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\Amelaye\BioPHP\Domain\Parser\Service ParseTransfacSiteManager

Class ParseTransfacSiteManager A site record describes one regulatory element : the stretch of DNA a factor was found to bind, where it sits relative to the transcription start site of its gene, and which factor binds it.

Summary

Methods
Properties
Constants
getFormat
parseDataFile
getSeqType
getDescription
getGeneRegion
getSequence
getFirstPosition
getBindingFactors
getOrganism
getMethod
getComments
__construct
isEntryStart
isEntryEnd
getEntryId
getAccession
getId
getDateCreated
getDateUpdated
No public properties found
No public constants found
readLabel
readData
parseCommonField
parseDate
append
splitList
accession
id
dateCreated
dateUpdated
No protected constants found
No private methods found
seqType
description
geneRegion
sequence
firstPosition
bindingFactors
organism
method
comments
No private constants found

Properties

$accession

$accession : string

Type

string —

$id

$id : string

Type

string —

$dateCreated

$dateCreated : string

Type

string —

$dateUpdated

$dateUpdated : string

Type

string —

$seqType

$seqType : string

Sequence type, e.g. "D" for a DNA element taken from a gene.

Type

string —

$description

$description : string

Type

string —

$geneRegion

$geneRegion : string

Type

string —

$sequence

$sequence : string

The sequence of the element itself.

Type

string —

$firstPosition

$firstPosition : string

Position of the first base, counted from the transcription start site, so a site sitting upstream of it reads negative.

Type

string —

$bindingFactors

$bindingFactors : array

Type

array<string|int, mixed> —

$organism

$organism : string

Type

string —

$method

$method : string

Type

string —

$comments

$comments : string

Type

string —

Methods

getFormat()

getFormat() : string

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

Returns

string —

parseDataFile()

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

Parses a TRANSFAC site 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

getSeqType()

getSeqType() : string

Returns

string —

getDescription()

getDescription() : string

Returns

string —

getGeneRegion()

getGeneRegion() : string

Returns

string —

getSequence()

getSequence() : string

Returns

string —

getFirstPosition()

getFirstPosition() : string

Returns

string —

getBindingFactors()

getBindingFactors() : array

Returns

array —

getOrganism()

getOrganism() : string

Returns

string —

getMethod()

getMethod() : string

Returns

string —

getComments()

getComments() : string

Returns

string —

__construct()

__construct() : mixed

Constructor.

Returns

mixed —

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new TRANSFAC record, which the accession number does.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a TRANSFAC record.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a TRANSFAC record, its accession number.

Parameters

array $aFlines

The whole file, buffered
string $sLine

The line opening the entry

Returns

string —

getAccession()

getAccession() : string

Returns

string —

getId()

getId() : string

Returns

string —

getDateCreated()

getDateCreated() : string

Returns

string —

getDateUpdated()

getDateUpdated() : string

Returns

string —

readLabel()

readLabel(string  $sLine) : string

Reads the two-letter label a line carries.

Parameters

string $sLine

The line to analyze

Returns

string —

readData()

readData(string  $sLine) : string

Reads the data a line carries, which starts at its fifth column.

Parameters

string $sLine

The line to analyze

Returns

string —

parseCommonField()

parseCommonField(string  $sLabel, string  $sData) : bool

Reads the fields every TRANSFAC record carries, and says whether it did : a subclass calls this first and only looks at the labels of its own record when it did not.

Parameters

string $sLabel
string $sData

Returns

bool —

parseDate()

parseDate(string  $sData) : mixed

Parses one DT line, which dates either the creation or the last update of the record and may carry a time of day.

Format : DT 20.06.90 11:00:03 (created); ewi.

Parameters

string $sData

Returns

mixed —

append()

append(string  $sBuffer, string  $sData) : string

Appends the data of a line to a field written over several of them.

Parameters

string $sBuffer
string $sData

Returns

string —

splitList()

splitList(string  $sText, string  $sSeparator = ";") : array

Splits a field listing its values, semicolon separated and possibly closed by a period, into its items.

Parameters

string $sText
string $sSeparator

Returns

array —