IntervalTree (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.util.IntervalTree<V>

All Implemented Interfaces:

java.lang.Iterable<IntervalTree.Node<V>>
```
public class IntervalTree<V>
extends java.lang.Object
implements java.lang.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).

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`class`	`IntervalTree.FwdIterator`
`static class`	`IntervalTree.Node<V1>`
`class`	`IntervalTree.OverlapIterator`
`class`	`IntervalTree.RevIterator`
`static class`	`IntervalTree.ValuesIterator<V1>`

Constructor Summary

Constructors
Constructor and Description

IntervalTree()

Constructors
Constructor and Description
`IntervalTree()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`checkMaxEnds()` This method is only for debugging.
`void`	`clear()` Remove all entries.
`IntervalTree.Node<V>`	`find(int start, int end)` Find an interval.
`IntervalTree.Node<V>`	`findByIndex(int idx)` Find the nth interval in the tree.
`int`	`getIndex(int start, int end)` Find the rank of the specified interval.
`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.
`java.util.Iterator<IntervalTree.Node<V>>`	`iterator()` Return an iterator over the entire tree.
`java.util.Iterator<IntervalTree.Node<V>>`	`iterator(int start, int end)` Return an iterator over all intervals greater than or equal to the specified interval.
`IntervalTree.Node<V>`	`max()` Find the greatest interval in the tree.
`IntervalTree.Node<V>`	`max(int start, int end)` Find the latest interval in the tree less than or equal to the specified interval.
`IntervalTree.Node<V>`	`min()` Find the least interval in the tree.
`IntervalTree.Node<V>`	`min(int start, int end)` Find the earliest interval in the tree greater than or equal to the specified interval.
`IntervalTree.Node<V>`	`minOverlapper(int start, int end)` Find the earliest interval in the tree that overlaps the specified interval.
`java.util.Iterator<IntervalTree.Node<V>>`	`overlappers(int start, int end)` Return an iterator over all intervals overlapping the specified range.
`void`	`printTree()` This method draws a nested picture of the tree on System.out.
`V`	`put(int start, int end, V value)` Put a new interval into the tree (or update the value associated with an existing interval).
`V`	`remove(int start, int end)` Remove an interval from the tree.
`java.util.Iterator<IntervalTree.Node<V>>`	`reverseIterator()` Return an iterator over the entire tree that returns intervals in reverse order.
`java.util.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.
`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.
`int`	`size()` Return the number of intervals in the tree.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - IntervalTree
```
public IntervalTree()
```
- Method Detail
  - 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.
  - 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 java.util.Iterator<IntervalTree.Node<V>> iterator()
```
    Return an iterator over the entire tree.
    
    Specified by:
    
    iterator in interface java.lang.Iterable<IntervalTree.Node<V>>
    
    Returns:
    
    An iterator.
  - iterator
```
public java.util.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 java.util.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 java.util.Iterator<IntervalTree.Node<V>> reverseIterator()
```
    Return an iterator over the entire tree that returns intervals in reverse order.
    
    Returns:
    
    An iterator.
  - reverseIterator
```
public java.util.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:
    
    java.lang.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.

Class IntervalTree<V>

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

IntervalTree

Method Detail

size

clear

put

remove

find

findByIndex

getIndex

min

min

minOverlapper

max

max

iterator

iterator

overlappers

reverseIterator

reverseIterator

getSentinel

setSentinel

checkMaxEnds

printTree