object Empty extends Region with Product with Serializable
An empty region. Empty has no chromosome, Blocks, or Orientation.
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
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def
<(that: Region): Boolean
- Definition Classes
- Ordered
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def
<=(that: Region): Boolean
- Definition Classes
- Ordered
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final
def
==(arg0: Any): Boolean
- Definition Classes
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-
def
>(that: Region): Boolean
- Definition Classes
- Ordered
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def
>=(that: Region): Boolean
- Definition Classes
- Ordered
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def
addBlock(block: Block): Region
Returns the Block.
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final
def
asInstanceOf[T0]: T0
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def
blocks: List[Block]
Returns Nil.
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def
chr: String
Throws an IllegalStateException.
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def
chrPos(relativePos: Int): Int
Throws an IllegalStateException.
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
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- @throws( ... )
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def
compare(that: Region): Int
Returns zero if other Region is Empty; a positive integer otherwise.
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def
compareTo(that: Region): Int
- Definition Classes
- Ordered → Comparable
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def
contains(feat: Region): Boolean
Returns false.
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def
containsCompatibleIntrons(o: Region): Boolean
Returns a boolean value representing whether this Region contains another Region and their introns are compatible.
Returns a boolean value representing whether this Region contains another Region and their introns are compatible.
That is, no INTERNAL block boundary for one of the Regions can fall strictly within a Block of the other Region.
- o
Other Region
- returns
True if this Region contains the other and their introns are compatible, false otherwise
- Definition Classes
- Region
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def
end: Int
Throws an IllegalStateException.
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
- Definition Classes
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def
finalize(): Unit
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final
def
getClass(): Class[_]
- Definition Classes
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def
getIntrons: List[Block]
Returns a list of Blocks representing the introns of this Region.
Returns a list of Blocks representing the introns of this Region.
The returned list is in order from left to right. Each Block in the returned list is the span of a gap between two Blocks of this Region. The returned Blocks have the same Orientation as this Region. The start position of each returned Block is equal to the end position (exclusive) of the previous adjacent Block in this Region. The end position of each returned Block (exclusive) is equal to the start position of the following adjacent Block in this Region.
If this Region is empty or has only one Block, Nil is returned.
- returns
A list of Blocks representing the gaps between the Blocks of this Region, or Nil if this Region has less than two Blocks.
- Definition Classes
- Region
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def
intersection(feat: Region): Region
Returns Empty.
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def
isEmpty: Boolean
Returns true.
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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def
minus(feat: Region): Region
Returns Empty.
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
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val
numBlocks: Int
Returns zero.
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def
orientation: Orientation
Throws an IllegalStateException.
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def
overlaps(feat: Region): Boolean
Returns false.
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def
overlapsCompatibleIntrons(o: Region): Boolean
Returns false.
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def
overlapsSpan(o: Region): Boolean
Returns a boolean value representing whether the span of this Region overlaps the span of another Region.
Returns a boolean value representing whether the span of this Region overlaps the span of another Region. That is, intron/exon structure is ignored and only the full span (from start to end) of the Regions are considered. Orientations must be compatible.
- Definition Classes
- Region
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def
relativePos(chrPos: Int): Option[Int]
Returns None.
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def
size: Int
Returns the sum of the lengths of the Blocks of this Region.
Returns the sum of the lengths of the Blocks of this Region.
Block length is the end position minus the start position, where, as always, start position is inclusive and end position is exclusive. Therefore, size is the number of individual genomic positions included in the Region.
The size of Empty is zero.
- Definition Classes
- Region
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def
start: Int
Throws an IllegalStateException.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
Returns "Empty".
Returns "Empty".
- Definition Classes
- Empty → AnyRef → Any
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def
trim(newStart: Int, newEnd: Int): Region
Returns Empty.
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def
union(feat: Region): Region
Returns the other Region.
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... )