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

NAME

       SWISS::Stars.pm

DESCRIPTION

       SWISS::Stars represents the ** lines within an SWISS-PROT + TrEMBL entry. These are the lines with the line tag ** which are normally not
       publicly visible.

       SWISS::Stars is a master object like SWISS::Entry. It contains subobjects which represent the different line types in the ** section. Each
       line type has a two letter tag in addition to the ** line tag. This module has been written to allow easy addition of new ** line types. To
       use a new ** line tag, just use the tag as an object dereference. Example:

	$entry->Stars->XX->add("New XX tag line.","Second new XX tag line.");

       If there is no class SWISS::Stars::XX, the class of the new object will be SWISS::Stars::default, which handles lines with the
       corresponding tag as an array of lines. If more specific handling is required, a new class SWISS::Stars::XX can be created following the
       template of SWISS::Stars::default. An example is SWISS::Stars::aa.

       Subclass names and new line tags have to be two-letter-tags. No checks are made wheter the dereferenced tag is allowed.

       Access to the (old) unstructured ANNOTATOR'S SECTION is provided by the line tag 'aa'.

	$entry->Stars->aa->add("Testline 1.","Second new test line.");

       will add these two lines to the ANNOTATOR'S SECTION.

Inherits from
       SWISS::BaseClass.pm

Attributes
	   No public attributes apart from the subclasses.

Methods
   Standard methods
       new
       fromText
       toText
       update

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