Package org.snpeff.interval.tree

Interface Itree

All Superinterfaces:
Iterable<Marker>
All Known Implementing Classes:
IntervalTree, IntervalTreeArray, IntervalTreeOri
public interface Itree extends Iterable<Marker>
Interval tree interface

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    add(Marker interval)
    Add an interval object to the interval tree's list
    void
    add(Markers markers)
    Add all intervals to interval tree's list
    void
    build()
    Build the interval tree to reflect the list of intervals.
    Markers
    getIntervals()
     
    boolean
    isEmpty()
     
    boolean
    isInSync()
    Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
    void
    load(String fileName, Genome genome)
    Load intervals from file
    Markers
    query(Interval interval)
    Perform an interval query, returning the intervals that intersect with 'interval'
    int
    size()
    Size: number of entries in this tree
    Markers
    stab(int point)
    Perform a stabbing query, returning the interval objects

    Methods inherited from interface java.lang.Iterable

    forEach, iterator, spliterator

  • Method Details

    • add

      void add(Marker interval)
      Add an interval object to the interval tree's list

    • add

      void add(Markers markers)
      Add all intervals to interval tree's list

    • build

      void build()
      Build the interval tree to reflect the list of intervals. Must not run if this is currently in sync

    • getIntervals

      Markers getIntervals()

    • isEmpty

      boolean isEmpty()

    • isInSync

      boolean isInSync()
      Is the tree 'in sync'? If false, the tree must be 'build()' before the next query

    • load

      void load(String fileName, Genome genome)
      Load intervals from file

    • query

      Markers query(Interval interval)
      Perform an interval query, returning the intervals that intersect with 'interval'
      Returns:
      All intervals that intersect 'interval'

    • size

      int size()
      Size: number of entries in this tree

    • stab

      Markers stab(int point)
      Perform a stabbing query, returning the interval objects
      Returns:
      All intervals intersecting 'point'