Documentation

ParseHgbaseManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParseHgbaseManager An HGBase entry describes a human mutation and the population it was observed in, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its lines are a label, a tab, then the data.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$allele  : string

$citation  : string

$freqIndiv  : int

$freqPerc  : float

$haplotypeId  : string

$isInBlock  : string

$popIndiv  : int

$popName  : string

$populationId  : string

$sourceComment  : string

$sourceId  : string

$submissionId  : string

$submitterName  : string

Methods

__construct()  : mixed

Constructor.

getAllele()  : string

getCitation()  : string

getEntryId()  : string

Extracts the identifier uniquely naming an HGBase entry.

getFormat()  : string

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

getFreqIndiv()  : int

getFreqPerc()  : float

getHaplotypeId()  : string

getIsInBlock()  : string

getPopIndiv()  : int

getPopName()  : string

getPopulationId()  : string

getSourceComment()  : string

getSourceId()  : string

getSubmissionId()  : string

getSubmitterName()  : string

isEntryEnd()  : bool

Tells whether a line closes an HGBase entry.

isEntryStart()  : bool

Tells whether a line opens a new HGBase entry.

parseDataFile()  : Sequence

Parses an HGBase data file and populates this manager's fields.

parseFrequency()  : void

Reads a FREQUENCY line, which gives a percentage then the population it was measured on.

parsePopulation()  : void

Reads a POPULATION line, which names the population then counts its individuals.

parseSubmitter()  : void

Reads a SUBMITTER line, which names the submitter then gives the submission identifier.

readData()  : string

Everything a line carries after its label.

readLabel()  : string

The label opening a line, upper cased. Labels are separated from their data by a tab or a run of spaces.