Package htsjdk.samtools.util

Class IntervalTree<V>

java.lang.Object
htsjdk.samtools.util.IntervalTree<V>
All Implemented Interfaces:
Iterable<IntervalTree.Node<V>>
public class IntervalTree<V> extends Object implements Iterable<IntervalTree.Node<V>>
A Red-Black tree with intervals for keys. Not thread-safe, and cannot be made so. 7/24/2008: This was copied from the tedUtils package. IMPORTANT!!! It has been modified to use the Reseq way of handling coordinates (end-inclusive).

  • Constructor Details

    • IntervalTree

      public IntervalTree()

  • Method Details

    • size

      public int size()
      Return the number of intervals in the tree.
      Returns:
      The number of intervals.

    • clear

      public void clear()
      Remove all entries.

    • put

      public V put(int start, int end, V value)
      Put a new interval into the tree (or update the value associated with an existing interval). If the interval is novel, the special sentinel value is returned.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      value - The associated value.
      Returns:
      The old value associated with that interval, or the sentinel.

    • merge

      public V merge(int start, int end, V value, BiFunction<? super V,? super V,? extends V> remappingFunction)
      If the specified start and end positions are not already associated with a value or are associated with the sentinel ( see getSentinel(), associates it with the given (non-sentinel) value. Otherwise, replaces the associated value with the results of the given remapping function, or removes if the result is equal to the sentinel value. This method may be of use when combining multiple values that have the same start and end position.
      Parameters:
      start - interval start position
      end - interval end position
      value - value to merge into the tree, must not be equal to the sentinel value
      remappingFunction - a function that merges the new value with the existing value for the same start and end position, if the function returns the sentinel value then the mapping will be unset
      Returns:
      the updated value that is stored in the tree after the completion of this merge operation, this will be the sentinel value if nothing ended up being stored

    • remove

      public V remove(int start, int end)
      Remove an interval from the tree. If the interval does not exist in the tree the special sentinel value is returned.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The value associated with that interval, or the sentinel.

    • find

      public IntervalTree.Node<V> find(int start, int end)
      Find an interval.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The Node that represents that interval, or null.

    • findByIndex

      public IntervalTree.Node<V> findByIndex(int idx)
      Find the nth interval in the tree.
      Parameters:
      idx - The rank of the interval sought (from 0 to size()-1).
      Returns:
      The Node that represents the nth interval.

    • getIndex

      public int getIndex(int start, int end)
      Find the rank of the specified interval. If the specified interval is not in the tree, then -1 is returned.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The rank of that interval, or -1.

    • min

      public IntervalTree.Node<V> min()
      Find the least interval in the tree.
      Returns:
      The earliest interval, or null if the tree is empty.

    • min

      public IntervalTree.Node<V> min(int start, int end)
      Find the earliest interval in the tree greater than or equal to the specified interval.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The earliest >= interval, or null if there is none.

    • minOverlapper

      public IntervalTree.Node<V> minOverlapper(int start, int end)
      Find the earliest interval in the tree that overlaps the specified interval.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The earliest overlapping interval, or null if there is none.

    • max

      public IntervalTree.Node<V> max()
      Find the greatest interval in the tree.
      Returns:
      The latest interval, or null if the tree is empty.

    • max

      public IntervalTree.Node<V> max(int start, int end)
      Find the latest interval in the tree less than or equal to the specified interval.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      The latest >= interval, or null if there is none.

    • iterator

      public Iterator<IntervalTree.Node<V>> iterator()
      Return an iterator over the entire tree.
      Specified by:
      iterator in interface Iterable<V>
      Returns:
      An iterator.

    • iterator

      public Iterator<IntervalTree.Node<V>> iterator(int start, int end)
      Return an iterator over all intervals greater than or equal to the specified interval.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      An iterator.

    • overlappers

      public Iterator<IntervalTree.Node<V>> overlappers(int start, int end)
      Return an iterator over all intervals overlapping the specified range.
      Parameters:
      start - The range start.
      end - The range end.
      Returns:
      An iterator.

    • reverseIterator

      public Iterator<IntervalTree.Node<V>> reverseIterator()
      Return an iterator over the entire tree that returns intervals in reverse order.
      Returns:
      An iterator.

    • reverseIterator

      public Iterator<IntervalTree.Node<V>> reverseIterator(int start, int end)
      Return an iterator over all intervals less than or equal to the specified interval, in reverse order.
      Parameters:
      start - The interval's start.
      end - The interval's end.
      Returns:
      An iterator.

    • getSentinel

      public V getSentinel()
      Get the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval. This is null by default.
      Returns:
      The sentinel value.

    • setSentinel

      public V setSentinel(V sentinel)
      Set the special sentinel value that will be used to signal novelty when putting a new interval into the tree, or to signal "not found" when removing an interval.
      Parameters:
      sentinel - The new sentinel value.
      Returns:
      The old sentinel value.

    • checkMaxEnds

      public void checkMaxEnds()
      This method is only for debugging. It verifies whether the tree is internally consistent with respect to the mMaxEnd cached on each node.
      Throws:
      IllegalStateException - If an inconsistency is detected.

    • printTree

      public void printTree()
      This method draws a nested picture of the tree on System.out. Useful for debugging.