Class BVGraph

  • All Implemented Interfaces:
    FlyweightPrototype<ImmutableGraph>, CompressionFlags

    public class BVGraph
    extends ImmutableGraph
    implements CompressionFlags
    An immutable graph represented using the techniques described in “The WebGraph Framework I: Compression Techniques”, by Paolo Boldi and Sebastiano Vigna, in Proc. of the Thirteenth World–Wide Web Conference, pages 595−601, 2004, ACM Press.

    This class provides a flexible and configurable way to store and access web graphs in a compressed form. Its main method can load an ImmutableGraph and compress it. The resulting compressed BVGraph is described by a graph file (with extension .graph), an offset file (with extension .offsets) and a property file (with extension .properties). The latter, not surprisingly, is a Java property file. Optionally, an offset big-list file (with extension .obl) can be created to load graphs faster.

    As a rule of thumb, random access is faster using successors(int), whereas while iterating using a NodeIterator it is better to use NodeIterator.successorArray().

    Parallel compression

    Starting with version 3.5.0, this classes uses ImmutableGraph.splitNodeIterators(int) to compress a graph using parallel compression threads. The number of parallel threads can be set at construction time, or using the property "it.unimi.dsi.webgraph.threads" from the command line; this approach is useful with classes such as Transform.

    Parallel compression requires the creation of possibly large temporary files. It might be necessary to set the property java.io.tmpdir to a suitable directory if you experience disk-full errors during compression.

    The Graph File

    This class stores a graph as an bit stream. The bit stream format depends on a number of parameters and encodings that can be mixed orthogonally. The parameters are:

    • the window size, a nonnegative integer;
    • the maximum reference count, a positive integer (it is meaningful only when the window is nonzero);
    • the minimum interval length, an integer larger than or equal to two, or 0, which is interpreted as infinity.

    Successor Lists

    The graph file is a sequence of successor lists, one for each node. The list of node x can be thought of as a sequence of natural numbers (even though, as we will explain later, this sequence is further coded suitably as a sequence of bits):

    1. The outdegree of the node; if it is zero, the list ends here.
    2. If the window size is not zero, the reference part, that is:
      1. a nonnegative integer, the reference, which never exceeds the window size; if the reference is r, the list of successors will be specified as a modified version of the list of successors of xr; if r is 0, then the list of successors will be specified explicitly;
      2. if r is nonzero:
        1. a natural number b, the block count;
        2. a sequence of b natural numbers B1, …, Bb, called the copy-block list; only the first number can be zero.
    3. Then comes the extra part, specifying some more entries that the list of successors contains (or all of them, if r is zero), that is:
      1. If the minimum interval length is finite,
        1. an integer i, the interval count;
        2. a sequence of i pairs, whose first component is the left extreme of an interval, and whose second component is the length of the interval (i.e., the number of integers contained in the interval).
      2. Finally, the list of residuals, which contain all successors not specified by previous methods.

    The above data should be interpreted as follows:

    • The reference part, if present (i.e., if both the window size and the reference are strictly positive), specifies that part of the list of successors of node xr should be copied; the successors of node xr that should be copied are described in the copy-block list; more precisely, one should copy the first B1 entries of this list, discard the next B2, copy the next B3 etc. (the last remaining elements of the list of successors will be copied if b is even, and discarded if b is odd).
    • The extra part specifies additional successors (or all of them, if the reference part is absent); the extra part is not present if the number of successors that are to be copied according to the reference part already coincides with the outdegree of x; the successors listed in the extra part are given in two forms:
      • some of them are specified as belonging to (integer) intervals, if the minimum interval length is finite; the interval count indicates how many intervals, and the intervals themselves are listed as pairs (left extreme, length);
      • the residuals are the remaining "scattered" successors.

    How Successor Lists Are Coded

    As we said before, the list of integers corresponding to each successor list should be coded into a sequence of bits. This is (ideally) done in two phases: we first modify the sequence in a suitable manner (as explained below) so to obtain another sequence of integers (some of them might be negative). Then each single integer is coded, using a coding that can be specified as an option; the integers that may be negative are first turned into natural numbers using Fast.int2nat(int).

