final case class MessengerRNA(blocks: Region, cdsStart: Int, cdsEnd: Int, name: Option[String], geneId: Option[String]) extends Transcript with Product with Serializable
A representation of a spliced messenger RNA.
A MessengerRNA has an underlying Region that specifies the chromosome, Blocks, and Orientation. In addition, a MessengerRNA has an optional name and parent gene name. Finally, it also has CDS start and end positions.
- blocks
Non-empty underlying Region
- cdsStart
Zero-based CDS start position (inclusive). The CDS start is the smallest (leftmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS start is the first position of the start codon. If Orientation is Minus, the CDS start is the 3'-most position of the stop codon. The CDS start must lie within one of the Blocks. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.
- cdsEnd
Zero-based CDS end position (exclusive). The CDS end is one plus the largest (rightmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS end is one plus the last position of the stop codon. If Orientation is Minus, the CDS end is the 5'-most position of the start codon. The CDS end must lie within one of the Blocks or be equal to one plus a Block end position. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.
- name
Optional feature name. Do not pass Some(""); use None in that case.
- geneId
Optional parent gene name. Do not pass Some(""); use None in that case.
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Instance Constructors
-
new
MessengerRNA(blocks: Region, cdsStart: Int, cdsEnd: Int, name: Option[String], geneId: Option[String])
- blocks
Non-empty underlying Region
- cdsStart
Zero-based CDS start position (inclusive). The CDS start is the smallest (leftmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS start is the first position of the start codon. If Orientation is Minus, the CDS start is the 3'-most position of the stop codon. The CDS start must lie within one of the Blocks. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.
- cdsEnd
Zero-based CDS end position (exclusive). The CDS end is one plus the largest (rightmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS end is one plus the last position of the stop codon. If Orientation is Minus, the CDS end is the 5'-most position of the start codon. The CDS end must lie within one of the Blocks or be equal to one plus a Block end position. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.
- name
Optional feature name. Do not pass Some(""); use None in that case.
- geneId
Optional parent gene name. Do not pass Some(""); use None in that case.
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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final
def
##(): Int
- Definition Classes
- AnyRef → Any
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def
<(that: Feature): Boolean
- Definition Classes
- Ordered
-
def
<=(that: Feature): Boolean
- Definition Classes
- Ordered
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
>(that: Feature): Boolean
- Definition Classes
- Ordered
-
def
>=(that: Feature): Boolean
- Definition Classes
- Ordered
-
final
def
addBlock(block: Block): Feature
Returns a GenericFeature representing this with a new Block merged in.
Returns a GenericFeature representing this with a new Block merged in.
The underlying Region of the returned Feature is the result of calling Region.addBlock on the underlying Region of this Feature. The name of the returned Feature is None.
- block
Block to add
- returns
GenericFeature whose underlying Region has the new Block merged in, with name None
- Definition Classes
- GenericFeature → Feature
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
val
blocks: Region
- Definition Classes
- MessengerRNA → Transcript → GenericFeature → Feature
-
def
canEqual(other: Any): Boolean
Returns true if other is an instance of MessengerRNA, false otherwise.
Returns true if other is an instance of MessengerRNA, false otherwise.
- Definition Classes
- MessengerRNA → Equals → Transcript → GenericFeature
- val cdsEnd: Int
- val cdsStart: Int
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
compare(that: Feature): Int
Returns the result of comparing this MessengerRNA to another Feature.
Returns the result of comparing this MessengerRNA to another Feature.
First compare the underlying Regions with Region.compare. If that result is non-zero, return it.
Next, compare the names. If both names are defined, use regular ordering on Strings. Otherwise, compare according to an ordering where name defined comes before name not defined. If the name comparison is non-zero, return it.
Next, if the other is a GenericFeature, return a positive integer.
Otherwise, compare the gene IDs. If both gene IDs are defined, use regular ordering on Strings. Otherwise, compare according to an ordering where gene ID defined comes before gene ID not defined. If the gene IDs comparison is non-zero, return it.
If the gene ID comparison was zero and other is a Transcript, return a positive integer.
If the gene ID comparison was zero and other is a MessengerRNA, compare the CDS start position, then finally the CDS end position.
