Documentation

ParseProdomManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

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.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$accession  : string

$domainCount  : int

$entryNo  : string

$freqNames  : array<string|int, mixed>

$keywords  : array<string|int, mixed>

$release  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getDomainCount()  : int

getEntryId()  : string

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

getEntryNo()  : string

getFormat()  : string

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

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

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

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

getRelease()  : string

isEntryEnd()  : bool

Tells whether a line closes a ProDom entry.

isEntryStart()  : bool

Tells whether a line opens a new ProDom entry.

parseDataFile()  : Sequence

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

parseIdentifier()  : void

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

parseKeywords()  : 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.