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

       Hey! The above document had some coding errors, which are explained below:

       Around line 731:
           =over without closing =back

perl v5.32.1                                       2021-08-15                                  SWISS::Entry(3pm)