Documentation

ParsePrositeManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParsePrositeManager A PROSITE entry describes a motif (pattern, or matrix/profile), not an annotated sequence, so - like ParsePdbManager - this class does not reuse the Sequence/Feature entities of ParseDbAbstractManager. It uses the same 2-char-tag/3-space layout as EMBL and Swiss-Prot, so multi-line fields are read with the same lookahead approach as ParseEmblManager. The MA (matrix) field, which Legacy/motif.inc.php itself only half-implemented (buggy 3-level nesting), is kept as a raw string here rather than ported as-is.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$accession  : string

$comments  : array<string|int, mixed>

$dates  : array<string|int, mixed>

$dbRefs  : array<string|int, PrositeDbRef>

$description  : string

$docXref  : string

$entryName  : string

$entryType  : string

$matrix  : string

$numericalResults  : array<string|int, mixed>

$pattern  : string

$pdbXrefs  : array<string|int, mixed>

$rule  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getComments()  : array<string|int, mixed>

getDates()  : array<string|int, mixed>

getDbRefs()  : array<string|int, PrositeDbRef>

getDescription()  : string

getDocXref()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a PROSITE entry.

getEntryName()  : string

getEntryType()  : string

getFormat()  : string

The name this format is known by in the collection records and in DatabaseParserFactory.

getMatrix()  : string

getNumericalResults()  : array<string|int, mixed>

getPattern()  : string

getPdbXrefs()  : array<string|int, mixed>

getRule()  : string

isEntryEnd()  : bool

Tells whether a line closes a PROSITE entry.

isEntryStart()  : bool

Tells whether a line opens a new PROSITE entry.

parseDataFile()  : Sequence

Parses a PROSITE data file and populates this manager's fields.

accumulate()  : string

Accumulates a multi-line field: the current line's data, plus every following line still tagged $sTag, joined with $sJoiner. Advances $aLines past what it reads.

parseDate()  : mixed

Parses the DT line.

parseDbRefs()  : array<string|int, PrositeDbRef>

Turns the DR field into a list of PrositeDbRef.

parseId()  : mixed

Parses the ID line.

parseList()  : array<string|int, mixed>

Turns a "item1; item2; item3." string into a plain array.

parseQualifiers()  : array<string|int, mixed>

Turns a "/qualifier=value; /qualifier=value;" string into an associative array.