Serialized Form

Package it.unimi.dsi.sux4j.bits

Class it.unimi.dsi.sux4j.bits.AbstractRank extends Object implements Serializable

Class it.unimi.dsi.sux4j.bits.HintedBsearchSelect extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

inventory

int[] inventory

onesPerInventory

int onesPerInventory

log2OnesPerInventory

int log2OnesPerInventory

numOnes

long numOnes

numWords

int numWords

count

long[] count

rank9

Rank9 rank9

Class it.unimi.dsi.sux4j.bits.JacobsonBalancedParentheses extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

bitVector

BitVector bitVector

openingPioneers

SparseSelect openingPioneers

openingPioneersRank

SparseRank openingPioneersRank

openingPioneerMatches

EliasFanoLongBigList openingPioneerMatches

closingPioneers

SparseSelect closingPioneers

closingPioneersRank

SparseRank closingPioneersRank

closingPioneerMatches

EliasFanoLongBigList closingPioneerMatches

Class it.unimi.dsi.sux4j.bits.Rank16 extends AbstractRank implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

superCount

long[] superCount

count

short[] count

numWords

int numWords

numOnes

long numOnes

lastOne

long lastOne

bitVector

BitVector bitVector

Class it.unimi.dsi.sux4j.bits.Rank9 extends AbstractRank implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

bitVector

BitVector bitVector

count

long[] count

numWords

int numWords

numOnes

long numOnes

lastOne

long lastOne

Class it.unimi.dsi.sux4j.bits.RankSelect extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

rank

Rank rank

A rank structure, or null.

select

Select select

A select structure, or null.

selectZero

SelectZero selectZero

A zero-select structure, or null.

Class it.unimi.dsi.sux4j.bits.Select9 extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

inventory

long[] inventory

subinventory

long[] subinventory

numOnes

long numOnes

numWords

int numWords

count

long[] count

rank9

Rank9 rank9

Class it.unimi.dsi.sux4j.bits.SimpleSelect extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

inventory

long[] inventory

subinventory

long[] subinventory

numOnes

long numOnes

numWords

int numWords

onesPerInventory

int onesPerInventory

log2OnesPerInventory

int log2OnesPerInventory

onesPerInventoryMask

int onesPerInventoryMask

log2LongwordsPerSubinventory

int log2LongwordsPerSubinventory

log2OnesPerSub64

int log2OnesPerSub64

log2OnesPerSub16

int log2OnesPerSub16

onesPerSub64

int onesPerSub64

onesPerSub16

int onesPerSub16

onesPerSub16Mask

int onesPerSub16Mask

exactSpill

long[] exactSpill

bitVector

BitVector bitVector

Class it.unimi.dsi.sux4j.bits.SimpleSelectZero extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

inventory

long[] inventory

subinventory

long[] subinventory

numOnes

long numOnes

numWords

int numWords

onesPerInventory

int onesPerInventory

log2OnesPerInventory

int log2OnesPerInventory

onesPerInventoryMask

int onesPerInventoryMask

log2LongwordsPerSubinventory

int log2LongwordsPerSubinventory

log2OnesPerSub64

int log2OnesPerSub64

log2OnesPerSub16

int log2OnesPerSub16

onesPerSub64

int onesPerSub64

onesPerSub16

int onesPerSub16

onesPerSub16Mask

int onesPerSub16Mask

exactSpill

long[] exactSpill

bitVector

BitVector bitVector

Class it.unimi.dsi.sux4j.bits.SparseRank extends AbstractRank implements Serializable

serialVersionUID: 2L

Serialized Fields

n

long n

The length of the underlying bit array.

m

long m

The number of ones in the underlying bit array.

l

int l

The number of lower bits.

lowerLBitsMask

long lowerLBitsMask

The mask for lower bits.

lowerBits

LongBigList lowerBits

The list of lower bits of the position of each one, stored explicitly.

upperBits

BitVector upperBits

The upper bits.

selectZeroUpper

SimpleSelectZero selectZeroUpper

The rank structure used to extract the upper bits.

fromSelect

boolean fromSelect

Whether this structure was built from a SparseSelect structure, and thus shares part of its internal state.

Class it.unimi.dsi.sux4j.bits.SparseSelect extends EliasFanoMonotoneLongBigList implements Serializable

serialVersionUID: 2L

Serialized Fields

n

long n

The number of bits in the underlying bit array.

fromRank

boolean fromRank

Whether this structure was built from a SparseRank structure, and thus shares part of its internal state.