    1. The outdegree of the node is left unchanged, as well as the reference and the block count;
    2. all blocks are decremented by 1, except for the first one;
    3. the interval count is left unchanged;
    4. all interval lengths are decremented by the minimum interval length;
    5. the first left extreme is expressed as its difference from x (it will be negative if the first extreme is less than x); the remaining left extremes are expressed as their distance from the previous right extreme plus 2 (e.g., if the interval is [5..11] and the previous one was [1..3], then the left extreme 5 is expressed as 5-(3+2)=5-5=0);
    6. the first residual is expressed as its difference from x (it will be negative if the first residual is less than x); the remaining residuals are expressed as decremented differences from the previous residual.

    The Offset File

    Since the graph is stored as a bit stream, we must have some way to know where each successor list starts. This information is stored in the offset file, which contains the bit offset of each successor list (in particular, the offset of the first successor list will be zero). As a commodity, the offset file contains an additional offset pointing just after the last successor list (providing, as a side-effect, the actual bit length of the graph file). Each offset (except for the first one) is stored as a suitably coded difference from the previous offset.

    The list of offsets can be additionally stored as a serialised EliasFanoMonotoneLongBigList using a suitable command-line option. If the serialised big list is detected, it is loaded instead of parsing the offset list.

    The Property File

    This file contains self-explaining entries that are necessary to correctly decode the graph and offset files, and moreover give some statistical information about the compressed graph (e.g., the number of bits per link).

    nodes
    the number of nodes of the graph.
    nodes
    the number of arcs of the graph.
    version
    a version number.
    graphclass
    the name of the class that should load this graph (ImmutableGraph convention).
    bitsperlink
    the number of bits per link (overall graph size in bits divided by the number of arcs).
    bitspernode
    the number of bits per node (overall graph size in bits divided by the number of nodes).
    compratio
    the ratio between the graph size and the information-theoretical lower bound (the binary logarithm of the number of subsets of size arcs out of a universe of nodes2 elements).
    compressionflags
    flags specifying the codes used for the components of the compression algorithm.
    zetak
    if ζ codes are selected for residuals, the parameter k.
    windowsize
    the window size.
    maxref
    the maximum reference count.
    minintervallength
    the minimum length of an interval.
    avgdist
    the average distance of a reference.
    avgref
    the average length of reference chains.
    bitsfor*
    number of bits used by a specific compoenent of the algorithm (the sum is the number of bits used to store the graph).
    avgbitsfor*
    number of bits used by a specific compoenent of the algorithm, divided by the number of nodes (the sum is the number of bits per node).
    *arcs
    the number of arcs stored by each component of the algorithm (the sum is the number of arcs).
    *expstats
    frequencies of the floor of the logarithm of successor gaps and residual gaps, separated by a comma; the statistics include the gap between each node and its first successor, after it has been passed through Fast.int2nat(int), but discarding zeroes (which happen in very rare circumstance, and should be considered immaterial).
    *avg[log]gap
    the average of the gaps (or of their logarithm) of successors and residuals: note that this data is computed from the exponential statistics above, and thus it is necessarily approximate.

    How The Graph File Is Loaded Into Memory

    The natural way of using a graph file is to load it into a byte array and then index its bits using the suitable offset. This class will use a byte array for graphs smaller than Integer.MAX_VALUE bytes, and a FastMultiByteArrayInputStream otherwise: in the latter case, expect a significant slowdown (as an InputBitStream can wrap directly a byte array).

    Offsets are loaded using an EliasFanoMonotoneLongBigList, which occupies exponentially less space than the graph itself (unless your graph is pathologically sparse). There is of course a cost involved in accessing the list with respect to accessing an array of longs.

    Note that by default the EliasFanoMonotoneLongBigList instance is created from scratch using the file of offsets. This is a long and tedious process, in particular with large graphs. The main method of this class has an option that will generate such a list once for all and serialise it in a file with extension .obl. The list will be quickly deserialised if its modification date is later than that of the offset file.

