\
Amelaye
BioPHP
Api
DTO
Interfaces
DependencyInjection
Domain
Database
Entity
Factory
Interfaces
Service
Parser
Entity
Interfaces
Service
Sequence
Builder
Entity
Interfaces
Service
Traits
ValueObject
Tools
Interfaces
Service

\Amelaye\BioPHP\Domain\Parser\Service ParseProdomManager

Class ParseProdomManager A ProDom entry describes a family of protein domains, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Only the fields the original BioPHP parser read are decomposed : the alignment block (AL/CO) and the cross-references (DR) are left aside, as they were there.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getEntryNo
getAccession
getRelease
getDomainCount
getFreqNames
getKeywords
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
parseIdentifier
parseKeywords
entryNo
accession
release
domainCount
freqNames
keywords
No private constants found

Properties

$entryNo

$entryNo : string

Type

string —

$accession

$accession : string

Type

string —

$release

$release : string

Type

string —

$domainCount

$domainCount : int

Type

int —

$freqNames

$freqNames : array

Type

array<string|int, mixed> —

$keywords

$keywords : array

Type

array<string|int, mixed> —

Methods

__construct()

__construct() : mixed

Constructor.

Returns

mixed —

getFormat()

getFormat() : string

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

Returns

string —

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new ProDom entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a ProDom entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a ProDom entry, read from its AC line.

Parameters

array $aFlines

The whole file, buffered
string $sLine

The line opening the entry

Returns

string —

parseDataFile()

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

Parses a ProDom 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

getEntryNo()

getEntryNo() : string

Returns

string —

getAccession()

getAccession() : string

Returns

string —

getRelease()

getRelease() : string

Returns

string —

getDomainCount()

getDomainCount() : int

Returns

int —

getFreqNames()

getFreqNames() : array

Frequent protein names, keyed by name, valued by how many times they occur.

Returns

array —

getKeywords()

getKeywords() : array

Returns

array —

parseIdentifier()

parseIdentifier(string  $sData) : void

Reads the ID line, which carries the entry number, the release and the domain count.

Example: ID 20167 p2002.1 10 seq.

Parameters

string $sData

The ID line, tag stripped

Returns

void —

parseKeywords()

parseKeywords(string  $sData) : void

Reads the KW line, which carries the frequent names and their occurrence count, then the keywords, the two halves being separated by a double slash.

Example: KW FADR(2) Y586(1) // COMPLETE PROTEOME DNA-BINDING FATTY

Parameters

string $sData

The KW line, tag stripped

Returns

void —