Class it.unimi.dsi.sux4j.bits.TrivialBalancedParentheses extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

v

BitVector v

Package it.unimi.dsi.sux4j.io

Class it.unimi.dsi.sux4j.io.ChunkedHashStore extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

n

int n

The number of elements that pass the current filter.

seed

long seed

The seed used to generate the hash triples.

count

int[] count

The number of triples in each disk chunk.

chunks

int chunks

The number of chunks.

file

File[] file

The files containing disk chunks.

diskChunkStep

int diskChunkStep

The number of disk chunks making up a chunk, or 1 if a chunk is smaller than or equal to a disk chunk.

chunkShift

int chunkShift

The shift to be applied to the first hash to obtain the chunk index, set by ChunkedHashStore.log2Chunks(int) (watch out: it can be Long.SIZE).

checkedForDuplicates

boolean checkedForDuplicates

If true, this store has been checked for duplicates.

transform

TransformationStrategy<T> transform

The transformation strategy provided at construction time.

pl

ProgressLogger pl

A progress logger.

dos

DataOutputStream[] dos

The data output streams for the disk chunks.

virtualDiskChunks

int virtualDiskChunks

The number of disk chunks divided by ChunkedHashStore.diskChunkStep.

filter

org.apache.commons.collections.Predicate filter

If not null, a filter that will be used to select triples.

maxCount

int maxCount

The maximum number of triples in a disk chunk.

locked

boolean locked

Whether this store is locked. Any attempt to ChunkedHashStore.reset(long) the store will cause an IllegalStateException if this variable is true.

closed

boolean closed

Whether this store has already been closed.

Class it.unimi.dsi.sux4j.io.ChunkedHashStore.DuplicateException extends RuntimeException implements Serializable

serialVersionUID: 1L

Class it.unimi.dsi.sux4j.io.FileLinesList extends AbstractObjectList<MutableString> implements Serializable

Serialized Fields

filename

String filename

The filename upon which this file-lines collection is based.

size

int size

The size of the list.

bufferSize

int bufferSize

The buffer size for all instances of FastBufferedInputStream.

terminators

EnumSet<E extends Enum<E>> terminators

The terminators that must be used to separate the file lines.

byteBuffer

ByteBuffer byteBuffer

A byte buffer for character decoding. It is enough large to hold any line in the file.

charBuffer

CharBuffer charBuffer

A character buffer for character decoding. It is enough large to hold any line in the file.

borders

EliasFanoMonotoneLongBigList borders

A sparse selection structure keeping track of the start of each line in the file.

inputStream

FastBufferedInputStream inputStream

The fast buffered input stream used by FileLinesList.get(int).

decoder

CharsetDecoder decoder

A decoder used by FileLinesList.get(int).

charset

Charset charset

The charset specified at construction time.

Package it.unimi.dsi.sux4j.mph

Class it.unimi.dsi.sux4j.mph.AbstractHashFunction extends AbstractObject2LongFunction<K> implements Serializable

serialVersionUID: 5315342712300777745L

Class it.unimi.dsi.sux4j.mph.HollowTrieDistributor extends AbstractObject2LongFunction<T> implements Serializable

serialVersionUID: 3L

Serialized Fields

transformationStrategy

TransformationStrategy<T> transformationStrategy

The transformation used to map object to bit vectors.

trie

LongArrayBitVector trie

The bitstream representing the hollow trie.

skips

EliasFanoLongBigList skips

The list of skips, indexed by the internal nodes (we do not need skips on the leaves).

externalBehaviour

MWHCFunction<T> externalBehaviour

For each external node and each possible path, the related behaviour.

size

int size

The number of (internal and external) nodes of the trie.

balParen

BalancedParentheses balParen

falseFollowsDetector

MWHCFunction<T> falseFollowsDetector

meanSkipLength

double meanSkipLength

The average skip length in bits (actually, the average length in bits of a skip length increased by one).

externalTestFunction

Object2LongFunction<K> externalTestFunction

A debug function used to store explicitly the internal behaviour.

falseFollows

Object2LongFunction<K> falseFollows

A debug function used to store explicitly the false follow detector.

Class it.unimi.dsi.sux4j.mph.HollowTrieDistributorMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 3L

Serialized Fields

size

int size

The number of elements.

bucketSize

int bucketSize

The size of a bucket.

log2BucketSize

int log2BucketSize

Fast.ceilLog2(int) of HollowTrieDistributorMonotoneMinimalPerfectHashFunction.bucketSize.

transform

TransformationStrategy<T> transform

The transformation strategy.

distributor

HollowTrieDistributor<T> distributor

A hollow trie distributor assigning keys to buckets.

offset

MWHCFunction<T> offset

The offset of each element into his bucket.

Class it.unimi.dsi.sux4j.mph.HollowTrieMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

skips

EliasFanoLongBigList skips

trie

LongArrayBitVector trie

The bit vector containing Jacobson's representation of the trie.

balParen

JacobsonBalancedParentheses balParen

A balanced parentheses structure over HollowTrieMonotoneMinimalPerfectHashFunction.trie.

transform

TransformationStrategy<T> transform

The transformation strategy.

size

int size

The number of elements in this hollow trie.

