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\Amelaye\BioPHP\Domain\Parser\Service ParsePrintsManager

Class ParsePrintsManager A PRINTS entry describes a protein fingerprint, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its data fields are lower case three-character tags ending with a semicolon (gc;, gn;, ga;, gd;), unlike every other format the library reads.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getEntryName
getEntryType
getCreateDate
getUpdDate
getDescription
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
parseDates
entryName
entryType
createDate
updDate
description
No private constants found

Properties

$entryName

$entryName : string

Type

string —

$entryType

$entryType : string

Type

string —

$createDate

$createDate : string

Type

string —

$updDate

$updDate : string

Type

string —

$description

$description : 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 PRINTS entry. The gc; field carries the entry name and comes first.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

PRINTS entries carry no end-of-entry marker, so a stream holding several of them cannot be split : reading stops at the end of the file. This mirrors the original BioPHP parser, which had the same limitation.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a PRINTS entry.

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 a PRINTS 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 —

getEntryType()

getEntryType() : string

Returns

string —

getCreateDate()

getCreateDate() : string

Returns

string —

getUpdDate()

getUpdDate() : string

Returns

string —

getDescription()

getDescription() : string

Returns

string —

parseDates()

parseDates(string  $sData) : void

Reads the ga; line, which carries the creation date then any number of "KEY value" pairs.

Example: ga; 16-NOV-1995; UPDATE 06-JUN-1999

Parameters

string $sData

The ga; line, tag stripped

Returns

void —