    Not Loading the Graph File at All

    For some applications (such as transposing a graph) it is not necessary to load the graph file in memory. Since this class is able to enumerate the links of a graph without using random access, it is possible not to load in memory any information at all, and obtain iterators that directly read from the graph file. To obtain this effect, you must call loadOffline(CharSequence).

    Memory–Mapping a Graph

    Another interesting alternative is memory mapping. When using loadMapped(CharSequence), the graph will be mapped into memory, and the offsets loaded. The graph will provide random access and behave as if it was loaded into memory, but of course the access will be slower.

    • Field Detail

      • SEQUENTIAL

        public static final int SEQUENTIAL
        The offset step parameter corresponding to sequential load.
        See Also:
        Constant Field Values
      • OFFLINE

        public static final int OFFLINE
        The offset step parameter corresponding to offline load.
        See Also:
        Constant Field Values
      • GRAPH_EXTENSION

        public static final String GRAPH_EXTENSION
        The standard extension for the graph bit stream.
        See Also:
        Constant Field Values
      • OFFSETS_EXTENSION

        public static final String OFFSETS_EXTENSION
        The standard extension for the graph-offsets bit stream.
        See Also:
        Constant Field Values
      • OFFSETS_BIG_LIST_EXTENSION

        public static final String OFFSETS_BIG_LIST_EXTENSION
        The standard extension for the cached LongBigList containing the graph offsets.
        See Also:
        Constant Field Values
      • OUTDEGREES_EXTENSION

        public static final String OUTDEGREES_EXTENSION
        The standard extension for the stream of node outdegrees.
        See Also:
        Constant Field Values
      • BVGRAPH_VERSION

        public static final int BVGRAPH_VERSION
        This number classifies the present graph format. When new features require introducing binary incompatibilities, this number is bumped so to ensure that old classes do not try to read graphs they cannot understand.
        See Also:
        Constant Field Values
      • INITIAL_SUCCESSOR_LIST_LENGTH

        protected static final int INITIAL_SUCCESSOR_LIST_LENGTH
        The initial length of an array that will contain a successor list.
        See Also:
        Constant Field Values
      • NO_INTERVALS

        public static final int NO_INTERVALS
        A special value for minIntervalLength interpreted as meaning that the minimum interval length is infinity.
        See Also:
        Constant Field Values
      • basename

        protected CharSequence basename
        The basename of the graph. This may be null, but trying to load the graph with an offset step of -1 will cause an exception.
      • n

        protected int n
        The number of nodes of the graph.
      • m

        protected long m
        The number of arcs of the graph.
      • isMapped

        protected boolean isMapped
        When offsetType is not -1, whether this graph is directly loaded into graphMemory, or rather memory-mapped.
      • graphMemory

        protected byte[] graphMemory
        The byte array storing the compressed graph, if isMemory is true and offsetType is not -1.

        This variable is loaded with a copy of the graph file, or with a rearrangement of the latter, depending on whether offsetType is smaller than or equal to one. If offsetType is -1, this variable is null, and node iterators are generated by opening streams directly on the graph file.

      • graphStream

        protected FastMultiByteArrayInputStream graphStream
        The multi-byte array input stream storing the compressed graph, if isMemory is false, isMapped is false and offsetType is not -1.

        It is loaded with a copy of the graph file. If offsetType is -1, this variable is null, and node iterators are generated by opening streams directly on the graph file.

      • mappedGraphStream

        protected ByteBufferInputStream mappedGraphStream
        The memory-mapped input stream storing the compressed graph, if isMapped is true.

        It is loaded with a copy of the graph file. If offsetType is -1, this variable is null, and node iterators are generated by opening streams directly on the graph file.

