Package bgu.bio.adt.graphs

Examples of bgu.bio.adt.graphs.FlexibleUndirectedGraph

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  }

  @Test
  public void testUnDirectedDegeneracy3() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 52;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    int[][] edges = new int[][] { { 0, 9 }, { 0, 10 }, { 0, 11 },
        { 0, 12 }, { 0, 13 }, { 0, 17 }, { 0, 18 }, { 0, 19 },
        { 0, 20 }, { 0, 24 }, { 0, 30 }, { 0, 41 }, { 0, 45 },
        { 0, 46 }, { 0, 47 }, { 0, 48 }, { 1, 9 }, { 1, 10 },
        { 1, 11 }, { 1, 12 }, { 1, 17 }, { 1, 18 }, { 1, 19 },
        { 1, 20 }, { 1, 24 }, { 1, 30 }, { 1, 37 }, { 1, 41 },
        { 1, 45 }, { 1, 46 }, { 1, 47 }, { 1, 48 }, { 1, 49 },
        { 2, 9 }, { 2, 10 }, { 2, 11 }, { 2, 14 }, { 2, 17 },
        { 2, 18 }, { 2, 19 }, { 2, 20 }, { 2, 24 }, { 2, 36 },
        { 2, 41 }, { 2, 45 }, { 2, 46 }, { 2, 47 }, { 2, 48 },
        { 2, 49 }, { 3, 5 }, { 3, 9 }, { 3, 10 }, { 3, 11 }, { 3, 14 },
        { 3, 17 }, { 3, 18 }, { 3, 19 }, { 3, 20 }, { 3, 24 },
        { 3, 36 }, { 3, 41 }, { 3, 45 }, { 3, 46 }, { 3, 47 },
        { 3, 48 }, { 4, 11 }, { 4, 18 }, { 4, 22 }, { 4, 28 },
        { 4, 40 }, { 4, 41 }, { 4, 44 }, { 4, 45 }, { 4, 46 },
        { 4, 50 }, { 4, 51 }, { 5, 14 }, { 5, 24 }, { 5, 36 },
        { 5, 41 }, { 5, 45 }, { 5, 46 }, { 5, 47 }, { 5, 48 },
        { 6, 18 }, { 6, 46 }, { 6, 51 }, { 7, 12 }, { 7, 24 },
        { 7, 31 }, { 7, 34 }, { 7, 37 }, { 7, 39 }, { 7, 41 },
        { 7, 45 }, { 7, 46 }, { 7, 47 }, { 8, 24 }, { 8, 41 },
        { 8, 46 }, { 8, 47 }, { 9, 15 }, { 9, 22 }, { 9, 26 },
        { 9, 28 }, { 9, 34 }, { 9, 35 }, { 9, 36 }, { 9, 40 },
        { 9, 41 }, { 9, 44 }, { 9, 46 }, { 9, 51 }, { 10, 13 },
        { 10, 15 }, { 10, 16 }, { 10, 21 }, { 10, 23 }, { 10, 26 },
        { 10, 31 }, { 10, 34 }, { 10, 36 }, { 10, 39 }, { 10, 40 },
        { 10, 41 }, { 10, 44 }, { 10, 45 }, { 10, 46 }, { 10, 50 },
        { 10, 51 }, { 11, 18 }, { 11, 35 }, { 11, 36 }, { 11, 46 },
        { 11, 51 }, { 12, 27 }, { 12, 34 }, { 12, 36 }, { 12, 40 },
        { 12, 41 }, { 12, 44 }, { 12, 45 }, { 12, 46 }, { 12, 50 },
        { 12, 51 }, { 13, 17 }, { 13, 28 }, { 13, 34 }, { 13, 35 },
        { 13, 41 }, { 13, 46 }, { 14, 31 }, { 14, 34 }, { 14, 37 },
        { 14, 39 }, { 14, 41 }, { 14, 45 }, { 14, 46 }, { 14, 47 },
        { 14, 49 }, { 15, 35 }, { 15, 46 }, { 15, 48 }, { 15, 51 },
        { 16, 17 }, { 16, 28 }, { 16, 34 }, { 16, 35 }, { 16, 40 },
        { 16, 41 }, { 16, 44 }, { 16, 46 }, { 16, 51 }, { 17, 26 },
        { 17, 34 }, { 17, 36 }, { 17, 40 }, { 17, 41 }, { 17, 44 },
        { 17, 46 }, { 17, 51 }, { 19, 26 }, { 19, 27 }, { 19, 31 },
        { 19, 34 }, { 19, 36 }, { 19, 39 }, { 19, 40 }, { 19, 41 },
        { 19, 44 }, { 19, 45 }, { 19, 46 }, { 19, 50 }, { 19, 51 },
        { 20, 21 }, { 20, 23 }, { 20, 26 }, { 20, 34 }, { 20, 36 },
        { 20, 40 }, { 20, 41 }, { 20, 44 }, { 20, 45 }, { 20, 46 },
        { 20, 50 }, { 20, 51 }, { 21, 28 }, { 21, 35 }, { 21, 51 },
        { 22, 48 }, { 22, 51 }, { 23, 35 }, { 23, 36 }, { 23, 40 },
        { 23, 41 }, { 23, 44 }, { 23, 51 }, { 24, 31 }, { 24, 34 },
        { 24, 35 }, { 24, 36 }, { 24, 40 }, { 24, 41 }, { 24, 44 },
        { 24, 45 }, { 24, 51 }, { 25, 41 }, { 25, 45 }, { 26, 35 },
        { 26, 48 }, { 26, 51 }, { 27, 34 }, { 27, 35 }, { 27, 39 },
        { 27, 49 }, { 28, 36 }, { 28, 48 }, { 28, 51 }, { 29, 41 },
        { 29, 45 }, { 30, 34 }, { 30, 36 }, { 30, 39 }, { 30, 40 },
        { 30, 41 }, { 30, 44 }, { 30, 45 }, { 30, 50 }, { 30, 51 },
        { 31, 34 }, { 31, 36 }, { 31, 40 }, { 31, 41 }, { 31, 44 },
        { 31, 51 }, { 33, 49 }, { 34, 40 }, { 34, 51 }, { 35, 36 },
        { 35, 51 }, { 37, 50 }, { 39, 45 }, { 39, 51 }, { 40, 51 },
        { 44, 51 }, { 47, 50 }, { 47, 51 }, { 48, 51 }, { 49, 50 } };

