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

Name
       SWISS::Entry

Description
       Main module to handle SWISS-PROT entries. One Entry object represents one SWISS-PROT entry and provides an API for its modification.

       The basic concept is the idea of lazy parsing. If an Entry object is created from the entry in flat file format, the text is simply stored
       in the private text attribute of the entry object. The member objects of the entry are only created if they are dereferenced.

Example
       This minimum program reads entries from a file in SWISS-PROT format and prints the primary accession number for each of the entries.

Attributes
       The following attributes represent member objects. They can be accessed like e.g. $entry->IDs

       IDs ID line object

       ACs
       DTs
       DEs
       GNs
       OSs
       OCs
       Refs
	   The reference block object

       CCs
       KWs
       DRs
       FTs
       Stars
	   Object for the annotator's section stored in the ** lines.

       SQs The sequence object.

Methods
       new Return a new Entry object

       initialize
	   Initialise an Entry object and return it.

       update [force]
	   Update an entry. The content of the member objects is written back into the private text attribute of the entry if necessary. If $force
	   is true, an update of all member objects is forced.

       reformat
	   Reformat all fields of an entry.

       fromText $text [, $fullParse[, $removeInternalComments]]
	   Create an Entry object from the text $text. If $fullParse is true, the entry is parsed at creation time. Otherwise the individual line
	   objects are only created if they are dereferenced. If $removeInternalComments is true, wild comments and indentation will be removed
	   from the text before the parsing is done. [NOTE: wild comments are lines starting with a double asterisk located outside the Stars
	   section, and indented lines are lines starting with spaces. Both are used internally by SWISS-PROT annotators during their work and
	   excluded from internal and external releases.]

       toText [$insertInternalComments]
	   Return the entry in flat file text format. If internal comments and indentation have been removed as specified in the parameters to
	   fromText(), you may wish to reinsert them in the text output by setting $insertInternalComments to true.

       toFasta
	   Return the entry in Fasta format.

       equal
	   Returns True if two entries are equal, False otherwise

       The following methods are provided for your convenience. They are shortcuts for methods of the individual line objects.

       ID  Returns the primary ID of the entry.

       AC  Returns the primary AC of the entry.

       SQ  Returns the sequence of the entry.

       EV  Returns the EV (evidence) object of an entry. SWISS-PROT internal method.

   Data access methods
       text
	   Returns the current text of the entry.  Quick and dirty! No update of the text is performed before.

       database_code
	   Is it a SWISS-PROT, TREMBL or TREMBLNEW entry?  database_code tries to find it out.	Return values are S for SWISS-PROT, 3 for TREMBL,
	   Q for TREMBLNEW, ? for unknown.

       isFragment
	   Returns true if the DE line indicates a fragment, or of the entry contains a NON_CONS or NON_TER feature.

       isCurated
	   Returns 1 if the entry is a curated entry, 0 otherwise.

	   SWISS-PROT internal use only.

perl v5.10.1							    2008-07-16							 SWISS::Entry(3pm)