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.
This minimum program reads entries from a file in SWISS-PROT
format and prints the primary accession number for each of the entries.
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.
- 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.
- 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.
Hey! The above document had some coding errors, which are
explained below:
- Around line 609:
- =over without closing =back