OpenReadingFrame
in package
frame follows the standard six-frame convention : +1/+2/+3 for the forward strand (the reading frame's zero-based offset plus one), -1/-2/-3 for the reverse strand (the same, on the reverse complement). start/end are always given as ascending 1-based inclusive positions in the ORIGINAL, forward-strand sequence - even for a reverse-strand ORF, the same convention GenBank's own complement(start..end) location uses, so a negative frame's coordinates stay directly comparable to a positive one's. end includes the stop codon's three bases when hasStopCodon() is true ; getPeptide() itself never includes the "*" stop symbol.
Class OpenReadingFrame
Tags
Table of Contents
Properties
- $end : int
- $frame : int
- $hasStopCodon : bool
- $peptide : string
- $start : int
Methods
- __construct() : mixed
- OpenReadingFrame constructor.
- getEnd() : int
- getFrame() : int
- getLength() : int
- getPeptide() : string
- getStart() : int
- hasStopCodon() : bool
- isReverseStrand() : bool
Properties
$end
private
int
$end
1-based inclusive, ascending, in the original forward-strand sequence
$frame
private
int
$frame
$hasStopCodon
private
bool
$hasStopCodon
$peptide
private
string
$peptide
$start
private
int
$start
1-based inclusive, ascending, in the original forward-strand sequence
Methods
__construct()
OpenReadingFrame constructor.
public
__construct(int $iFrame, int $iStart, int $iEnd, string $sPeptide, bool $bHasStopCodon) : mixed
Parameters
- $iFrame : int
-
One of -3, -2, -1, 1, 2, 3
- $iStart : int
- $iEnd : int
- $sPeptide : string
- $bHasStopCodon : bool
-
False for an ORF still open at the end of the sequence
getEnd()
public
getEnd() : int
Return values
intgetFrame()
public
getFrame() : int
Return values
intgetLength()
public
getLength() : int
Return values
intgetPeptide()
public
getPeptide() : string
Return values
stringgetStart()
public
getStart() : int
Return values
inthasStopCodon()
public
hasStopCodon() : bool
Return values
boolisReverseStrand()
public
isReverseStrand() : bool