Documentation

ParseTransfacSiteManager extends ParseTransfacAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

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.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$accession  : string

$dateCreated  : string

$dateUpdated  : string

$id  : string

$bindingFactors  : array<string|int, mixed>

$comments  : string

$description  : string

$firstPosition  : string

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

$geneRegion  : string

$method  : string

$organism  : string

$seqType  : string

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

$sequence  : string

The sequence of the element itself.

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getBindingFactors()  : array<string|int, mixed>

getComments()  : string

getDateCreated()  : string

getDateUpdated()  : string

getDescription()  : string

getEntryId()  : string

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

getFirstPosition()  : string

getFormat()  : string

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

getGeneRegion()  : string

getId()  : string

getMethod()  : string

getOrganism()  : string

getSeqType()  : string

getSequence()  : string

isEntryEnd()  : bool

Tells whether a line closes a TRANSFAC record.

isEntryStart()  : bool

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

parseDataFile()  : Sequence

Parses a TRANSFAC site data file and populates this manager's fields.

append()  : string

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

parseCommonField()  : 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.

parseDate()  : mixed

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

readData()  : string

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

readLabel()  : string

Reads the two-letter label a line carries.

splitList()  : array<string|int, mixed>

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