PlasmidFeatureRecord
in package
The storage shape of a PlasmidFeature. Coordinates keep the value object's convention : 1-based inclusive, with start greater than end meaning the feature crosses the origin. $position records the feature's rank within its plasmid, because Plasmid preserves the order it was built with.
Class PlasmidFeatureRecord
Tags
Attributes
- #[Entity]
- #[Table]
- $name: "plasmid_feature"
Table of Contents
Properties
- $color : string|null
- $endPosition : int
- $externalId : string|null
- $id : int|null
- $metadata : array<string|int, mixed>
- $name : string
- $note : string|null
- $phase : int|null
- $plasmid : PlasmidRecord|null
- $position : int
- $startPosition : int
- $strand : string
- $type : string
Methods
- getColor() : string|null
- getEndPosition() : int
- getExternalId() : string|null
- getId() : int|null
- getMetadata() : array<string|int, mixed>
- getName() : string
- getNote() : string|null
- getPhase() : int|null
- getPlasmid() : PlasmidRecord|null
- getPosition() : int
- getStartPosition() : int
- getStrand() : string
- getType() : string
- setColor() : $this
- setEndPosition() : $this
- setExternalId() : $this
- setMetadata() : $this
- setName() : $this
- setNote() : $this
- setPhase() : $this
- setPlasmid() : $this
- setPosition() : $this
- setStartPosition() : $this
- setStrand() : $this
- setType() : $this
Properties
$color
private
string|null
$color
= null
Strict "#RRGGBB" hexadecimal notation
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::STRING
- $length: 7
- $nullable: true
$endPosition
private
int
$endPosition
= 1
1-based inclusive
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::INTEGER
$externalId
private
string|null
$externalId
= null
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::STRING
- $length: 255
- $nullable: true
$id
private
int|null
$id
= null
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::INTEGER
- #[GeneratedValue]
- #[Id]
$metadata
private
array<string|int, mixed>
$metadata
= []
Only scalars, null and arrays of the same, recursively
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::JSON
$name
private
string
$name
= ""
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::STRING
- $length: 255
$note
private
string|null
$note
= null
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::TEXT
- $nullable: true
$phase
private
int|null
$phase
= null
GFF3 phase (0, 1 or 2), CDS only ; GenBank /codon_start minus 1
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::SMALLINT
- $nullable: true
$plasmid
private
PlasmidRecord|null
$plasmid
= null
Attributes
- #[JoinColumn]
- $name: "plasmid_id"
- $referencedColumnName: "id"
- $nullable: false
- $onDelete: "CASCADE"
- #[ManyToOne]
- $targetEntity: \Amelaye\BioPHP\Domain\Cloning\Entity\PlasmidRecord::class
- $inversedBy: "features"
$position
private
int
$position
= 0
Zero-based rank of the feature within the plasmid's feature list
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::INTEGER
$startPosition
private
int
$startPosition
= 1
1-based inclusive
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::INTEGER
$strand
private
string
$strand
= ""
One of Strand::VALID_STRANDS
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::STRING
- $length: 8
$type
private
string
$type
= ""
One of FeatureType::VALID_TYPES
Attributes
- #[Column]
- $type: \Doctrine\DBAL\Types\Types::STRING
- $length: 32
Methods
getColor()
public
getColor() : string|null
Return values
string|nullgetEndPosition()
public
getEndPosition() : int
Return values
intgetExternalId()
public
getExternalId() : string|null
Return values
string|nullgetId()
public
getId() : int|null
Return values
int|null —Null until the record has been flushed
getMetadata()
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|nullgetPlasmid()
public
getPlasmid() : PlasmidRecord|null
Return values
PlasmidRecord|nullgetPosition()
public
getPosition() : int
Return values
intgetStartPosition()
public
getStartPosition() : int
Return values
intgetStrand()
public
getStrand() : string
Return values
stringgetType()
public
getType() : string
Return values
stringsetColor()
public
setColor(string|null $sColor) : $this
Parameters
- $sColor : string|null
Return values
$thissetEndPosition()
public
setEndPosition(int $iEndPosition) : $this
Parameters
- $iEndPosition : int
Return values
$thissetExternalId()
public
setExternalId(string|null $sExternalId) : $this
Parameters
- $sExternalId : string|null
Return values
$thissetMetadata()
public
setMetadata(array<string|int, mixed> $aMetadata) : $this
Parameters
- $aMetadata : array<string|int, mixed>
Return values
$thissetName()
public
setName(string $sName) : $this
Parameters
- $sName : string
Return values
$thissetNote()
public
setNote(string|null $sNote) : $this
Parameters
- $sNote : string|null
Return values
$thissetPhase()
public
setPhase(int|null $iPhase) : $this
Parameters
- $iPhase : int|null
Return values
$thissetPlasmid()
public
setPlasmid(PlasmidRecord|null $oPlasmid) : $this
Parameters
- $oPlasmid : PlasmidRecord|null
Return values
$thissetPosition()
public
setPosition(int $iPosition) : $this
Parameters
- $iPosition : int
Return values
$thissetStartPosition()
public
setStartPosition(int $iStartPosition) : $this
Parameters
- $iStartPosition : int
Return values
$thissetStrand()
public
setStrand(string $sStrand) : $this
Parameters
- $sStrand : string
Return values
$thissetType()
public
setType(string $sType) : $this
Parameters
- $sType : string