    for (int i = 0; i < edges.length; i++) {
      graph.addEdge(edges[i][0], edges[i][1]);
    }
    Assert.assertEquals("wrong degeneracy", 9, graph.degeneracy());

  }
View Full Code Here
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  }

  @Test
  public void testJSON() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 52;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    int[][] edges = new int[][] { { 0, 9 }, { 0, 10 }, { 0, 11 },
        { 0, 12 }, { 0, 13 }, { 0, 17 }, { 0, 18 }, { 0, 19 },
        { 0, 20 }, { 0, 24 }, { 0, 30 }, { 0, 41 }, { 0, 45 },
        { 0, 46 }, { 0, 47 }, { 0, 48 }, { 1, 9 }, { 1, 10 },
        { 1, 11 }, { 1, 12 }, { 1, 17 }, { 1, 18 }, { 1, 19 },
        { 1, 20 }, { 1, 24 }, { 1, 30 }, { 1, 37 }, { 1, 41 },
        { 1, 45 }, { 1, 46 }, { 1, 47 }, { 1, 48 }, { 1, 49 },
        { 2, 9 }, { 2, 10 }, { 2, 11 }, { 2, 14 }, { 2, 17 },
        { 2, 18 }, { 2, 19 }, { 2, 20 }, { 2, 24 }, { 2, 36 },
        { 2, 41 }, { 2, 45 }, { 2, 46 }, { 2, 47 }, { 2, 48 },
        { 2, 49 }, { 3, 5 }, { 3, 9 }, { 3, 10 }, { 3, 11 }, { 3, 14 },
        { 3, 17 }, { 3, 18 }, { 3, 19 }, { 3, 20 }, { 3, 24 },
        { 3, 36 }, { 3, 41 }, { 3, 45 }, { 3, 46 }, { 3, 47 },
        { 3, 48 }, { 4, 11 }, { 4, 18 }, { 4, 22 }, { 4, 28 },
        { 4, 40 }, { 4, 41 }, { 4, 44 }, { 4, 45 }, { 4, 46 },
        { 4, 50 }, { 4, 51 }, { 5, 14 }, { 5, 24 }, { 5, 36 },
        { 5, 41 }, { 5, 45 }, { 5, 46 }, { 5, 47 }, { 5, 48 },
        { 6, 18 }, { 6, 46 }, { 6, 51 }, { 7, 12 }, { 7, 24 },
        { 7, 31 }, { 7, 34 }, { 7, 37 }, { 7, 39 }, { 7, 41 },
        { 7, 45 }, { 7, 46 }, { 7, 47 }, { 8, 24 }, { 8, 41 },
        { 8, 46 }, { 8, 47 }, { 9, 15 }, { 9, 22 }, { 9, 26 },
        { 9, 28 }, { 9, 34 }, { 9, 35 }, { 9, 36 }, { 9, 40 },
        { 9, 41 }, { 9, 44 }, { 9, 46 }, { 9, 51 }, { 10, 13 },
        { 10, 15 }, { 10, 16 }, { 10, 21 }, { 10, 23 }, { 10, 26 },
        { 10, 31 }, { 10, 34 }, { 10, 36 }, { 10, 39 }, { 10, 40 },
        { 10, 41 }, { 10, 44 }, { 10, 45 }, { 10, 46 }, { 10, 50 },
        { 10, 51 }, { 11, 18 }, { 11, 35 }, { 11, 36 }, { 11, 46 },
        { 11, 51 }, { 12, 27 }, { 12, 34 }, { 12, 36 }, { 12, 40 },
        { 12, 41 }, { 12, 44 }, { 12, 45 }, { 12, 46 }, { 12, 50 },
        { 12, 51 }, { 13, 17 }, { 13, 28 }, { 13, 34 }, { 13, 35 },
        { 13, 41 }, { 13, 46 }, { 14, 31 }, { 14, 34 }, { 14, 37 },
