Documentation

ParseEpdManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParseEpdManager An EPD entry describes a promoter. It borrows the two character tag layout of EMBL, but its fields carry different things, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The three dated events the format defines are all read here, where the original BioPHP parser had commented two of them out.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$accessions  : array<string|int, mixed>

$comments  : string

$createDate  : string

$createRel  : string

$dataClass  : string

$description  : string

$entryName  : string

$insiteType  : string

$notupdDate  : string

$notupdRel  : string

$sequpdDate  : string

$sequpdRel  : string

$taxDiv  : string

Methods

__construct()  : mixed

Constructor.

getAccessions()  : array<string|int, mixed>

getComments()  : string

getCreateDate()  : string

getCreateRel()  : string

getDataClass()  : string

getDescription()  : string

getEntryId()  : string

Extracts the identifier uniquely naming an EPD entry, read from its AC line.

getEntryName()  : string

getFormat()  : string

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

getInsiteType()  : string

getNotupdDate()  : string

getNotupdRel()  : string

getSequpdDate()  : string

getSequpdRel()  : string

getTaxDiv()  : string

isEntryEnd()  : bool

Tells whether a line closes an EPD entry.

isEntryStart()  : bool

Tells whether a line opens a new EPD entry.

parseDataFile()  : Sequence

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

parseDate()  : void

Reads a DT line, which dates one event and names the release it happened in.

parseIdentifier()  : void

Reads the ID line, which names the entry then qualifies it.