      • offsets

        protected LongBigList offsets
        This variable is null iff offsetType is zero or less (implying that offsets have not been loaded). Otherwise, it is an Elias–Fano monotone list containing the pointers of the bit streams of one each offsetType nodes.
      • offsetType

        protected int offsetType
        The offset type: 2 is memory-mapping, 1 is normal random-access loading, 0 means that we do not want to load offsets at all, -1 that the we do not want even load the graph file.
      • cachedNode

        protected int cachedNode
        If not -1, the node whose degree is cached in cachedOutdegree.
      • maxRefCount

        protected int maxRefCount
        The maximum reference count.
      • DEFAULT_MAX_REF_COUNT

        public static final int DEFAULT_MAX_REF_COUNT
        Default backward reference maximum length.
        See Also:
        Constant Field Values
      • windowSize

        protected int windowSize
        The window size. Zero means no references.
      • DEFAULT_WINDOW_SIZE

        public static final int DEFAULT_WINDOW_SIZE
        Default window size.
        See Also:
        Constant Field Values
      • minIntervalLength

        protected int minIntervalLength
        The minimum interval length.
      • DEFAULT_MIN_INTERVAL_LENGTH

        public static final int DEFAULT_MIN_INTERVAL_LENGTH
        Default minimum interval length.
        See Also:
        Constant Field Values
      • zetaK

        protected int zetaK
        The value of k for ζk coding (for residuals).
      • DEFAULT_ZETA_K

        public static final int DEFAULT_ZETA_K
        Default value of k.
        See Also:
        Constant Field Values
      • OUTDEGREES_GAMMA

        public static final int OUTDEGREES_GAMMA
        Flag: write outdegrees using γ coding (default).
        See Also:
        Constant Field Values
      • OUTDEGREES_DELTA

        public static final int OUTDEGREES_DELTA
        Flag: write outdegrees using δ coding.
        See Also:
        Constant Field Values
      • BLOCKS_GAMMA

        public static final int BLOCKS_GAMMA
        Flag: write copy-block lists using γ coding (default).
        See Also:
        Constant Field Values
      • BLOCKS_DELTA

        public static final int BLOCKS_DELTA
        Flag: write copy-block lists using δ coding.
        See Also:
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      • RESIDUALS_GAMMA

        public static final int RESIDUALS_GAMMA
        Flag: write residuals using γ coding.
        See Also:
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      • RESIDUALS_ZETA

        public static final int RESIDUALS_ZETA
        Flag: write residuals using ζk coding (default).
        See Also:
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      • RESIDUALS_DELTA

        public static final int RESIDUALS_DELTA
        Flag: write residuals using δ coding.
        See Also:
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      • RESIDUALS_NIBBLE

        public static final int RESIDUALS_NIBBLE
        Flag: write residuals using variable-length nibble coding.
        See Also:
        Constant Field Values
      • RESIDUALS_GOLOMB

        public static final int RESIDUALS_GOLOMB
        Flag: write residuals using Golomb coding.
        See Also:
        Constant Field Values
      • REFERENCES_GAMMA

        public static final int REFERENCES_GAMMA
        Flag: write references using γ coding.
        See Also:
        Constant Field Values
      • REFERENCES_DELTA

        public static final int REFERENCES_DELTA
        Flag: write references using δ coding.
        See Also:
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      • REFERENCES_UNARY

        public static final int REFERENCES_UNARY
        Flag: write references using unary coding (default).
        See Also:
        Constant Field Values
      • BLOCK_COUNT_GAMMA

        public static final int BLOCK_COUNT_GAMMA
        Flag: write block counts using γ coding (default).
        See Also:
        Constant Field Values
      • BLOCK_COUNT_DELTA

        public static final int BLOCK_COUNT_DELTA
        Flag: write block counts using δ coding.
        See Also:
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      • BLOCK_COUNT_UNARY

        public static final int BLOCK_COUNT_UNARY
        Flag: write block counts using unary coding.
        See Also:
        Constant Field Values
      • OFFSETS_GAMMA

        public static final int OFFSETS_GAMMA
        Flag: write offsets using γ coding (default).
        See Also:
        Constant Field Values
      • OFFSETS_DELTA

        public static final int OFFSETS_DELTA
        Flag: write offsets using δ coding.
        See Also:
        Constant Field Values
      • outdegreeCoding

        protected int outdegreeCoding
        The coding for outdegrees. By default, we use γ coding.
      • blockCoding

        protected int blockCoding
        The coding for copy-block lists. By default, we use γ coding.
      • residualCoding

        protected int residualCoding
        The coding for residuals. By default, we use ζ coding.
      • referenceCoding

        protected int referenceCoding
        The coding for references. By default, we use unary coding.
      • blockCountCoding

        protected int blockCountCoding
        The coding for block counts. By default, we use γ coding.
      • offsetCoding

        protected int offsetCoding
        The coding for offsets. By default, we use γ coding.
    • Constructor Detail

      • BVGraph

        protected BVGraph()
    • Method Detail

      • numNodes

        public int numNodes()
        Description copied from class: ImmutableGraph
        Returns the number of nodes of this graph.