        { 14, 39 }, { 14, 41 }, { 14, 45 }, { 14, 46 }, { 14, 47 },
        { 14, 49 }, { 15, 35 }, { 15, 46 }, { 15, 48 }, { 15, 51 },
        { 16, 17 }, { 16, 28 }, { 16, 34 }, { 16, 35 }, { 16, 40 },
        { 16, 41 }, { 16, 44 }, { 16, 46 }, { 16, 51 }, { 17, 26 },
        { 17, 34 }, { 17, 36 }, { 17, 40 }, { 17, 41 }, { 17, 44 },
        { 17, 46 }, { 17, 51 }, { 19, 26 }, { 19, 27 }, { 19, 31 },
        { 19, 34 }, { 19, 36 }, { 19, 39 }, { 19, 40 }, { 19, 41 },
        { 19, 44 }, { 19, 45 }, { 19, 46 }, { 19, 50 }, { 19, 51 },
        { 20, 21 }, { 20, 23 }, { 20, 26 }, { 20, 34 }, { 20, 36 },
        { 20, 40 }, { 20, 41 }, { 20, 44 }, { 20, 45 }, { 20, 46 },
        { 20, 50 }, { 20, 51 }, { 21, 28 }, { 21, 35 }, { 21, 51 },
        { 22, 48 }, { 22, 51 }, { 23, 35 }, { 23, 36 }, { 23, 40 },
        { 23, 41 }, { 23, 44 }, { 23, 51 }, { 24, 31 }, { 24, 34 },
        { 24, 35 }, { 24, 36 }, { 24, 40 }, { 24, 41 }, { 24, 44 },
        { 24, 45 }, { 24, 51 }, { 25, 41 }, { 25, 45 }, { 26, 35 },
        { 26, 48 }, { 26, 51 }, { 27, 34 }, { 27, 35 }, { 27, 39 },
        { 27, 49 }, { 28, 36 }, { 28, 48 }, { 28, 51 }, { 29, 41 },
        { 29, 45 }, { 30, 34 }, { 30, 36 }, { 30, 39 }, { 30, 40 },
        { 30, 41 }, { 30, 44 }, { 30, 45 }, { 30, 50 }, { 30, 51 },
        { 31, 34 }, { 31, 36 }, { 31, 40 }, { 31, 41 }, { 31, 44 },
        { 31, 51 }, { 33, 49 }, { 34, 40 }, { 34, 51 }, { 35, 36 },
        { 35, 51 }, { 37, 50 }, { 39, 45 }, { 39, 51 }, { 40, 51 },
        { 44, 51 }, { 47, 50 }, { 47, 51 }, { 48, 51 }, { 49, 50 } };

    for (int i = 0; i < edges.length; i++) {
      graph.addEdge(edges[i][0], edges[i][1]);
    }

    try {
      JSONObject json = graph.toJSON();
      FlexibleUndirectedGraph graph2 = FlexibleUndirectedGraph
          .fromJSON(json);
      Assert.assertEquals("Wrong number of nodes", graph.getNodeNum(),
          graph2.getNodeNum());
      Assert.assertEquals("Wrong number of edges", graph.getEdgeNum(),
          graph2.getEdgeNum());
      for (int i = 0; i < edges.length; i++) {
        Assert.assertEquals("Missed an edge in the new graph "
            + edges[i][0] + " " + edges[i][1], true,
            graph2.isNeighbours(edges[i][0], edges[i][1]));
      }
    } catch (JSONException e) {
      Assert.fail("Got error in JSON format " + e.getMessage());
    }
View Full Code Here
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public class TestWeightedClique {

