Class IntervalAndSubIntervals<T extends Marker>

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, java.lang.Iterable<T>, TxtSerializable
    Direct Known Subclasses:
    Gene, Transcript

    public class IntervalAndSubIntervals<T extends Marker>
    extends Marker
    implements java.lang.Iterable<T>
    Interval that contains sub intervals.
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • IntervalAndSubIntervals

        public IntervalAndSubIntervals()
      • IntervalAndSubIntervals

        public IntervalAndSubIntervals​(Marker parent,
                                       int start,
                                       int end,
                                       boolean strandMinus,
                                       java.lang.String id)
    • Method Detail

      • add

        public void add​(T t)
        Add a subinterval
      • addAll

        public void addAll​(java.lang.Iterable<T> ts)
        Add all intervals
      • addAll

        public void addAll​(Markers markers)
        Add all markers
      • containsId

        public boolean containsId​(java.lang.String id)
        Is 'id' in the subintervals?
      • get

        public T get​(java.lang.String id)
        Obtain a subinterval
      • invalidateSorted

        protected void invalidateSorted()
        Invalidate sorted collections
      • iterator

        public java.util.Iterator<T> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<T extends Marker>
      • markers

        public Markers markers()
        A list of all markers in this transcript
      • numChilds

        public int numChilds()
      • query

        public Markers query​(Marker marker)
        Query all genomic regions that intersect 'marker'
        Overrides:
        query in class Marker
      • remove

        public void remove​(T t)
        Remove a subinterval
      • reset

        public void reset()
        Remove all intervals
      • setStrandMinus

        public void setStrandMinus​(boolean strandMinus)
        Overrides:
        setStrandMinus in class Interval
      • sorted

        public java.util.List<T> sorted()
        Return a collection of sub intervals sorted by natural order
      • sortedStrand

        public java.util.List<T> sortedStrand()
        Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strans < 0)
      • subIntervals

        public java.util.Collection<T> subIntervals()
        Return a collection of sub intervals