        Albeit this method is not optional, it is allowed that this method throws an UnsupportedOperationException if this graph has never been entirely traversed using a node iterator. This apparently bizarre behaviour is necessary to support implementations as ArcListASCIIGraph, which do not know the actual number of nodes until a traversal has been completed.

        Specified by:
        numNodes in class ImmutableGraph
        Returns:
        the number of nodes.
      • numArcs

        public long numArcs()
        Description copied from class: ImmutableGraph
        Returns the number of arcs of this graph (optional operation).
        Overrides:
        numArcs in class ImmutableGraph
        Returns:
        the number of arcs.
      • randomAccess

        public boolean randomAccess()
        Description copied from class: ImmutableGraph
        Checks whether this graph provides random access to successor lists.
        Specified by:
        randomAccess in class ImmutableGraph
        Returns:
        true if this graph provides random access to successor lists.
      • basename

        public CharSequence basename()
        Description copied from class: ImmutableGraph
        Returns a symbolic basename for this graph (optional operation).

        Implementors of this class may provide a basename (usually a pathname from which various files storing the graph are stemmed). This method is optional because it is sometimes unmeaningful (e.g., for one-off anonymous classes).

        Overrides:
        basename in class ImmutableGraph
        Returns:
        the basename.
      • maxRefCount

        public int maxRefCount()
        Returns the maximum reference count of this graph.
        Returns:
        the maximum reference count.
      • windowSize

        public int windowSize()
        Returns the window size of this graph.
        Returns:
        the window size.
      • readOffset

        protected final long readOffset​(InputBitStream ibs)
                                 throws IOException
        Reads an offset difference from the given stream.
        Parameters:
        ibs - an offset-file input bit stream.
        Returns:
        the next offset difference.
        Throws:
        IOException
      • writeOffset

        protected final int writeOffset​(OutputBitStream obs,
                                        long x)
                                 throws IOException
        Writes an offset difference to the given stream.
        Parameters:
        obs - an offset-file output bit stream.
        x - an offset difference to be stored in the stream.
        Returns:
        the number of bits written.
        Throws:
        IOException
      • readOutdegree

        protected final int readOutdegree​(InputBitStream ibs)
                                   throws IOException
        Reads an outdegree from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next outdegree.
        Throws:
        IOException
      • readOutdegree

        protected final int readOutdegree​(InputBitStream ibs,
                                          long offset)
                                   throws IOException
        Reads an outdegree from the given stream at a given offset.
        Parameters:
        ibs - a graph-file input bit stream.
        offset - the offset at which the stream must be positioned.
        Returns:
        the next outdegree.
        Throws:
        IOException
      • writeOutdegree

        protected final int writeOutdegree​(OutputBitStream obs,
                                           int d)
                                    throws IOException
        Writes an outdegree to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        d - an outdegree to be stored in the stream.
        Returns:
        the number of bits written.
        Throws:
        IOException
      • readReference

        protected final int readReference​(InputBitStream ibs)
                                   throws IOException
        Reads a reference from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next reference.
        Throws:
        IOException
      • writeReference

        protected final int writeReference​(OutputBitStream obs,
                                           int ref)
                                    throws IOException
        Writes a reference to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        ref - the reference.
        Returns:
        the number of bits written.
        Throws:
        IOException
      • readBlockCount

        protected final int readBlockCount​(InputBitStream ibs)
                                    throws IOException
        Reads a block count from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next block count.
        Throws:
        IOException
      • writeBlockCount

        protected final int writeBlockCount​(OutputBitStream obs,
                                            int count)
                                     throws IOException
        Writes a block count to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        count - the block count.
        Returns:
        the number of written bits.
        Throws:
        IOException
      • readBlock