- that
Other Feature to compare
- returns
Negative integer if this is less than other, zero if neither is greater, positive integer if this is greater than other
- Definition Classes
- MessengerRNA → Transcript → GenericFeature → Ordered
-
def
compareTo(that: Feature): Int
- Definition Classes
- Ordered → Comparable
-
def
contains(other: Feature): Boolean
Returns a boolean value representing whether this Feature contains another Feature.
-
def
containsCompatibleIntrons(other: Feature): Boolean
Returns a boolean value representing whether this Feature contains another Feature and their introns are compatible.
Returns a boolean value representing whether this Feature contains another Feature and their introns are compatible.
That is, no INTERNAL block boundary for one of the Features can fall strictly within a Block of the other Feature.
- other
Other Feature
- returns
True if this Feature contains the other and their introns are compatible, false otherwise
- Definition Classes
- Feature
-
def
distance(other: Feature): Int
Returns the distance between this Feature and another Feature.
Returns the distance between this Feature and another Feature.
Orientation is ignored.
If the spans of the Features (including introns) overlap, 0 is returned. Otherwise, if the other Feature lies to the right of this Feature, distance is defined as the first position of the other Feature minus the last position of this Feature. The definition is similar for the opposite direction. Therefore, the returned distance is a nonnegative number.
If the Features are on different chromosomes, an IllegalArgumentException is thrown.
- Definition Classes
- Feature
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(other: Any): Boolean
Returns an equality comparison of this with another object.
Returns an equality comparison of this with another object.
Returns true if other is a MessengerRNA that can equal this according to MessengerRNA.canEqual, the underlying Regions are equal, the names are equal, the gene IDs are equal, the CDS starts are equal, and the CDS ends are equal. Returns false otherwise.
- other
Other object
- returns
True if this equals other, false otherwise
- Definition Classes
- MessengerRNA → Equals → Transcript → GenericFeature → AnyRef → Any
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
val
geneId: Option[String]
- Definition Classes
- MessengerRNA → Transcript
-
def
get3UTR: Option[Region]
Returns a Region representing the 3'-UTR of this MessengerRNA.
Returns a Region representing the 3'-UTR of this MessengerRNA.
If the Orientation is Plus, the 3'-UTR has start position cdsEnd and end position equal to getEnd. In other words, the 3'-UTR is equal to the value of calling Region.trim(cdsEnd, getEnd) on the underlying Region of this MessengerRNA.
If the Orientation is Minus, the 3'-UTR has start position getStart and end position equal to cdsStart. In other words, the 3'-UTR is equal to the value of calling Region.trim(getStart, cdsStart) on the underlying Region of this MessengerRNA.
If the stop codon is at one end of the MessengerRNA, returns None.
- returns
A Region representing the 3'-UTR, or None if the stop codon is at one end of the MessengerRNA.
-
def
get5UTR: Option[Region]
Returns a Region representing the 5'-UTR of this MessengerRNA.
Returns a Region representing the 5'-UTR of this MessengerRNA.
If the Orientation is Plus, the 5'-UTR has start position getStart and end position cdsStart. In other words, the 5'-UTR is equal to the value of calling Region.trim(getStart, cdsStart) on the underlying Region of this MessengerRNA.
If the Orientation is Minus, the 5'-UTR has start position cdsEnd and end position getEnd. In other words, the 5'-UTR is equal to the value of calling Region.trim(cdsEnd, getEnd) on the underlying Region of this MessengerRNA.
If the start codon is at one end of the MessengerRNA, returns None.
- returns
A Region representing the 5'-UTR, or None if the start codon is at one end of the MessengerRNA.
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def
getBlocks: List[Block]
Returns the list of Blocks of the underlying Region as in Region.blocks.
Returns the list of Blocks of the underlying Region as in Region.blocks.
- Definition Classes
- Feature
-
lazy val
getCDS: Region
A Region representing the coding region of this MessengerRNA.
A Region representing the coding region of this MessengerRNA.
The CDS includes the start and stop codons. It is equal to the value of calling Region.trim(cdsStart, cdsEnd) on the underlying Region of this MessengerRNA.
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def
getChr: String
Returns the chromosome name.
Returns the chromosome name.
- Definition Classes
- Feature
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
getEnd: Int
Returns the end position of the underlying Region as in Region.end.
Returns the end position of the underlying Region as in Region.end.
