\Amelaye\BioPHP\Domain\Database\Factory DatabaseParserFactory

The single place that knows which parsers exist. Everything a format implies - its name, how an entry starts, how its identifier reads, how it is parsed - lives in the parser itself, so supporting a new format means writing one class and adding one line below.

Class DatabaseParserFactory

Summary

Methods
Properties
Constants
getFormats
getParserClass
createParser
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
No private methods found
No private properties found
PARSERS

Constant

PARSERS

PARSERS = [\Amelaye\BioPHP\Domain\Parser\Service\ParseGenbankManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseSwissprotManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseEmblManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePdbManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePrositeManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseExpasyEnzymeManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePdbstrManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseUnigeneManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePrintsManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseBlocksManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseAaindexManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseProdomManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseNcbiLitManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePmdManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseHgbaseManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePrfManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParsePirManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseEpdManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseGenomeManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseEntrezManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacMatrixManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacGeneManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacClassManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacCellManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacFactorManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseTransfacSiteManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseKeggCompoundManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseKeggReactionManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseKeggEnzymeManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseKeggOrthologManager::class, \Amelaye\BioPHP\Domain\Parser\Service\ParseKeggGenomeManager::class]

Every parser the library ships with.

Methods

getFormats()

getFormats() : array

The format names accepted by the library, in registration order.

Returns

array —

getParserClass()

getParserClass(string  $sFormat) : string

Resolves a format name to the class handling it.

Parameters

string $sFormat

Database format, e.g. "GENBANK"

Throws

\Exception

When no parser claims that format

Returns

string —

Fully qualified name of the parser class

createParser()

createParser(string  $sFormat) : \Amelaye\BioPHP\Domain\Database\Interfaces\ParseDatabaseInterface

Builds a fresh parser for a format. A parser holds the state of the record it has read, so each call returns its own instance.

Parameters

string $sFormat

Database format, e.g. "GENBANK"

Throws

\Exception

When no parser claims that format

Returns

\Amelaye\BioPHP\Domain\Database\Interfaces\ParseDatabaseInterface —