HopscotchCollection (gatk 4.2.4.0 API)

java.lang.Object
- java.util.AbstractCollection<T>
- - org.broadinstitute.hellbender.utils.collections.HopscotchCollection<T>

All Implemented Interfaces:

java.lang.Iterable<T>, java.util.Collection<T>

Direct Known Subclasses:

HopscotchCollectionSpark, HopscotchMultiMap, HopscotchSet
```
public class HopscotchCollection<T>
extends java.util.AbstractCollection<T>
```
Multiset implementation that provides low memory overhead with a high load factor by using the hopscotch algorithm. Retrieval times are usually a little slower than for the JDK's HashSet (neglecting GC time), but this class uses much less memory. Insertion and deletion times are typically a little better than HashSet. It's probably a nice choice for very large collections. You can make it faster than HashSet by replacing the prime-number table sizing with power-of-2 table sizing, but then it'll behave just as badly as HashSet given poor hashCode implementations. (The extra time in retrieval is mostly due to having to take the hash value mod the capacity, rather than masking off a few bits.) Very rarely, and usually when your element type's hashCode implementation is poor, the hopscotching will fail even after the table is (automatically) resized to be 1.4 times larger. In this case an IllegalStateException will be thrown. To be honest, I haven't ever seen it happen with this version of the code, but it might. If it happens to you, you might want to take a look at your T's hashCode implementation to make certain it has good avalanche characteristics. The ones you see recommended everywhere that add in the final piece of state, don't have good avalanche. We try to take care of this common defect with the SPREADER, but that's not a perfect solution.

Field Summary

Fields
Modifier and Type Field and Description

protected static double LOAD_FACTOR

protected static int SPREADER

Fields
Modifier and Type	Field and Description
`protected static double`	`LOAD_FACTOR`
`protected static int`	`SPREADER`

Constructor Summary

Constructors
Constructor and Description
`HopscotchCollection()` make a small HopscotchCollection
`HopscotchCollection(java.util.Collection<? extends T> collection)` make a HopscotchCollection from a collection
`HopscotchCollection(int capacity)` make a HopscotchCollection for a specified capacity (or good guess)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(T entry)`
`int`	`capacity()` maximum number of elements that can be held without resizing.
`java.util.stream.Stream<T>`	`chainHeads()`
`void`	`clear()`
`boolean`	`contains(java.lang.Object key)`
`protected java.util.function.BiPredicate<T,T>`	`entryCollides()` in a general multiset there is no uniqueness criterion, so there is never a collision
`T`	`find(java.lang.Object key)` find an entry equivalent to the key, or return null
`java.util.Iterator<T>`	`findEach(java.lang.Object key)` get an iterator over each of the elements equivalent to the key
`T`	`findOrAdd(java.lang.Object key, java.util.function.Function<java.lang.Object,T> producer)` find an entry equivalent to the key, or use producer to add a new value
`protected int`	`hashToIndex(java.lang.Object entry)`
`boolean`	`isEmpty()`
`java.util.Iterator<T>`	`iterator()`
`boolean`	`remove(java.lang.Object key)`
`boolean`	`removeAll(java.util.Collection<?> collection)` unlike the AbstractCollection implementation, this one iterates over the supplied collection
`boolean`	`removeEach(java.lang.Object key)` remove each of the elements equivalent to the key
`int`	`size()`
`java.util.stream.Stream<T>`	`squatters()`
`protected java.util.function.Function<T,java.lang.Object>`	`toKey()` in a general multiset, the entry is the key

Methods inherited from class java.util.AbstractCollection
addAll, containsAll, retainAll, toArray, toArray, toString

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

Methods inherited from interface java.util.Collection
equals, hashCode, parallelStream, removeIf, spliterator, stream

Methods inherited from interface java.lang.Iterable
forEach

- Field Detail
  - LOAD_FACTOR
```
protected static final double LOAD_FACTOR
```
    See Also:
    
    Constant Field Values
  - SPREADER
```
protected static final int SPREADER
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - HopscotchCollection
```
public HopscotchCollection()
```
    make a small HopscotchCollection
  - HopscotchCollection
```
public HopscotchCollection(int capacity)
```
    make a HopscotchCollection for a specified capacity (or good guess)
  - HopscotchCollection
```
public HopscotchCollection(java.util.Collection<? extends T> collection)
```
    make a HopscotchCollection from a collection
- Method Detail
  - add
```
public final boolean add(T entry)
```
    Specified by:
    
    add in interface java.util.Collection<T>
    
    Overrides:
    
    add in class java.util.AbstractCollection<T>
  - clear
```
public final void clear()
```
    Specified by:
    
    clear in interface java.util.Collection<T>
    
    Overrides:
    
    clear in class java.util.AbstractCollection<T>
  - capacity
```
public final int capacity()
```
    maximum number of elements that can be held without resizing. (but we may have to resize earlier.)
  - contains
```
public final boolean contains(java.lang.Object key)
```
    Specified by:
    
    contains in interface java.util.Collection<T>
    
    Overrides:
    
    contains in class java.util.AbstractCollection<T>
  - find
```
public final T find(java.lang.Object key)
```
    find an entry equivalent to the key, or return null
  - findOrAdd
```
public final T findOrAdd(java.lang.Object key,
                         java.util.function.Function<java.lang.Object,T> producer)
```
    find an entry equivalent to the key, or use producer to add a new value
  - findEach
```
public final java.util.Iterator<T> findEach(java.lang.Object key)
```
    get an iterator over each of the elements equivalent to the key
  - isEmpty
```
public final boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface java.util.Collection<T>
    
    Overrides:
    
    isEmpty in class java.util.AbstractCollection<T>
  - iterator
```
public final java.util.Iterator<T> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<T>
    
    Specified by:
    
    iterator in interface java.util.Collection<T>
    
    Specified by:
    
    iterator in class java.util.AbstractCollection<T>
  - remove
```
public final boolean remove(java.lang.Object key)
```
    Specified by:
    
    remove in interface java.util.Collection<T>
    
    Overrides:
    
    remove in class java.util.AbstractCollection<T>
  - removeEach
```
public final boolean removeEach(java.lang.Object key)
```
    remove each of the elements equivalent to the key
  - removeAll
```
public final boolean removeAll(java.util.Collection<?> collection)
```
    unlike the AbstractCollection implementation, this one iterates over the supplied collection
    
    Specified by:
    
    removeAll in interface java.util.Collection<T>
    
    Overrides:
    
    removeAll in class java.util.AbstractCollection<T>
  - size
```
public final int size()
```
    Specified by:
    
    size in interface java.util.Collection<T>
    
    Specified by:
    
    size in class java.util.AbstractCollection<T>
  - chainHeads
```
public java.util.stream.Stream<T> chainHeads()
```
  - squatters
```
public java.util.stream.Stream<T> squatters()
```
  - entryCollides
```
protected java.util.function.BiPredicate<T,T> entryCollides()
```
    in a general multiset there is no uniqueness criterion, so there is never a collision
  - toKey
```
protected java.util.function.Function<T,java.lang.Object> toKey()
```
    in a general multiset, the entry is the key
  - hashToIndex
```
protected int hashToIndex(java.lang.Object entry)
```

Class HopscotchCollection<T>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.util.AbstractCollection

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Field Detail

LOAD_FACTOR

SPREADER

Constructor Detail

HopscotchCollection

HopscotchCollection

HopscotchCollection

Method Detail

add

clear

capacity

contains

find

findOrAdd

findEach

isEmpty

iterator

remove

removeEach

removeAll

size

chainHeads

squatters

entryCollides

toKey

hashToIndex