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 [isoformName]
           Return the entry in Fasta format (canonical/displayed sequence if no isoform name
           provided)

       isoFormNames [all]
           Return the list of (filtered for not: External|Displayed|Not described|Unknown)
           isoform names.  If all is true: list all isoform names

       isoIds [isoformName]
           Return list of isoform Ids for a particular isoform name (isoIds for
           canonical/displayed if no isoform name provided)

       isoId [isoformName]
           Return primary isoform Id for a particular isoform name (primary isoId for
           canonical/displayed if no isoform name provided)

       isoFormSequence [isoform name]
           Return the raw sequence for a specified isoform name (raw canonical sequence if no
           isoform name provided)

       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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       Around line 731:
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