\
Amelaye
BioPHP
Api
DTO
Interfaces
DependencyInjection
Domain
Database
Entity
Factory
Interfaces
Service
Parser
Entity
Interfaces
Service
Sequence
Builder
Entity
Interfaces
Service
Traits
ValueObject
Tools
Interfaces
Service

\Amelaye\BioPHP\Domain\Parser\Service ParseUnigeneManager

Class ParseUnigeneManager A UniGene entry groups the sequences believed to come from one gene. It carries no sequence of its own, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The PROTSIM lines are kept raw, as ParsePrositeManager does for its matrix field: their layout varies and the original BioPHP parser never decomposed them.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getClusterId
getTitle
getExpression
getProtSims
getSeqCount
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
No private methods found
clusterId
title
expression
protSims
seqCount
No private constants found

Properties

$clusterId

$clusterId : string

Type

string —

$title

$title : string

Type

string —

$expression

$expression : array

Type

array<string|int, mixed> —

$protSims

$protSims : array

Type

array<string|int, mixed> —

$seqCount

$seqCount : int

Type

int —

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 UniGene entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a UniGene entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a UniGene 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 UniGene 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

getClusterId()

getClusterId() : string

Returns

string —

getTitle()

getTitle() : string

Returns

string —

getExpression()

getExpression() : array

The tissues the cluster was observed in, one entry per semicolon separated item.

Returns

array —

getProtSims()

getProtSims() : array

The PROTSIM lines, kept as written.

Returns

array —

getSeqCount()

getSeqCount() : int

Returns

int —