Packages

c

feature

Feature

sealed abstract class Feature extends Ordered[Feature]

A genomic feature.

Includes a non-empty underlying Region and an optional feature name.

Linear Supertypes
Ordered[Feature], Comparable[Feature], AnyRef, Any
Known Subclasses
GenericFeature, MessengerRNA, Transcript, SamMapping
Ordering
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Inherited
  1. Feature
  2. Ordered
  3. Comparable
  4. AnyRef
  5. Any
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def addBlock(block: Block): Feature

    Returns a Feature representing this with an additional Block merged in.

    Returns a Feature representing this with an additional Block merged in.

    See subclass documentation for class-specific details.

    block

    Block to add

    returns

    New Feature with the new Block merged in

  2. abstract def compare(that: Feature): Int
    Definition Classes
    Ordered
  3. abstract def intersection(other: Feature): Option[Feature]

    Returns a Feature representing the intersection of this with another Feature.

    Returns a Feature representing the intersection of this with another Feature.

    See subclass documentation for class-specific details.

    other

    Other Feature

    returns

    Feature representing the intersection of the two Features, or None if they do not overlap

  4. abstract def minus(other: Feature): Option[Feature]

    Returns a Feature representing this minus the overlap with another Feature.

    Returns a Feature representing this minus the overlap with another Feature.

    See subclass documentation for class-specific details.

    other

    Other Feature

    returns

    Feature representing this minus the other, or None if the remaining region is empty

  5. abstract def union(other: Feature): Feature

    Returns a Feature representing the union of this with another Feature.

    Returns a Feature representing the union of this with another Feature.

    See subclass documentation for class-specific details.

    other

    Other Feature

    returns

    Feature representing the union of the two Features

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def <(that: Feature): Boolean
    Definition Classes
    Ordered
  4. def <=(that: Feature): Boolean
    Definition Classes
    Ordered
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. def >(that: Feature): Boolean
    Definition Classes
    Ordered
  7. def >=(that: Feature): Boolean
    Definition Classes
    Ordered
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. val blocks: Region
  10. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  11. def compareTo(that: Feature): Int
    Definition Classes
    Ordered → Comparable
  12. def contains(other: Feature): Boolean

    Returns a boolean value representing whether this Feature contains another Feature.

    Returns a boolean value representing whether this Feature contains another Feature.

    Ignores feature name and calls Region.contains on the two underlying Regions.

    other

    Other Feature

    returns

    True if this Feature contains the other, false otherwise

  13. 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

  14. 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.

    other

    Other Feature

    returns

    The distance in base pairs between this Feature and the other Feature

  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. def getBlocks: List[Block]

    Returns the list of Blocks of the underlying Region as in Region.blocks.

  19. def getChr: String

    Returns the chromosome name.

  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  21. def getEnd: Int

    Returns the end position of the underlying Region as in Region.end.

  22. def getOrientation: Orientation

    Returns the orientation of the underlying Region as in Region.orientation.

  23. def getStart: Int

    Returns the start position of the underlying Region as in Region.start.

  24. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  25. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  26. val name: Option[String]
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  30. def numBlocks: Int

    Returns the number of Blocks in the underlying region.

  31. def overlaps(other: Feature): Boolean

    Returns a boolean value representing whether this Feature overlaps another Feature.

    Returns a boolean value representing whether this Feature overlaps another Feature.

    Ignores feature name and calls Region.overlaps on the two underlying Regions.

    other

    Other Feature

    returns

    True if the Features overlap, false otherwise

  32. 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

  33. def overlapsSpan(other: Feature): Boolean

    Returns a boolean value representing whether the span of this Feature overlaps the span of another Feature.

    Returns a boolean value representing whether the span of this Feature overlaps the span of another Feature.

    Ignores feature name and calls Region.overlapsSpan on the two underlying Regions.

    other

    Other Feature

    returns

    True if the spans of the Features overlap, false otherwise

  34. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  35. def toString(): String
    Definition Classes
    AnyRef → Any
  36. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Ordered[Feature]

Inherited from Comparable[Feature]

Inherited from AnyRef

Inherited from Any

Ungrouped