PlasmidFeature
in package
Coordinates are 1-based inclusive, the convention used by GenBank and EMBL feature tables. Start and end are only validated to be at least 1 here : since a lone feature does not know the length of the plasmid it will belong to, the upper bound is checked by Plasmid when the feature is attached. A start strictly greater than end is valid and means the feature crosses the origin.
The optional phase is GFF3's column 8 (0, 1 or 2 : how many bases to skip from the feature's 5' end, in its own orientation, to reach the first complete codon), equivalent to GenBank's /codon_start minus 1. It is only meaningful on a CDS, the only type that accepts one. Class PlasmidFeature
Tags
Table of Contents
Properties
- $color : string|null
- $end : int
- $externalId : string|null
- $metadata : array<string|int, mixed>
- $name : string
- $note : string|null
- $phase : int|null
- $start : int
- $strand : string
- $type : string
Methods
- __construct() : mixed
- PlasmidFeature constructor.
- crossesOrigin() : bool
- getColor() : string|null
- getEnd() : int
- getExternalId() : string|null
- getLength() : int
- Number of symbols covered by the feature. Requires the length of the plasmid the feature belongs to, since an origin-crossing feature wraps past the last symbol back to the first.
- getMetadata() : array<string|int, mixed>
- getName() : string
- getNote() : string|null
- getPhase() : int|null
- getStart() : int
- getStrand() : string
- getType() : string
- assertSerializableMetadata() : void
- Rejects metadata holding anything but scalars, null, or arrays of the same, recursively.
Properties
$color
private
string|null
$color
= null
Strict "#RRGGBB" hexadecimal notation
$end
private
int
$end
1-based inclusive
$externalId
private
string|null
$externalId
= null
$metadata
private
array<string|int, mixed>
$metadata
Only scalars, null and arrays of the same, recursively
$name
private
string
$name
$note
private
string|null
$note
= null
$phase
private
int|null
$phase
= null
0, 1 or 2 ; CDS only
$start
private
int
$start
1-based inclusive
$strand
private
string
$strand
One of Strand::VALID_STRANDS
$type
private
string
$type
One of FeatureType::VALID_TYPES
Methods
__construct()
PlasmidFeature constructor.
public
__construct(string $sName, string $sType, int $iStart, int $iEnd[, string $sStrand = Strand::NONE ][, string|null $sColor = null ][, string|null $sNote = null ][, string|null $sExternalId = null ][, array<string|int, mixed>|null $aMetadata = null ][, int|null $iPhase = null ]) : mixed
Parameters
- $sName : string
-
Must not be empty
- $sType : string
-
One of FeatureType::VALID_TYPES
- $iStart : int
-
1-based inclusive, at least 1
- $iEnd : int
-
1-based inclusive, at least 1
- $sStrand : string = Strand::NONE
-
One of Strand::VALID_STRANDS, defaults to Strand::NONE
- $sColor : string|null = null
-
Strict "#RRGGBB" notation, or null
- $sNote : string|null = null
- $sExternalId : string|null = null
- $aMetadata : array<string|int, mixed>|null = null
-
Only scalars, null and arrays thereof ; a source format's original type or attributes that don't map onto a dedicated property (e.g. a GenBank feature key) belong here rather than being folded into $sNote
- $iPhase : int|null = null
-
0, 1 or 2, only on a CDS ; null when unknown
crossesOrigin()
public
crossesOrigin() : bool
Return values
bool —True when start is strictly after end, meaning the feature crosses the origin of the circular molecule it belongs to.
getColor()
public
getColor() : string|null
Return values
string|nullgetEnd()
public
getEnd() : int
Return values
int —1-based inclusive
getExternalId()
public
getExternalId() : string|null
Return values
string|nullgetLength()
Number of symbols covered by the feature. Requires the length of the plasmid the feature belongs to, since an origin-crossing feature wraps past the last symbol back to the first.
public
getLength(int $iPlasmidLength) : int
Parameters
- $iPlasmidLength : int
-
Length of the plasmid sequence this feature is on
Return values
intgetMetadata()
public
getMetadata() : array<string|int, mixed>
Return values
array<string|int, mixed>getName()
public
getName() : string
Return values
stringgetNote()
public
getNote() : string|null
Return values
string|nullgetPhase()
public
getPhase() : int|null
Return values
int|null —0, 1 or 2 ; null when unknown or not a CDS
getStart()
public
getStart() : int
Return values
int —1-based inclusive
getStrand()
public
getStrand() : string
Return values
stringgetType()
public
getType() : string
Return values
stringassertSerializableMetadata()
Rejects metadata holding anything but scalars, null, or arrays of the same, recursively.
private
assertSerializableMetadata(string $sName, array<string|int, mixed> $aMetadata) : void
Parameters
- $sName : string
-
The feature's name, for the exception message
- $aMetadata : array<string|int, mixed>