Class it.unimi.dsi.sux4j.mph.LcpMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

n

int n

The number of elements.

bucketSize

int bucketSize

The size of a bucket.

log2BucketSize

int log2BucketSize

Fast.ceilLog2(int) of LcpMonotoneMinimalPerfectHashFunction.bucketSize.

bucketSizeMask

int bucketSizeMask

The mask for LcpMonotoneMinimalPerfectHashFunction.log2BucketSize bits.

offsetLcpLength

MWHCFunction<T> offsetLcpLength

A function mapping each element to the offset inside its bucket (lowest LcpMonotoneMinimalPerfectHashFunction.log2BucketSize bits) and to the length of the longest common prefix of its bucket (remaining bits).

lcp2Bucket

MWHCFunction<T> lcp2Bucket

A function mapping each longest common prefix to its bucket.

transform

TransformationStrategy<T> transform

The transformation strategy.

seed

long seed

Class it.unimi.dsi.sux4j.mph.MinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

n

int n

The number of elements.

chunkShift

int chunkShift

The shift for chunks.

globalSeed

long globalSeed

The seed used to generate the initial hash triple.

seed

long[] seed

The seed of the underlying 3-hypergraphs.

offset

int[] offset

The start offset of each block.

values

LongBigList values

The final magick—the list of modulo-3 values that define the output of the minimal hash function.

bitVector

LongArrayBitVector bitVector

The bit vector underlying MinimalPerfectHashFunction.values.

count

int[] count

The number of nonzero bit pairs up to a given block of MinimalPerfectHashFunction.BITS_PER_BLOCK bits.

transform

TransformationStrategy<T> transform

The transformation strategy.

Class it.unimi.dsi.sux4j.mph.MWHCFunction extends AbstractObject2LongFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

chunkShift

int chunkShift

The shift for chunks.

n

int n

The number of elements.

m

int m

The number of vertices of the intermediate hypergraph.

width

int width

The data width.

globalSeed

long globalSeed

The seed used to generate the initial hash triple.

seed

long[] seed

The seed of the underlying 3-hypergraphs.

offset

int[] offset

The start offset of each block.

data

LongBigList data

The final magick—the list of modulo-3 values that define the output of the minimal hash function.

marker

LongArrayBitVector marker

Optionally, a MWHCFunction.rank structure built on this bit array is used to mark positions containing non-zero value; indexing in MWHCFunction.data is made by ranking if this field is non-null.

rank

Rank16 rank

The ranking structure on MWHCFunction.marker.

transform

TransformationStrategy<T> transform

The transformation strategy to turn objects of type T into bit vectors.

Class it.unimi.dsi.sux4j.mph.PaCoTrieDistributor extends AbstractObject2LongFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

trie

byte[] trie

The bitstream representing the PaCo trie.

numberOfLeaves

int numberOfLeaves

The number of leaves in the trie.

transformationStrategy

TransformationStrategy<T> transformationStrategy

The transformation used to map object to bit vectors.

Class it.unimi.dsi.sux4j.mph.PaCoTrieDistributorMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

size

int size

The number of elements.

bucketSize

int bucketSize

The size of a bucket.

log2BucketSize

int log2BucketSize

Fast.ceilLog2(int) of PaCoTrieDistributorMonotoneMinimalPerfectHashFunction.bucketSize.

transform

TransformationStrategy<T> transform

The transformation strategy.

distributor

PaCoTrieDistributor<T> distributor

A PaCo trie assigning keys to buckets.

offset

MWHCFunction<T> offset

The offset of each element into his bucket.

Class it.unimi.dsi.sux4j.mph.TwoStepsLcpMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

n

int n

The number of elements.

bucketSize

int bucketSize

The size of a bucket.

log2BucketSize

int log2BucketSize

Fast.ceilLog2(int) of TwoStepsLcpMonotoneMinimalPerfectHashFunction.bucketSize.

bucketSizeMask

int bucketSizeMask

The mask for TwoStepsLcpMonotoneMinimalPerfectHashFunction.log2BucketSize bits.

offsets

MWHCFunction<T> offsets

A function mapping each element to the offset inside its bucket.

lcpLengths

TwoStepsMWHCFunction<T> lcpLengths

A function mapping each element to the length of the longest common prefix of its bucket.

lcp2Bucket

MWHCFunction<T> lcp2Bucket

A function mapping each longest common prefix to its bucket.

transform

TransformationStrategy<T> transform

The transformation strategy.

seed

long seed

The seed to be used when converting keys to triples.

