bionic (3) SWISS::Entry.3pm.gz

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.

POD ERRORS

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