Documentation

ParseAaindexManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

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.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$accession  : string

$author  : string

$description  : string

$journal  : string

$litRefs  : array<string|int, mixed>

$title  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getAuthor()  : string

getDescription()  : string

getEntryId()  : string

Extracts the identifier uniquely naming an AAINDEX1 entry.

getFormat()  : string

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

getJournal()  : string

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

Cross-references, keyed by database name.

getTitle()  : string

isEntryEnd()  : bool

Tells whether a line closes an AAINDEX1 entry.

isEntryStart()  : bool

Tells whether a line opens a new AAINDEX1 entry.

parseDataFile()  : Sequence

Parses an AAINDEX1 data file and populates this manager's fields.

parseReferences()  : void

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