Package cern.jet.random.engine

Examples of cern.jet.random.engine.MersenneTwister


    if(!(argForward > 0 && argForward < 1) || !(argBackward > 0 && argBackward <= 1))
      throw new IllegalArgumentException("invalid scopes for backwards or forwards");
    visited = new HashSet<DeterministicVertex>();
    machine = new DirectedSparseGraph();
    vertices = new ArrayList<DeterministicVertex>();
    generator  = new MersenneTwister(seed);
    boolGenerator = new Random(seed);
    DeterministicVertex v=new DeterministicVertex(new VertexID(VertexID.VertKind.NEUTRAL,0));
    annotateVertex(v);
    machine.addVertex(v);
    vertices.add(v);// permits v to be chosen as a target, creating self-loops
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    if(!(argForward > 0 && argForward < 1) || !(argBackward > 0 && argBackward <= 1))
      throw new IllegalArgumentException("invalid scopes for backwards or forwards");
    visited = new HashSet<CmpVertex>();
    machine = new LearnerGraphND(Configuration.getDefaultConfiguration());
    vertices = new ArrayList<CmpVertex>();
    generator  = new MersenneTwister(seed);
    this.alphabet = alphabet;
    boolGenerator = new Random(seed);
    CmpVertex v= machine.generateNewCmpVertex(new VertexID(VertexID.VertKind.NEUTRAL,0), Configuration.getDefaultConfiguration())//new ();
    annotateVertex(v);
    vertices.add(v);// permits v to be chosen as a target, creating self-loops
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    if(!(argForward > 0 && argForward < 1) || !(argBackward > 0 && argBackward <= 1))
      throw new IllegalArgumentException("invalid scopes for backwards or forwards");
    visited = new HashSet<DeterministicVertex>();
    machine = new DirectedSparseGraph();
    vertices = new ArrayList<DeterministicVertex>();
    generator  = new MersenneTwister(seed);
    boolGenerator = new Random(seed);
    DeterministicVertex v=new DeterministicVertex(new VertexID(VertexID.VertKind.NEUTRAL,0));
    annotateVertex(v);
    machine.addVertex(v);
    vertices.add(v);// permits v to be chosen as a target, creating self-loops
View Full Code Here

    if(!(argForward > 0 && argForward < 1) || !(argBackward > 0 && argBackward <= 1))
      throw new IllegalArgumentException("invalid scopes for backwards or forwards");
    visited = new HashSet<DeterministicVertex>();
    machine = new DirectedSparseGraph();
    vertices = new ArrayList<DeterministicVertex>();
    generator  = new MersenneTwister(seed);
    boolGenerator = new Random(seed);
    DeterministicVertex v=new DeterministicVertex(new VertexID(VertexID.VertKind.NEUTRAL,0));
    annotateVertex(v);
    machine.addVertex(v);
    vertices.add(v);// permits v to be chosen as a target, creating self-loops
View Full Code Here

    if(!(argForward > 0 && argForward < 1) || !(argBackward > 0 && argBackward <= 1))
      throw new IllegalArgumentException("invalid scopes for backwards or forwards");
    visited = new HashSet<CmpVertex>();
    machine = new LearnerGraphND(Configuration.getDefaultConfiguration());
    vertices = new ArrayList<CmpVertex>();
    generator  = new MersenneTwister(seed);
    this.alphabet = alphabetArg;
    boolGenerator = new Random(seed);
    CmpVertex v= AbstractLearnerGraph.generateNewCmpVertex(new VertexID(VertexID.VertKind.NEUTRAL,0), Configuration.getDefaultConfiguration())//new ();
    annotateVertex(v);
    vertices.add(v);// permits v to be chosen as a target, creating self-loops
View Full Code Here

        if ((generatorClassValue == null)
                || generatorClassValue.equals("DRand")) {
            _randomNumberGenerator = new DRand((int) seedValue);
        } else if (generatorClassValue.equals("MersenneTwister (MT19937)")) {
            _randomNumberGenerator = new MersenneTwister((int) seedValue);
        } else if (generatorClassValue.equals("Ranecu")) {
            _randomNumberGenerator = new Ranecu((int) seedValue);
        } else if (generatorClassValue.equals("Ranlux")) {
            _randomNumberGenerator = new Ranlux((int) seedValue);
        } else if (generatorClassValue.equals("Ranmar")) {
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                dof[i]++;
                Csum[i] += C.get(i, j);
            }
        }

        mt = new MersenneTwister();

        // init beta distributions
        rowDistribution = new Beta[Csum.length];
        for ( int i = 0; i < Csum.length; i++ )
        {
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        for (int i = 0; i < Csum.length; i++)
        {
            //double alpha = Csum[i] - C.get(i, i) + 1;
            double alpha = Csum[i] + dof[i] - C.get(i, i) - 1;
            double beta = C.get(i, i) + 1;
            rowDistribution[i] = new Beta(alpha, beta, new MersenneTwister());
        }

        // check counts.
        if (!checkCounts())
        {
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        halfReadLength = readLength / 2;
        errorRate = QualityUtils.qualToErrorProb((byte)phredErrorRate);
        readQuals = new byte[readLength];
        Arrays.fill(readQuals, (byte)phredErrorRate);
        if ( samplingMode == ReadSamplingMode.POISSON )
           poissonRandom = new Poisson(readDepth, new MersenneTwister((int)RANDOM_SEED));
    }
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    }
    // LOGGING ->

    this.seed = seed;
    generators = new HashMap<String, RandomEngine>();
    generators.put(null, new MersenneTwister(seed));
   
    distributions = new HashMap<String, AbstractDistribution>();

    if (logger.isDebugEnabled()) {
      distributions.put(UNIFORM_DEFAULT, new UUniformDistributionController(generators.get(null)));
View Full Code Here

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