Class it.unimi.dsi.sux4j.mph.TwoStepsMWHCFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 2L

Serialized Fields

n

int n

The number of elements.

transform

TransformationStrategy<T> transform

The transformation strategy to turn objects of type T into bit vectors.

firstFunction

MWHCFunction<T> firstFunction

The first function, or null. The special output value TwoStepsMWHCFunction.escape denotes that TwoStepsMWHCFunction.secondFunction should be queried instead.

secondFunction

MWHCFunction<T> secondFunction

The second function. All queries for which TwoStepsMWHCFunction.firstFunction returns TwoStepsMWHCFunction.escape (or simply all queries, if TwoStepsMWHCFunction.firstFunction is null) will be rerouted here.

remap

long[] remap

A mapping from values of the first function to actual values, provided that there is a first function.

escape

int escape

The escape value returned by TwoStepsMWHCFunction.firstFunction to suggest that TwoStepsMWHCFunction.secondFunction should be queried instead, provided that there is a first function.

seed

long seed

rankMean

double rankMean

The mean of the rank distribution.

width

int width

The width of the output of this function, in bits.

Class it.unimi.dsi.sux4j.mph.ZFastTrieDistributor extends AbstractObject2LongFunction<T> implements Serializable

serialVersionUID: 1L

Serialized Fields

leaves

Rank9 leaves

A ranking structure on the vector containing leaves plus p0,p1, etc.

transformationStrategy

TransformationStrategy<T> transformationStrategy

The transformation used to map object to bit vectors.

behaviour

MWHCFunction<T> behaviour

For each external node and each possible path, the related behaviour.

size

int size

The number of elements of the set upon which the trie is built.

signatures

MWHCFunction<T> signatures

ranker

TwoStepsLcpMonotoneMinimalPerfectHashFunction<T> ranker

logWMask

long logWMask

logW

int logW

signatureMask

long signatureMask

numDelimiters

int numDelimiters

mistakeSignatures

IntOpenHashSet mistakeSignatures

corrections

MWHCFunction<T> corrections

emptyTrie

boolean emptyTrie

Whether the underlying probabilistic trie is empty.

noDelimiters

boolean noDelimiters

Whether there are no delimiters.

seed

long seed

Class it.unimi.dsi.sux4j.mph.ZFastTrieDistributorMonotoneMinimalPerfectHashFunction extends AbstractHashFunction<T> implements Serializable

serialVersionUID: 1L

Serialized Fields

size

int size

The number of elements.

log2BucketSize

int log2BucketSize

The logarithm of the bucket size.

transform

TransformationStrategy<T> transform

The transformation strategy.

distributor

ZFastTrieDistributor<T> distributor

A hollow trie distributor assigning keys to buckets.

offset

MWHCFunction<T> offset

The offset of each element into his bucket.

Package it.unimi.dsi.sux4j.util

Class it.unimi.dsi.sux4j.util.EliasFanoLongBigList extends AbstractLongBigList implements Serializable

serialVersionUID: 1L

Serialized Fields

length

long length

The number of elements in this list.

bits

LongArrayBitVector bits

The storage for small elements.

offset

long offset

The offset (derived from the lower bound computed or provided at construction time) that must be added before returning a value.

borders

EliasFanoMonotoneLongBigList borders

The position of the initial bit of each element, plus a final marker for the end of the bit array.

Class it.unimi.dsi.sux4j.util.EliasFanoMonotoneLongBigList extends AbstractLongBigList implements Serializable

serialVersionUID: 2L

Serialized Fields

length

long length

The length of the sequence.

l

int l

The number of lower bits.

lowerBits

LongBigList lowerBits

The list of lower bits of each element, stored explicitly.

selectUpper

SimpleSelect selectUpper

The select structure used to extract the upper bits.

Class it.unimi.dsi.sux4j.util.EliasFanoPrefixSumLongBigList extends EliasFanoMonotoneLongBigList implements Serializable

serialVersionUID: 1L

Serialized Fields

upperBits

BitVector upperBits

Class it.unimi.dsi.sux4j.util.ShiftAddXorSignedStringMap extends AbstractObject2LongFunction<CharSequence> implements Serializable

serialVersionUID: 0L

Serialized Fields

hash

Object2LongFunction<K> hash

Deprecated.

The underlying map.

signatures

LongBigList signatures

Deprecated.

Signatures.

width

int width

Deprecated.

The width in bits of each signature.

shift

int shift

Deprecated.

The left shift to get only ShiftAddXorSignedStringMap.width nonzero bits.

mask

long mask

Deprecated.

The mask to get only ShiftAddXorSignedStringMap.width nonzero bits.

Class it.unimi.dsi.sux4j.util.TwoSizesLongBigList extends AbstractLongBigList implements Serializable

serialVersionUID: 1L

Serialized Fields

length

long length

The number of elements in this list.

small

LongBigList small

The storage for small elements.

large

LongBigList large

The storage for large elements.

marker

LongArrayBitVector marker

A bit array marking whether an element is stored in the small or large storage.

rank

Rank9 rank

A ranking structure to index small and large.

numBits

long numBits

The number of bits used by this structure.