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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.