Documentation

ParseTransfacMatrixManager extends ParseTransfacAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

Class ParseTransfacMatrixManager A matrix record holds the nucleotide weight matrix describing what a transcription factor binds : one row per position of the binding site, counting how often each of A, C, G and T was observed there.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$accession  : string

$dateCreated  : string

$dateUpdated  : string

$id  : string

$basis  : string

$comments  : string

$description  : string

$matrix  : array<string|int, mixed>

One row per position : ["A" => 1, "C" => 2, "G" => 2, "T" => 0, "consensus" => "N"].

$name  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getBasis()  : string

getComments()  : string

getDateCreated()  : string

getDateUpdated()  : string

getDescription()  : string

getEntryId()  : string

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

getFormat()  : string

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

getId()  : string

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

getName()  : 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 matrix 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.

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

Parses one row of the weight matrix, the label being the position it describes.