ParseExpasyEnzymeManager
in package
implements
ParseDatabaseInterface
Class ParseExpasyEnzymeManager ExPASy ENZYME entries describe an enzyme by its EC number, not a sequence - like ParsePdbManager and ParsePrositeManager, this class does not reuse the Sequence/Feature entities of ParseDbAbstractManager. Not to be confused with RestrictionEnzymeManager, which covers restriction endonucleases (a completely different Legacy/ExPASy database).
Tags
Table of Contents
Interfaces
- ParseDatabaseInterface
- Interface ParseDatabaseInterface
Properties
- $aCaLines : array<string|int, mixed>
- $alternateNames : array<string|int, mixed>
- $catalyticActivities : array<string|int, mixed>
- One entry per reaction the enzyme catalyses : an enzyme acting on several substrates has as many, and the file numbers them "(1)", "(2)".
- $cofactors : array<string|int, mixed>
- $comments : string
- $description : string
- $diseases : array<string|int, ExpasyDisease>
- $id : string
- $prositeRefs : array<string|int, mixed>
- $swissprotRefs : array<string|int, mixed>
Methods
- __construct() : mixed
- Constructor.
- getAlternateNames() : array<string|int, mixed>
- getCatalyticActivities() : array<string|int, mixed>
- getCofactors() : array<string|int, mixed>
- getComments() : string
- getDescription() : string
- getDiseases() : array<string|int, ExpasyDisease>
- getEntryId() : string
- Extracts the identifier uniquely naming a ExPASy ENZYME entry.
- getFormat() : string
- The name this format is known by in the collection records and in DatabaseParserFactory.
- getId() : string
- getPrositeRefs() : array<string|int, mixed>
- getSwissprotRefs() : array<string|int, mixed>
- isEntryEnd() : bool
- Tells whether a line closes a ExPASy ENZYME entry.
- isEntryStart() : bool
- Tells whether a line opens a new ExPASy ENZYME entry.
- parseDataFile() : Sequence
- Parses an ExPASy ENZYME data file and populates this manager's fields.
- accumulate() : string
- Accumulates a multi-line field: the current line's data, plus every following line still tagged $sTag, joined with $sJoiner. Advances $aLines past what it reads.
- parseCatalyticActivities() : array<string|int, mixed>
- Reads the CA field into one entry per reaction. An enzyme acting on several substrates has several, which the file numbers "(1)", "(2)"; an unnumbered line continues the reaction above it, a long reaction being wrapped rather than repeated.
- parseCofactors() : array<string|int, mixed>
- Parses the CF field.
- parseDisease() : ExpasyDisease
- Parses one DI line.
- parsePrositeRef() : string
- Parses one PR line.
- parseSwissprotRefs() : array<string|int, mixed>
- Parses the DR field into an accession => entry name map.
Properties
$aCaLines
private
array<string|int, mixed>
$aCaLines
= []
$alternateNames
private
array<string|int, mixed>
$alternateNames
= []
$catalyticActivities
One entry per reaction the enzyme catalyses : an enzyme acting on several substrates has as many, and the file numbers them "(1)", "(2)".
private
array<string|int, mixed>
$catalyticActivities
= []
$cofactors
private
array<string|int, mixed>
$cofactors
= []
$comments
private
string
$comments
= ""
$description
private
string
$description
= ""
$diseases
private
array<string|int, ExpasyDisease>
$diseases
= []
$id
private
string
$id
= ""
$prositeRefs
private
array<string|int, mixed>
$prositeRefs
= []
$swissprotRefs
private
array<string|int, mixed>
$swissprotRefs
= []
Methods
__construct()
Constructor.
public
__construct() : mixed
getAlternateNames()
public
getAlternateNames() : array<string|int, mixed>
Return values
array<string|int, mixed>getCatalyticActivities()
public
getCatalyticActivities() : array<string|int, mixed>
Return values
array<string|int, mixed>getCofactors()
public
getCofactors() : array<string|int, mixed>
Return values
array<string|int, mixed>getComments()
public
getComments() : string
Return values
stringgetDescription()
public
getDescription() : string
Return values
stringgetDiseases()
public
getDiseases() : array<string|int, ExpasyDisease>
Return values
array<string|int, ExpasyDisease>getEntryId()
Extracts the identifier uniquely naming a ExPASy ENZYME entry.
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
stringgetFormat()
The name this format is known by in the collection records and in DatabaseParserFactory.
public
static getFormat() : string
Return values
stringgetId()
public
getId() : string
Return values
stringgetPrositeRefs()
public
getPrositeRefs() : array<string|int, mixed>
Return values
array<string|int, mixed>getSwissprotRefs()
public
getSwissprotRefs() : array<string|int, mixed>
Return values
array<string|int, mixed>isEntryEnd()
Tells whether a line closes a ExPASy ENZYME entry.
public
static isEntryEnd(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolisEntryStart()
Tells whether a line opens a new ExPASy ENZYME entry.
public
static isEntryStart(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolparseDataFile()
Parses an ExPASy ENZYME data file and populates this manager's fields.
public
parseDataFile(array<string|int, mixed> $aFlines) : Sequence
Parameters
- $aFlines : array<string|int, mixed>
-
The lines the script has to parse
Tags
Return values
Sequence —$oSequence
accumulate()
Accumulates a multi-line field: the current line's data, plus every following line still tagged $sTag, joined with $sJoiner. Advances $aLines past what it reads.
private
accumulate(ArrayIterator $aLines, array<string|int, mixed> $aFlines, string $sTag, string $sJoiner) : string
Parameters
- $aLines : ArrayIterator
- $aFlines : array<string|int, mixed>
- $sTag : string
- $sJoiner : string
Return values
stringparseCatalyticActivities()
Reads the CA field into one entry per reaction. An enzyme acting on several substrates has several, which the file numbers "(1)", "(2)"; an unnumbered line continues the reaction above it, a long reaction being wrapped rather than repeated.
private
parseCatalyticActivities(array<string|int, mixed> $aLines) : array<string|int, mixed>
Parameters
- $aLines : array<string|int, mixed>
Return values
array<string|int, mixed>parseCofactors()
Parses the CF field.
private
parseCofactors(string $sText) : array<string|int, mixed>
Format : CF Cofactor1; Cofactor2.
Parameters
- $sText : string
Return values
array<string|int, mixed>parseDisease()
Parses one DI line.
private
parseDisease(string $sLine) : ExpasyDisease
Format : DI Disease name; MIM: 123456.
Parameters
- $sLine : string
Return values
ExpasyDiseaseparsePrositeRef()
Parses one PR line.
private
parsePrositeRef(string $sLine) : string
Format : PR PROSITE; PDOC00061;
Parameters
- $sLine : string
Return values
stringparseSwissprotRefs()
Parses the DR field into an accession => entry name map.
private
parseSwissprotRefs(string $sText) : array<string|int, mixed>
Format : DR ACCESSION, ENTRY_NAME; ACCESSION, ENTRY_NAME; ...
Parameters
- $sText : string