        protected final int readBlock​(InputBitStream ibs)
                               throws IOException
        Reads a block from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next block.
        Throws:
        IOException
      • writeBlock

        protected final int writeBlock​(OutputBitStream obs,
                                       int block)
                                throws IOException
        Writes a block to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        block - the block.
        Returns:
        the number of written bits.
        Throws:
        IOException
      • readResidual

        protected final int readResidual​(InputBitStream ibs)
                                  throws IOException
        Reads a residual from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next residual.
        Throws:
        IOException
      • readLongResidual

        protected final long readLongResidual​(InputBitStream ibs)
                                       throws IOException
        Reads a long residual from the given stream.
        Parameters:
        ibs - a graph-file input bit stream.
        Returns:
        the next residual.
        Throws:
        IOException
      • writeResidual

        protected final int writeResidual​(OutputBitStream obs,
                                          int residual)
                                   throws IOException
        Writes a residual to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        residual - the residual.
        Returns:
        the number of written bits.
        Throws:
        IOException
      • writeResidual

        protected final int writeResidual​(OutputBitStream obs,
                                          long residual)
                                   throws IOException
        Writes a residual to the given stream.
        Parameters:
        obs - a graph-file output bit stream.
        residual - the residual.
        Returns:
        the number of written bits.
        Throws:
        IOException
      • successors

        public LazyIntIterator successors​(int x)
        Returns an iterator over the successors of a given node.
        Overrides:
        successors in class ImmutableGraph
        Parameters:
        x - a node.
        Returns:
        an iterator over the successors of the node.
      • successors

        protected LazyIntIterator successors​(int x,
                                             InputBitStream ibs,
                                             int[][] window,
                                             int[] outd)
                                      throws IllegalStateException
        Given an InputBitStream wrapping a graph file, returns an iterator over the successors of a given node x.

        This method can be used in two different ways:

        1. by providing a node and an input bit stream wrapping a graph file, it is possible to access the successor list of the node (provided that offsets have been loaded);
        2. by providing additional data, which essentially are used to keep some state about the graph, it is possible to perform an efficient sequential visit of all successor lists (even when no offsets were loaded).

        This method may modify the offset and the outdegree caches if window is null.

        Parameters:
        x - a node.
        ibs - an input bit stream wrapping a graph file. After this method returns, the state of ibs is undefined: however, after the iterator returned is exhausted, ibs will positioned just after the successor list of x.
        window - either null, or a double array with the following meaning: window[(x-i) mod windowSize] contains, for all i between 1 (inclusive) and windowSize (exclusive), the list of successors of node xi. If window is not null then ibs must be positioned before the successor list of x. This parameter will not be modified.
        outd - if window is not null, this is an array with as many elements as windowSize; outd[(x-i) mod windowSize] contains the outdegree of node xi for i greater than 0; at the end, this will be true also for i equal to 0.
        Returns:
        an iterator over the successors of x.
        Throws:
        IllegalStateException - if window is null and offsetType is 0.
      • nodeIterator

        public NodeIterator nodeIterator​(int from)
        This method returns a node iterator for scanning the graph sequentially, starting from the given node. It keeps track of a sliding window of windowSize() previous successor lists to speed up the iteration of graphs with significant referentiation.
        Overrides:
        nodeIterator in class ImmutableGraph
        Parameters:
        from - the node from which the iterator will iterate.
        Returns:
        a NodeIterator for accessing nodes and successors sequentially.
      • load

        public static BVGraph load​(CharSequence basename,
                                   int offsetType,
                                   ProgressLogger pl)
                            throws IOException
        Creates a new BVGraph by loading a compressed graph file from disk to memory.
        Parameters:
        basename - the basename of the graph.
        offsetType - the desired offset type (2 is memory mapping, 1 is normal random-access loading, 0 means that we do not want to load offsets at all, -1 that the we do not want even load the graph file).
        pl - a progress logger used while loading the graph, or null.
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the graph.
      • load

