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\Amelaye\BioPHP\Domain\Parser\Service ParseNcbiLitManager

Class ParseNcbiLitManager The NCBI journal list describes periodicals, not sequences, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. It is the only format the library reads whose fields are "Label: value" pairs and whose entries are closed by a row of dashes rather than a double slash.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getId
getTitle
getMedAbbr
getIssn
getEssn
getIsoAbbr
getNlmId
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
No private methods found
id
title
medAbbr
issn
essn
isoAbbr
nlmId
No private constants found

Properties

$id

$id : string

Type

string —

$title

$title : string

Type

string —

$medAbbr

$medAbbr : string

Type

string —

$issn

$issn : string

Type

string —

$essn

$essn : string

Type

string —

$isoAbbr

$isoAbbr : string

Type

string —

$nlmId

$nlmId : 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 journal entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a journal entry. The NCBI list separates its records with a row of dashes.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a journal 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 an NCBI journal list 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

getId()

getId() : string

Returns

string —

getTitle()

getTitle() : string

Returns

string —

getMedAbbr()

getMedAbbr() : string

Returns

string —

getIssn()

getIssn() : string

Returns

string —

getEssn()

getEssn() : string

Returns

string —

getIsoAbbr()

getIsoAbbr() : string

Returns

string —

getNlmId()

getNlmId() : string

Returns

string —