ParseTransfacAbstractManager
in package
implements
ParseDatabaseInterface
Class ParseTransfacAbstractManager TRANSFAC ships one flat file per kind of record - matrix.dat, gene.dat, class.dat, cell.dat, factor.dat, site.dat - which all share the same grammar : a two-letter label in the first columns, its data from the fifth, "XX" lines spacing the fields apart and "//" closing the record. That grammar, the AC/ID/DT fields every record carries and the way a field spanning several lines is joined, live here; each subclass adds the fields of its own record.
The date reads by tokens rather than at the fixed offset Legacy/transfac.inc.php used for five of its six record types : that offset assumed a two-digit year ("20.06.90") and misses the marker as soon as the file writes the year in full, which TRANSFAC has long been doing.
Tags
Table of Contents
Interfaces
- ParseDatabaseInterface
- Interface ParseDatabaseInterface
Properties
- $accession : string
- $dateCreated : string
- $dateUpdated : string
- $id : string
Methods
- __construct() : mixed
- Constructor.
- getAccession() : string
- getDateCreated() : string
- getDateUpdated() : string
- getEntryId() : string
- Extracts the identifier uniquely naming a TRANSFAC record, its accession number.
- getId() : 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.
- 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.
Properties
$accession
protected
string
$accession
= ""
$dateCreated
protected
string
$dateCreated
= ""
$dateUpdated
protected
string
$dateUpdated
= ""
$id
protected
string
$id
= ""
Methods
__construct()
Constructor.
public
__construct() : mixed
getAccession()
public
getAccession() : string
Return values
stringgetDateCreated()
public
getDateCreated() : string
Return values
stringgetDateUpdated()
public
getDateUpdated() : string
Return values
stringgetEntryId()
Extracts the identifier uniquely naming a TRANSFAC record, its accession number.
public
static getEntryId(array<string|int, mixed> $aFlines, string $sLine) : string
Parameters
- $aFlines : array<string|int, mixed>
-
The whole file, buffered
- $sLine : string
-
The line opening the entry
Return values
stringgetId()
public
getId() : string
Return values
stringisEntryEnd()
Tells whether a line closes a TRANSFAC record.
public
static isEntryEnd(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolisEntryStart()
Tells whether a line opens a new TRANSFAC record, which the accession number does.
public
static isEntryStart(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolappend()
Appends the data of a line to a field written over several of them.
protected
append(string $sBuffer, string $sData) : string
Parameters
- $sBuffer : string
- $sData : string
Return values
stringparseCommonField()
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.
protected
parseCommonField(string $sLabel, string $sData) : bool
Parameters
- $sLabel : string
- $sData : string
Return values
boolparseDate()
Parses one DT line, which dates either the creation or the last update of the record and may carry a time of day.
protected
parseDate(string $sData) : mixed
Format : DT 20.06.90 11:00:03 (created); ewi.
Parameters
- $sData : string
readData()
Reads the data a line carries, which starts at its fifth column.
protected
static readData(string $sLine) : string
Parameters
- $sLine : string
-
The line to analyze
Return values
stringreadLabel()
Reads the two-letter label a line carries.
protected
static readLabel(string $sLine) : string
Parameters
- $sLine : string
-
The line to analyze
Return values
stringsplitList()
Splits a field listing its values, semicolon separated and possibly closed by a period, into its items.
protected
splitList(string $sText[, string $sSeparator = ";" ]) : array<string|int, mixed>
Parameters
- $sText : string
- $sSeparator : string = ";"