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\Amelaye\BioPHP\Domain\Parser\Service ParseEpdManager

Class ParseEpdManager An EPD entry describes a promoter. It borrows the two character tag layout of EMBL, but its fields carry different things, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The three dated events the format defines are all read here, where the original BioPHP parser had commented two of them out.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getEntryName
getDataClass
getInsiteType
getTaxDiv
getAccessions
getCreateDate
getCreateRel
getSequpdDate
getSequpdRel
getNotupdDate
getNotupdRel
getDescription
getComments
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
parseIdentifier
parseDate
entryName
dataClass
insiteType
taxDiv
accessions
createDate
createRel
sequpdDate
sequpdRel
notupdDate
notupdRel
description
comments
No private constants found

Properties

$entryName

$entryName : string

Type

string —

$dataClass

$dataClass : string

Type

string —

$insiteType

$insiteType : string

Type

string —

$taxDiv

$taxDiv : string

Type

string —

$accessions

$accessions : array

Type

array<string|int, mixed> —

$createDate

$createDate : string

Type

string —

$createRel

$createRel : string

Type

string —

$sequpdDate

$sequpdDate : string

Type

string —

$sequpdRel

$sequpdRel : string

Type

string —

$notupdDate

$notupdDate : string

Type

string —

$notupdRel

$notupdRel : string

Type

string —

$description

$description : string

Type

string —

$comments

$comments : string

Type

string —

Methods

__construct()

__construct() : mixed

Constructor.

Returns

mixed —

getFormat()

getFormat() : string

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

Returns

string —

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new EPD entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes an EPD entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

getEntryId(array  $aFlines, string  $sLine) : string

Extracts the identifier uniquely naming an EPD entry, read from its AC line.

Parameters

array $aFlines

The whole file, buffered
string $sLine

The line opening the entry

Returns

string —

parseDataFile()

parseDataFile(array  $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

Parses an EPD data file and populates this manager's fields.

Parameters

array $aFlines

The lines the script has to parse

Throws

\Exception

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence —

$oSequence

getEntryName()

getEntryName() : string

Returns

string —

getDataClass()

getDataClass() : string

Returns

string —

getInsiteType()

getInsiteType() : string

Returns

string —

getTaxDiv()

getTaxDiv() : string

Returns

string —

getAccessions()

getAccessions() : array

Returns

array —

getCreateDate()

getCreateDate() : string

Returns

string —

getCreateRel()

getCreateRel() : string

Returns

string —

getSequpdDate()

getSequpdDate() : string

Returns

string —

getSequpdRel()

getSequpdRel() : string

Returns

string —

getNotupdDate()

getNotupdDate() : string

Returns

string —

getNotupdRel()

getNotupdRel() : string

Returns

string —

getDescription()

getDescription() : string

Returns

string —

getComments()

getComments() : string

Returns

string —

parseIdentifier()

parseIdentifier(string  $sData) : void

Reads the ID line, which names the entry then qualifies it.

Example: ID HS_ACHA_1 standard; single; HUM.

Parameters

string $sData

The ID line, tag stripped

Returns

void —

parseDate()

parseDate(string  $sData) : void

Reads a DT line, which dates one event and names the release it happened in.

Example: DT 15-JUN-2001 (REL. 75, CREATED)

Parameters

string $sData

The DT line, tag stripped

Returns

void —