Class GV4CompressedFunction<T>

java.lang.Object
it.unimi.dsi.fastutil.objects.AbstractObject2LongFunction<T>
it.unimi.dsi.sux4j.mph.GV4CompressedFunction<T>
All Implemented Interfaces:
it.unimi.dsi.fastutil.Function<T,Long>, it.unimi.dsi.fastutil.objects.Object2LongFunction<T>, it.unimi.dsi.fastutil.Size64, Serializable, Function<T,Long>, ToLongFunction<T>

public class GV4CompressedFunction<T> extends it.unimi.dsi.fastutil.objects.AbstractObject2LongFunction<T> implements Serializable, it.unimi.dsi.fastutil.Size64
An immutable function stored in a compressed form.

Instances of this class store a function from keys to values. Keys are provided by an iterable object (whose iterators must return elements in a consistent order), whereas values are provided by a LongIterable. If you do not specify values, each key will be assigned its rank (e.g., its position in iteration order starting from zero).

The values must have a skewed distribution: some values must be much more frequent than others. In that case, this data structure uses much less space than, say, a GOV4Function because it is able to use, for each key, a number of bits close to the empirical entropy of the value list (with an additional ≈3%). It is slower than a GV3CompressedFunction, and it takes more time to build, but it uses less space.

For convenience, this class provides a main method that reads from standard input a (possibly gzip'd) sequence of newline-separated strings, and writes a serialised function mapping each element of the list to its position, or to a given list of values.

Building a function

This class provides a great amount of flexibility when creating a new function; such flexibility is exposed through the builder. To exploit the various possibilities, you must understand some details of the construction.

In a first phase, we build a BucketedHashStore containing hashes of the keys. By default, the store will associate each hash with the rank of the key. If you specify values, the store will associate with each hash the corresponding value.

However, if you further require an indirect construction the store will associate again each hash with the rank of the corresponding key, and access randomly the values (which must be either a LongList or a LongBigList). Indirect construction is useful only in complex, multi-layer hashes (such as an LcpMonotoneMinimalPerfectHashFunction) in which we want to reuse a checked BucketedHashStore. Storing values in the BucketedHashStore is extremely scalable because the values must just be a LongIterable that will be scanned sequentially during the store construction. On the other hand, if you have already a store that associates ordinal positions, and you want to build a new function for which a LongList or LongBigList of values needs little space (e.g., because it is described implicitly), you can opt for an indirect construction using the already built store.

Note that if you specify a store it will be used before building a new one (possibly because of a DuplicateException), with obvious benefits in terms of performance. If the store is not checked, and a DuplicateException is thrown, the constructor will try to rebuild the store, but this requires, of course, that the keys, and possibly the values, are available. Note that it is your responsibility to pass a correct store.

Multithreading

This implementation is multithreaded: each bucket returned by the BucketedHashStore is processed independently. By default, this class uses Runtime.availableProcessors() parallel threads, but by default no more than 4. If you wish to set a specific number of threads, you can do so through the system property "it.unimi.dsi.sux4j.mph.threads"<T>.

Implementation Details

The detail of the data structure can be found in “Engineering Compressed Functions”, by Marco Genuzio and Sebastiano Vigna, 2017. The theoretical basis for the construction is described by Jóhannes B. Hreinsson, Morten Krøyer, and Rasmus Pagh in “Storing a compressed function with constant time access”, Algorithms - ESA 2009, 17th Annual European Symposium, 2009, pages 730−741. Each output value is represented by a codeword from a prefix-free code (by default, a length-limited Huffman code). We generate a random 4-regular linear system on F2, where the known term of the k-th equation is a bit in a bit array. When we read the bit array at four suitable positions depending on an input key, we can recover the codeword representing the output value.

Since:
4.2.0
Author:
Sebastiano Vigna, Marco Genuzio
See Also:
  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static class 
     
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    The expected bucket size.
    protected final it.unimi.dsi.bits.BitVector
    A bit vector storing the main data array.
    protected final Codec.Decoder
    The decoder that will be used to yield output values.
    static final double
     
    static final int
     
    protected final int
    protected final int
    protected final int
    Length of longest codeword
    protected long
    The seed used to generate the initial signature.
    protected final long
    The number of keys.
    static final String
    The system property used to set the number of parallel threads.
    protected static final int
     
    protected final long[]
    A long containing three values per bucket: the top SEED_BITS bits contain the seed (note that it must not be shifted right); the remaining lower bits contain the starting position in data of the bits associated with the bucket.
    protected static final int
     
    protected final it.unimi.dsi.bits.TransformationStrategy<? super T>
    The transformation strategy to turn objects of type T into bit vectors.

