Documentation

Feature

in package

• Amelaye
• BioPHP
• Domain
• Sequence
• Entity

Class GbFeatures

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$ftDesc  : string

$ftFrom  : int

$ftKey  : string

$ftLocation  : string|null

The location exactly as the record wrote it (INSDC syntax, e.g. "join(94..300,401..1482)").

$ftQual  : string

$ftTo  : int

$ftValue  : string

$id  : int|null

$primAcc  : string

The primary accession of the sequence this row belongs to : a plain column, so that a parsed record can be stored as the parser builds it, with its accession as a string.

$strand  : string|null

The strand the feature was read from : "+" (direct/sense) or "-" (the location was wrapped in "complement(...)"). Null when the format has no strand concept (e.g. Swiss-Prot, whose features are positions on a protein sequence), when the feature lies on both strands (a trans-spliced join(complement(a..b),c..d)) or when none was recorded.

Methods

getFtDesc()  : string

getFtFrom()  : int|null

getFtKey()  : string

getFtLocation()  : string|null

getFtQual()  : string

getFtTo()  : int|null

getFtValue()  : string

getId()  : int|null

getPrimAcc()  : string

getStrand()  : string|null

isPartial()  : bool

Tells whether the feature extends beyond the bases its location gives ("<1..206", the start lies before base 1 ; "1..>888", the end lies after base 888), as the location was written.

setFtDesc()  : void

setFtFrom()  : void

setFtKey()  : void

setFtLocation()  : void

setFtQual()  : void

setFtTo()  : void

setFtValue()  : void

setPrimAcc()  : void

setStrand()  : void