        public static BVGraph load​(CharSequence basename,
                                   int offsetType)
                            throws IOException
        Creates a new BVGraph by loading a compressed graph file from disk to memory, with no progress logger.
        Parameters:
        basename - the basename of the graph.
        offsetType - the desired offset type (2 is memory mapping, 1 is normal random-access loading, 0 means that we do not want to load offsets at all, -1 that the we do not want even load the graph file).
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the graph.
      • load

        public static BVGraph load​(CharSequence basename)
                            throws IOException
        Creates a new BVGraph by loading a compressed graph file from disk to memory, with no progress logger and all offsets.
        Parameters:
        basename - the basename of the graph.
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the graph.
      • load

        public static BVGraph load​(CharSequence basename,
                                   ProgressLogger pl)
                            throws IOException
        Creates a new BVGraph by loading a compressed graph file from disk to memory, with all offsets.
        Parameters:
        basename - the basename of the graph.
        pl - a progress logger used while loading the graph, or null.
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the graph.
      • loadMapped

        public static BVGraph loadMapped​(CharSequence basename,
                                         ProgressLogger pl)
                                  throws IOException
        Creates a new BVGraph by memory-mapping a graph file.
        Parameters:
        basename - the basename of the graph.
        pl - a progress logger used while loading the offsets, or null.
        Returns:
        an BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while memory-mapping the graph or reading the offsets.
      • loadMapped

        public static BVGraph loadMapped​(CharSequence basename)
                                  throws IOException
        Creates a new BVGraph by memory-mapping a graph file.
        Parameters:
        basename - the basename of the graph.
        Returns:
        an BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while memory-mapping the graph or reading the offsets.
      • loadOffline

        public static BVGraph loadOffline​(CharSequence basename,
                                          ProgressLogger pl)
                                   throws IOException
        Creates a new BVGraph by loading just the metadata of a compressed graph file.
        Parameters:
        basename - the basename of the graph.
        pl - a progress logger, or null.
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the metadata.
      • loadOffline

        public static BVGraph loadOffline​(CharSequence basename)
                                   throws IOException
        Creates a new BVGraph by loading just the metadata of a compressed graph file.
        Parameters:
        basename - the basename of the graph.
        Returns:
        a BVGraph containing the specified graph.
        Throws:
        IOException - if an I/O exception occurs while reading the metadata.
      • loadInternal

        protected BVGraph loadInternal​(CharSequence basename,
                                       int offsetType,
                                       ProgressLogger pl)
                                throws IOException
        Loads a compressed graph file from disk into this graph. Note that this method should be called only on a newly created graph.
        Parameters:
        basename - the basename of the graph.
        offsetType - the desired offset type (2 is memory-mapping, 1 is normal random-access loading, 0 means that we do not want to load offsets at all, -1 that the we do not want even load the graph file).
        pl - a progress logger used while loading the graph, or null.
        Returns:
        this graph.
        Throws:
        IOException - if an I/O exception occurs while reading the graph.
      • intervalize

        protected static int intervalize​(IntArrayList x,
                                         int minInterval,
                                         IntArrayList left,
                                         IntArrayList len,
                                         IntArrayList residuals)
        This method tries to express an increasing sequence of natural numbers x as a union of an increasing sequence of intervals and an increasing sequence of residual elements. More precisely, this intervalization works as follows: first, one looks at x as a sequence of intervals (i.e., maximal sequences of consecutive elements); those intervals whose length is ≥ minInterval are stored in the lists left (the list of left extremes) and len (the list of lengths; the length of an integer interval is the number of integers in that interval). The remaining integers, called residuals are stored in the residual list.

        Note that the previous content of left, len and residual is lost.

