Packages

c

collection

GTF22FeatureSet

final class GTF22FeatureSet extends FeatureSet[Feature]

A FeatureSet constructed from annotations specified in a GTF2.2 file.

GTF2.2 feature.format specification. See GTF22Record for details on how GTF2.2 records are interpreted and incorporated into Features.

Linear Supertypes
FeatureSet[Feature], AnyRef, Any
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  1. GTF22FeatureSet
  2. FeatureSet
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Instance Constructors

  1. new GTF22FeatureSet(file: File)

    file

    GTF2.2 file

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. def contains(t: Feature): Boolean

    Returns a boolean value representing whether this set contains the given Feature.

    Returns a boolean value representing whether this set contains the given Feature.

    t

    Feature to look for

    Definition Classes
    GTF22FeatureSet → FeatureSet
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  11. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. def iterator: Iterator[Feature]

    Returns an iterator over the entire set.

    Returns an iterator over the entire set.

    The returned iterator is not guaranteed to conform to any particular ordering.

    returns

    Iterator over the set in no particular order

    Definition Classes
    GTF22FeatureSet → FeatureSet
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def nearest(chr: String, start: Int, end: Int): Iterator[Feature]

    Returns an iterator over the nearest Features to a genomic interval.

    Returns an iterator over the nearest Features to a genomic interval.

    If this set contains one or more Features whose span (including introns) overlaps the given interval, an iterator over those overlappers is returned.

    Otherwise, all Features tied for the minimum distance are returned. Distance is defined as in Feature.distance.

    Orientation is ignored.

    The returned iterator is not guaranteed to conform to any particular ordering.

    chr

    Chromosome name of query interval

    start

    Zero-based inclusive start position of query interval

    end

    Zero-based exclusive end position of query interval

    returns

    Iterator over nearest Features in no particular order, or Iterator.empty if there are no Features on the chromosome

    Definition Classes
    GTF22FeatureSet → FeatureSet
  16. def nearest(feat: Feature): Iterator[Feature]

    Returns an iterator over the nearest Features to a given Feature.

    Returns an iterator over the nearest Features to a given Feature.

    If this set contains one or more Features whose span (including introns) overlaps the span (including introns) of the given Feature, an iterator over those overlappers is returned.

    Otherwise, all Features tied for the minimum distance are returned. Distance is defined as in Feature.distance.

    Orientation is ignored.

    The returned iterator is not guaranteed to conform to any particular ordering.

    feat

    Query Feature

    returns

    Iterator over nearest Features in no particular order, or Iterator.empty if there are no Features on the chromosome

    Definition Classes
    FeatureSet
  17. final def notify(): Unit
    Definition Classes
    AnyRef
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  19. def overlappers(feat: Feature): Iterator[Feature]

    Returns an iterator over overlappers of a given Feature.

    Returns an iterator over overlappers of a given Feature.

    Overlappers are the Features contained in this set that overlap the given Feature as defined by Feature.overlaps.

    The returned iterator is not guaranteed to conform to any particular ordering.

    feat

    Query Feature

    returns

    Iterator over overlappers of the given Feature in no particular order, or Iterator.empty if there are no overlappers

    Definition Classes
    GTF22FeatureSet → FeatureSet
  20. def overlappers(chr: String, start: Int, end: Int, orientation: Orientation): Iterator[Feature]

    Returns an iterator over overlappers of a genomic interval.

    Returns an iterator over overlappers of a genomic interval.

    Overlappers are the Features contained in this set that overlap the interval accounting for Orientation, as defined by Feature.overlaps.

    The returned iterator is not guaranteed to conform to any particular ordering.

    chr

    Chromosome name of query interval

    start

    Zero-based inclusive start position of query interval

    end

    Zero-based exclusive end position of query interval

    orientation

    Orientation of query interval. Only overlappers with a compatible Orientation (as defined by Orientation.isCompatible) will be returned.

    returns

    Iterator over overlappers in no particular order, or Iterator.empty if there are no overlappers

    Definition Classes
    GTF22FeatureSet → FeatureSet
  21. def overlappersSpan(feat: Feature): Iterator[Feature]

    Returns an iterator over Features whose span overlaps that of a given Feature.

    Returns an iterator over Features whose span overlaps that of a given Feature.

    Overlappers are the Features contained in this set whose span overlaps that of the given Feature as defined by Feature.overlapsSpan.

    The returned iterator is not guaranteed to conform to any particular ordering.

    feat

    Query Feature

    returns

    Iterator over span overlappers of the given Feature in no particular order, or Iterator.empty if there are none

    Definition Classes
    GTF22FeatureSet → FeatureSet
  22. def overlappersSpan(chr: String, start: Int, end: Int, orientation: Orientation): Iterator[Feature]

    Returns an iterator over Features whose span overlaps a genomic interval.

    Returns an iterator over Features whose span overlaps a genomic interval.

    Overlappers are the Features contained in this set whose span overlaps the interval accounting for Orientation, as defined by Feature.overlapsSpan.

    The returned iterator is not guaranteed to conform to any particular ordering.

    chr

    Chromosome name of query interval

    start

    Zero-based inclusive start position of query interval

    end

    Zero-based exclusive end position of query interval

    orientation

    Orientation of query interval. Only overlappers with a compatible Orientation (as defined by Orientation.isCompatible) will be returned.

    returns

    Iterator over span overlappers in no particular order, or Iterator.empty if there are none

    Definition Classes
    GTF22FeatureSet → FeatureSet
  23. lazy val size: Long

    The number of features contained in this set.

    The number of features contained in this set.

    Definition Classes
    GTF22FeatureSet → FeatureSet
  24. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  25. def toString(): String
    Definition Classes
    AnyRef → Any
  26. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from FeatureSet[Feature]

Inherited from AnyRef

Inherited from Any

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