Documentation

ParseAaindexManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

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 field lists the entries the index correlates with, and the I field the index values themselves, one per amino acid : the original BioPHP parser left both aside, so the data of the entry was never available.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$accession  : string

$author  : string

$correlations  : array<string, float>

The entries this index correlates with (C field), accession => correlation coefficient

$description  : string

$index  : array<string, float|null>

The index value of each amino acid (I field), one-letter code => value, null for "NA"

$journal  : string

$litRefs  : array<string|int, mixed>

$title  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : string

getAuthor()  : string

getCorrelations()  : array<string, float>

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.

getIndex()  : array<string, float|null>

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.

parseCorrelations()  : array<string, float>

Reads the C field : pairs of an entry's accession and its correlation coefficient.

parseIndex()  : array<string, float|null>

Reads the I field : a header of ten pairs naming the amino acids ("A/L R/K ..."), then a row of values for the first residue of each pair and a row for the second one. A value missing from the original study is written "NA".

parseReferences()  : void

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