        Parameters:
        x - the list to be intervalized (an increasing list of natural numbers).
        minInterval - the least length that a maximal sequence of consecutive elements must have in order for it to be considered as an interval.
        left - the resulting list of left extremes of the intervals.
        len - the resulting list of interval lengths.
        residuals - the resulting list of residuals.
        Returns:
        the number of intervals.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 int windowSize,
                                 int maxRefCount,
                                 int minIntervalLength,
                                 int zetaK,
                                 int flags,
                                 int numberOfThreads,
                                 ProgressLogger pl)
                          throws IOException
        Writes the given graph using a given base name.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        windowSize - the window size (-1 for the default value).
        maxRefCount - the maximum reference count (-1 for the default value).
        minIntervalLength - the minimum interval length (-1 for the default value, NO_INTERVALS to disable).
        zetaK - the parameter used for residual ζ-coding, if used (-1 for the default value).
        flags - the flag mask.
        numberOfThreads - the number of threads to use; if 0 or negative, it will be replaced by Runtime.availableProcessors(). Note that if ImmutableGraph.numNodes() is not implemented by graph, the number of threads will be automatically set to one, possibly logging a warning.
        pl - a progress logger to log the state of compression, or null if no logging is required.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 int windowSize,
                                 int maxRefCount,
                                 int minIntervalLength,
                                 int zetaK,
                                 int flags,
                                 ProgressLogger pl)
                          throws IOException
        Writes the given graph using a given base name.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        windowSize - the window size (-1 for the default value).
        maxRefCount - the maximum reference count (-1 for the default value).
        minIntervalLength - the minimum interval length (-1 for the default value, NO_INTERVALS to disable).
        zetaK - the parameter used for residual ζ-coding, if used (-1 for the default value).
        flags - the flag mask.
        pl - a progress logger to log the state of compression, or null if no logging is required.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 int windowSize,
                                 int maxRefCount,
                                 int minIntervalLength,
                                 int zetaK,
                                 int flags)
                          throws IOException
        Writes the given graph using a given base name, without any progress logger.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        windowSize - the window size (-1 for the default value).
        maxRefCount - the maximum reference count (-1 for the default value).
        minIntervalLength - the minimum interval length (-1 for the default value, NO_INTERVALS to disable).
        zetaK - the parameter used for residual ζ-coding, if used (-1 for the default value).
        flags - the flag mask.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 int windowSize,
                                 int maxRefCount,
                                 int minIntervalLength,
                                 int zetaK,
                                 int flags,
                                 int numberOfThreads)
                          throws IOException
        Writes the given graph using a given base name, without any progress logger.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        windowSize - the window size (-1 for the default value).
        maxRefCount - the maximum reference count (-1 for the default value).
        minIntervalLength - the minimum interval length (-1 for the default value, NO_INTERVALS to disable).
        zetaK - the parameter used for residual ζ-coding, if used (-1 for the default value).
        flags - the flag mask.
        numberOfThreads - the number of threads to use; if 0 or negative, it will be replaced by Runtime.availableProcessors(). Note that if ImmutableGraph.numNodes() is not implemented by graph, the number of threads will be automatically set to one, possibly logging a warning.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 ProgressLogger pl)
                          throws IOException
        Writes the given graph using a given base name, with all parameters set to their default values.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        pl - a progress logger to log the state of compression, or null if no logging is required.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename,
                                 int numberOfThreads,
                                 ProgressLogger pl)
                          throws IOException
        Writes the given graph using a given base name, with all parameters set to their default values.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        numberOfThreads - the number of threads to use; if 0 or negative, it will be replaced by Runtime.availableProcessors(). Note that if ImmutableGraph.numNodes() is not implemented by graph, the number of threads will be automatically set to one, possibly logging a warning.
        pl - a progress logger to log the state of compression, or null if no logging is required.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • store

        public static void store​(ImmutableGraph graph,
                                 CharSequence basename)
                          throws IOException
        Writes the given graph using a given base name, without any progress logger and with all parameters set to their default values.
        Parameters:
        graph - a graph to be compressed.
        basename - a base name.
        Throws:
        IOException - if some exception is raised while writing the graph.
      • updateBins

        protected static void updateBins​(int currNode,
                                         int[] list,
                                         int length,
                                         long[] bin)
        Updates a list of exponential bins using the gaps a given list of strinctly increasing integers.
        Parameters:
        currNode - the current node.
        list - a strictly increasing list of integers.
        length - the number of valid elements in list.
        bin - the bins.
      • writeOffsets

        public void writeOffsets​(OutputBitStream obs,
                                 ProgressLogger pl)
                          throws IOException
        Write the offset file to a given bit stream.
        Parameters:
        obs - the output bit stream to which offsets will be written.
        pl - a progress logger, or null.
        Throws:
        IOException