    Fields inherited from class it.unimi.dsi.fastutil.objects.AbstractObject2LongFunction

    defRetValue
  • Constructor Summary

    Constructors
    Modifier
    Constructor
    Description
    protected
    GV4CompressedFunction(Iterable<? extends T> keys, it.unimi.dsi.bits.TransformationStrategy<? super T> transform, it.unimi.dsi.fastutil.longs.LongIterable values, boolean indirect, File tempDir, BucketedHashStore<T> bucketedHashStore, Codec codec)
    Creates a new function for the given keys and values.
  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
     
    void
    dump(String file)
     
    long
     
    static void
    main(String[] arg)
     
    long
    Returns the number of bits used by this structure.
    int
    Deprecated.
    long
    Returns the number of keys in the function domain.

    Methods inherited from class it.unimi.dsi.fastutil.objects.AbstractObject2LongFunction

    defaultReturnValue, defaultReturnValue

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface it.unimi.dsi.fastutil.Function

    apply, clear

    Methods inherited from interface java.util.function.Function

    compose

    Methods inherited from interface it.unimi.dsi.fastutil.objects.Object2LongFunction

    andThen, andThenByte, andThenChar, andThenDouble, andThenFloat, andThenInt, andThenLong, andThenObject, andThenReference, andThenShort, applyAsLong, composeByte, composeChar, composeDouble, composeFloat, composeInt, composeLong, composeObject, composeReference, composeShort, get, getOrDefault, getOrDefault, put, put, remove, removeLong
  • Field Details

    • SEED_BITS

      protected static final int SEED_BITS
      See Also:
    • OFFSET_BITS

      protected static final int OFFSET_BITS
      See Also:
    • NUMBER_OF_THREADS_PROPERTY

      public static final String NUMBER_OF_THREADS_PROPERTY
      The system property used to set the number of parallel threads.
      See Also:
    • DELTA

      public static final double DELTA
      See Also:
    • DELTA_TIMES_256

      public static final int DELTA_TIMES_256
    • BUCKET_SIZE

      public static final int BUCKET_SIZE
      The expected bucket size.
      See Also:
    • n

      protected final long n
      The number of keys.
    • globalMaxCodewordLength

      protected final int globalMaxCodewordLength
      Length of longest codeword
    • globalSeed

      protected long globalSeed
      The seed used to generate the initial signature.
    • offsetAndSeed

      protected final long[] offsetAndSeed
      A long containing three values per bucket:
      • the top SEED_BITS bits contain the seed (note that it must not be shifted right);
      • the remaining lower bits contain the starting position in data of the bits associated with the bucket.
    • data

      protected final it.unimi.dsi.bits.BitVector data
      A bit vector storing the main data array.
    • transform

      protected final it.unimi.dsi.bits.TransformationStrategy<? super T> transform
      The transformation strategy to turn objects of type T into bit vectors.
    • decoder

      protected final Codec.Decoder decoder
      The decoder that will be used to yield output values.
    • escapeLength

      protected final int escapeLength
    • escapedSymbolLength

      protected final int escapedSymbolLength
  • Constructor Details

    • GV4CompressedFunction

      protected GV4CompressedFunction(Iterable<? extends T> keys, it.unimi.dsi.bits.TransformationStrategy<? super T> transform, it.unimi.dsi.fastutil.longs.LongIterable values, boolean indirect, File tempDir, BucketedHashStore<T> bucketedHashStore, Codec codec) throws IOException
      Creates a new function for the given keys and values.
      Parameters:
      keys - the keys in the domain of the function, or null.
      transform - a transformation strategy for the keys.
      values - values to be assigned to each element, in the same order of the iterator returned by keys; if null, the assigned value will the ordinal number of each element.
      indirect - if true, bucketedHashStore contains ordinal positions, and values is a LongIterable that must be accessed to retrieve the actual values.
      tempDir - a temporary directory for the store files, or null for the standard temporary directory.
      bucketedHashStore - a bucketed hash store containing the keys associated with their values and counting value frequencies, or null; the store can be unchecked, but in this case keys and transform must be non-null.
      codec - the Codec used to encode values.
      Throws:
      IOException
  • Method Details

    • getLong

      public long getLong(Object o)
      Specified by:
      getLong in interface it.unimi.dsi.fastutil.objects.Object2LongFunction<T>
    • size64

      public long size64()
      Returns the number of keys in the function domain.
      Specified by:
      size64 in interface it.unimi.dsi.fastutil.Size64
      Returns:
      the number of the keys in the function domain.
    • size

      @Deprecated public int size()
      Deprecated.
      Specified by:
      size in interface it.unimi.dsi.fastutil.Function<T,Long>
      Specified by:
      size in interface it.unimi.dsi.fastutil.Size64
    • numBits

      public long numBits()
      Returns the number of bits used by this structure.
      Returns:
      the number of bits used by this structure.
    • containsKey

      public boolean containsKey(Object o)
      Specified by:
      containsKey in interface it.unimi.dsi.fastutil.Function<T,Long>
    • dump

      public void dump(String file) throws IOException
      Throws:
      IOException
    • main

      public static void main(String[] arg) throws NoSuchMethodException, IOException, com.martiansoftware.jsap.JSAPException
      Throws:
      NoSuchMethodException
      IOException
      com.martiansoftware.jsap.JSAPException