Documentation

ParsePrintsManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParsePrintsManager A PRINTS entry describes a protein fingerprint, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its data fields are lower case three-character tags ending with a semicolon (gc;, gn;, ga;, gd;), unlike every other format the library reads.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$createDate  : string

$description  : string

$entryName  : string

$entryType  : string

$updDate  : string

Methods

__construct()  : mixed

Constructor.

getCreateDate()  : string

getDescription()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a PRINTS entry.

getEntryName()  : string

getEntryType()  : string

getFormat()  : string

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

getUpdDate()  : string

isEntryEnd()  : bool

PRINTS entries carry no end-of-entry marker, so a stream holding several of them cannot be split : reading stops at the end of the file. This mirrors the original BioPHP parser, which had the same limitation.

isEntryStart()  : bool

Tells whether a line opens a new PRINTS entry. The gc; field carries the entry name and comes first.

parseDataFile()  : Sequence

Parses a PRINTS data file and populates this manager's fields.

parseDates()  : void

Reads the ga; line, which carries the creation date then any number of "KEY value" pairs.