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FeatureSet

trait FeatureSet[T <: Feature] extends AnyRef

A data structure storing a set of Features.

Supports common operations on collections of genomic features, such as extracting overlappers of a given locus, and some common collection operations such as contains.

T

The type of Features contained in the set

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GTF22FeatureSet
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Abstract Value Members

  1. abstract def contains(t: T): 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

  2. abstract def iterator: Iterator[T]

    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

  3. abstract def nearest(chr: String, start: Int, end: Int): Iterator[T]

    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

  4. abstract def overlappers(feat: Feature): Iterator[T]

    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

  5. abstract def overlappers(chr: String, start: Int, end: Int, orientation: Orientation): Iterator[T]

    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

  6. abstract def overlappersSpan(feat: Feature): Iterator[T]

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

    Returns an iterator over Ts 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

  7. abstract def overlappersSpan(chr: String, start: Int, end: Int, orientation: Orientation): Iterator[T]

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

    Returns an iterator over Ts 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

  8. abstract val size: Long

    The number of features contained in this set.

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  13. def nearest(feat: Feature): Iterator[T]

    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

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