- Definition Classes
- Feature
-
def
getOrientation: Orientation
Returns the orientation of the underlying Region as in Region.orientation.
Returns the orientation of the underlying Region as in Region.orientation.
- Definition Classes
- Feature
-
def
getStart: Int
Returns the start position of the underlying Region as in Region.start.
Returns the start position of the underlying Region as in Region.start.
- Definition Classes
- Feature
-
def
getStartCodon: Region
Returns a Region representing the start codon of this MessengerRNA.
Returns a Region representing the start codon of this MessengerRNA.
If the Orientation is Plus, the start codon has start position cdsStart and size 3. If the orientation is Minus, the start codon has end position cdsEnd and size 3.
The start codon may include multiple Blocks if the CDS boundary lies near a Block boundary.
- returns
A Region of size 3, possibly spliced, representing the start codon of this MessengerRNA.
-
def
getStopCodon: Region
Returns a Region representing the stop codon of this MessengerRNA.
Returns a Region representing the stop codon of this MessengerRNA.
If the Orientation is Plus, the stop codon has end position cdsEnd and size 3. If the Orientation is Minus, the stop codon has start position cdsStart and size 3.
The stop codon may include multiple Blocks if the CDS boundary lies near a Block boundary.
- returns
A Region of size 3, possibly spliced, representing the stop codon of this MessengerRNA.
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lazy val
hashCode: Int
A hashCode based on the underlying Region, name, geneId, cdsStart, and cdsEnd.
- Definition Classes
- MessengerRNA → Transcript → GenericFeature → AnyRef → Any
-
def
hc: Int
- Attributes
- protected
- Definition Classes
- GenericFeature
-
final
def
intersection(other: Feature): Option[Feature]
Returns a GenericFeature representing the intersection of this with another Feature.
Returns a GenericFeature representing the intersection of this with another Feature.
If the underlying Regions do not overlap according to Region.overlaps, returns None.
Otherwise, the returned feature has underlying Region equal to the intersection of the two underlying Regions as computed by Region.intersection. The returned feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the intersection of the underlying Regions with name None, or None if the underlying Regions do not overlap
- Definition Classes
- GenericFeature → Feature
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
final
def
minus(other: Feature): Option[Feature]
Returns a GenericFeature representing this minus the overlap with another Feature.
Returns a GenericFeature representing this minus the overlap with another Feature.
If the underlying Region of this Feature is contained in the underlying Region of the other, returns None.
Otherwise, the returned Feature has underlying Region equal to the result of Region.minus on the two underlying Regions. The returned Feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the subtraction of the underlying Regions with name None, or None if that subtraction is empty
- Definition Classes
- GenericFeature → Feature
-
val
name: Option[String]
- Definition Classes
- MessengerRNA → GenericFeature → Feature
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
-
def
numBlocks: Int
Returns the number of Blocks in the underlying region.
-
def
overlaps(other: Feature): Boolean
Returns a boolean value representing whether this Feature overlaps another Feature.
-
def
overlapsCompatibleIntrons(other: Feature): Boolean
Returns a boolean value representing whether this Feature overlaps another Feature and their introns are compatible.
Returns a boolean value representing whether this Feature overlaps another Feature and their introns are compatible.
That is, no INTERNAL block boundary for one of the Features can fall strictly within a Block of the other Feature.
- other
Other Feature
- returns
True if the Features overlap and their introns are compatible, false otherwise
- Definition Classes
- Feature
-
def
overlapsSpan(other: Feature): Boolean
Returns a boolean value representing whether the span of this Feature overlaps the span of another Feature.
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
Returns a string representation of this MessengerRNA.
Returns a string representation of this MessengerRNA.
- Definition Classes
- MessengerRNA → Transcript → GenericFeature → AnyRef → Any
-
def
unapply(t: Transcript): Option[(Region, Option[String], Option[String])]
- Definition Classes
- Transcript
-
final
def
union(other: Feature): Feature
Returns a GenericFeature representing the union of this with another Feature.
Returns a GenericFeature representing the union of this with another Feature.
The returned feature has underlying Region equal to the union of the two underlying Regions as computed by Region.union. The returned feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the union of the underlying Regions, with name None
- Definition Classes
- GenericFeature → Feature
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )