\
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 ParseAaindexManager

Class ParseAaindexManager An AAINDEX1 entry describes a numerical property of the twenty amino acids, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its data fields are single letter tags whose continuation lines start with a space, the GenBank way. The C (correlated entries) and I (index values) fields are not decomposed : they are fixed numeric tables the original BioPHP parser never touched either.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getAccession
getDescription
getAuthor
getTitle
getJournal
getLitRefs
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
parseReferences
accession
description
author
title
journal
litRefs
No private constants found

Properties

$accession

$accession : string

Type

string —

$description

$description : string

Type

string —

$author

$author : string

Type

string —

$title

$title : string

Type

string —

$journal

$journal : string

Type

string —

$litRefs

$litRefs : 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 AAINDEX1 entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes an AAINDEX1 entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming an AAINDEX1 entry.

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 an AAINDEX1 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

getAccession()

getAccession() : string

Returns

string —

getDescription()

getDescription() : string

Returns

string —

getAuthor()

getAuthor() : string

Returns

string —

getTitle()

getTitle() : string

Returns

string —

getJournal()

getJournal() : string

Returns

string —

getLitRefs()

getLitRefs() : array

Cross-references, keyed by database name.

Returns

array —

parseReferences()

parseReferences(string  $sData) : void

Reads the R line, which lists cross-references as "DBNAME:ID" pairs. The line is allowed to be empty.

Example: R LIT:1810048b PMID:1575719

Parameters

string $sData

The R line, tag stripped

Returns

void —