   28-FEB-2003 (Rel. 41, Last annotation update)

       to:

	DT   01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
	DT   01-JUL-1993, sequence version 36.
	DT   28-FEB-2003, entry version 54.

       This module supports both formats. To convert an entry from the old to the new format, do:

	$entry->DTs->CREATED_rel("UniProtKB/Swiss-Prot");
	$entry->DTs->ANN_version(54);
	$entry->DTs->SQ_version(36);

perl v5.10.1							    2008-07-11							   SWISS::DTs(3pm)

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

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 v5.10.1							    2006-01-26							   SWISS::DRs(3pm)