Examples of IIntGraph

Examples of stallone.api.graph.IIntGraph

120
121
122
123
124
125
126
127
128
129
130
        return (true);
    }

    private void calculateComponents()
    {
        IIntGraph g = new MatrixIntGraph(T);
        IntStrongConnectivity connectivity = new IntStrongConnectivity(g);
        connectivity.perform();

        List<IIntArray> C = connectivity.getStrongComponents();
//        int[][] C = g.BFS_mult();
View Full Code Here

Examples of stallone.api.graph.IIntGraph

42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
    {
        this.Q = _Q;
        this.A = _A;
        this.B = _B;

        IIntGraph g = graphNew.intMatrixGraph(_F);

        this.inA = new boolean[_F.rows()];
        for (int i = 0; i < A.length; i++)
            inA[A[i]] = true;
       
        inB = new boolean[_F.rows()];
        for (int i = 0; i < B.length; i++)
            inB[B[i]] = true;

        // convert double matrix into Big Decimals
        this.F = new SparseObjectMatrix2D(_F.rows(), _F.rows());
        for (int i=0; i<_F.rows(); i++)
            for (int j=0; j<_F.rows(); j++)
                if (_F.get(i,j) != 0)
                    F.set(i,j, new BigDecimal(_F.get(i,j)));

        // collect in- and outflux of every node
        this.influxes = new BigDecimal[_F.rows()];
        this.outfluxes = new BigDecimal[_F.rows()];
        for (int i=0; i<influxes.length; i++)
            {
                influxes[i] = BigDecimal.ZERO;
                outfluxes[i] = BigDecimal.ZERO;
            }

        for (int i=0; i<F.rows(); i++)
            for (int j=0; j<F.rows(); j++)
                {
                    if (F.get(i,j) != null)
                        {
                            influxes[j] = influxes[j].add((BigDecimal)F.get(i,j));
                            outfluxes[i] = outfluxes[i].add((BigDecimal)F.get(i,j));
                        }
                }

        // correct for rounding errors by iterating nodes with increasing committor.
        int[] IQ = doubleArrays.sortedIndexes(Q);
        for (int i=0; i<IQ.length; i++)
            {
                int s = IQ[i]; // this is the current node

                if (influxes[s].equals(BigDecimal.ZERO) ||
                    outfluxes[s].equals(BigDecimal.ZERO))
                    continue;

                BigDecimal err = outfluxes[s].subtract(influxes[s]); // difference between in and out

                // correct outflux.
                int[] neighbors = g.getNeighbors(s).getArray();

                int ilargest = 0;
                double flargest = _F.get(s,neighbors[0]);
                for (int j=1; j<neighbors.length; j++)
                    if (_F.get(s, neighbors[j]) > flargest)
View Full Code Here

Examples of stallone.api.graph.IIntGraph

343
344
345
346
347
348
349
350
351
352
353
    /**
       Checks if the current graph structure has a A->B reaction pathway
     */
    public boolean hasConnection(int[][] _E)
    {
  IIntGraph g = graphNew.intListGraph(_E);
  for (int i=0; i<A.length; i++)
      {
                int[] found = graph.bfs(g, A[i]);
    for (int j=0; j<found.length; j++)
        if (inB[found[j]])
View Full Code Here

Examples of stallone.api.graph.IIntGraph

44
45
46
47
48
49
50
51
52
53
54
        return (connectedComponents(P).size() == 1);
    }

    public List<IIntArray> connectedComponents(IDoubleArray P)
    {
        IIntGraph g = new MatrixIntGraph(P);
        IntStrongConnectivity connectivity = new IntStrongConnectivity(g);
        connectivity.perform();

        List<IIntArray> C = connectivity.getStrongComponents();
        return C;
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.