  @Test
  public void testClique1() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 9;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    graph.addEdge(1, 2);
    graph.addEdge(1, 3);
    graph.addEdge(2, 3);
    graph.addEdge(3, 4);
    graph.addEdge(3, 5);
    graph.addEdge(3, 6);
    graph.addEdge(4, 5);
    graph.addEdge(4, 6);
    graph.addEdge(5, 6);

    WeightedCliqueTree clique = new WeightedCliqueTree();
    clique.setGraph(graph);
    double[] weights = new double[] { 1, 1, 1, 1, 1, 1, 1, 1 };
    IntDoublePair[] nodesAsPairs = new IntDoublePair[8];
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        clique.potential());
  }

  @Test
  public void testClique2() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 8;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    graph.addEdge(1, 2);
    graph.addEdge(1, 3);
    graph.addEdge(1, 4);
    graph.addEdge(1, 7);

    graph.addEdge(2, 3);
    graph.addEdge(2, 5);
    graph.addEdge(2, 7);

    graph.addEdge(3, 6);
    double[] weights = new double[] { 1, 1, 10, 3.4, 1, 1, 1, 1 };
    IntDoublePair[] nodesAsPairs = new IntDoublePair[8];
    for (int i = 0; i < nodesAsPairs.length; i++) {
      nodesAsPairs[i] = new IntDoublePair(i, weights[i]);
    }
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public class TestMaximalWeightedClique {
  private boolean useTimeout = true;

  @Test
  public void testUnDirectedClique1() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addEdge(0, 1);
    graph.addEdge(0, 4);
    graph.addEdge(0, 3);
    graph.addEdge(3, 2);
    graph.addEdge(5, 3);
    graph.addEdge(4, 3);
    MaximalWeightedClique maximalWeightedClique = new MaximalWeightedClique();
    maximalWeightedClique.setGraph(graph);
    TIntArrayList ans = maximalWeightedClique
        .findMaximumWeightedClique(new double[] { 1, 1, 1, 1, 1, 1, 1 });
    ans.sort();
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        new int[] { 0, 3, 4 }, arr);
  }
 
  @Test
  public void testUnDirectedCliqueOnSingles() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    graph.addNode();
    MaximalWeightedClique maximalWeightedClique = new MaximalWeightedClique();
    maximalWeightedClique.setGraph(graph);
    TIntArrayList ans = maximalWeightedClique
        .findMaximumWeightedClique(new double[] { 1, 1, 5, 1, 1, 1, 1 });
    ans.sort();
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        new int[] { 2 }, arr);
  }

  @Test
  public void testUnDirectedClique2() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 10;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    for (int i = 0; i < nodes; i++) {
      for (int j = i + 1; j < nodes; j++) {
        graph.addEdge(i, j);
      }
    }
    double[] weights = new double[nodes];
    for (int i = 0; i < nodes; i++) {
      weights[i] = 1;
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    Assert.assertArrayEquals("Found the wrong clique", expected, arr);
  }

  @Test
  public void testUnDirectedClique3() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 6;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    graph.addEdge(0, 5);
    graph.addEdge(2, 5);
    double[] weights = new double[] { 23.7600228881836, 10.149999618530273,
        10.559999465942383, 12.0100228881836, 18.53999900817871,
        29.6900534057617 };
    MaximalWeightedClique maximalWeightedClique = new MaximalWeightedClique();
    maximalWeightedClique.setGraph(graph);
View Full Code Here
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    Assert.assertArrayEquals("Found the wrong clique", expected, arr);
  }

  @Test
  public void testUnDirectedCliqueMandatory1() {
    FlexibleUndirectedGraph graph = new FlexibleUndirectedGraph();
    int nodes = 9;
    for (int i = 0; i < nodes; i++) {
      graph.addNode();
    }

    graph.addEdge(1, 2);
    graph.addEdge(1, 3);
    graph.addEdge(2, 3);
    graph.addEdge(3, 4);
    graph.addEdge(3, 5);
    graph.addEdge(3, 6);
    graph.addEdge(4, 5);
    graph.addEdge(4, 6);
    graph.addEdge(5, 6);
    double[] weights = new double[] { 20, 10, 10, 10, 2, 11, 2, 1, 1 };
    MaximalWeightedClique maximalWeightedClique = new MaximalWeightedClique();
    maximalWeightedClique.setGraph(graph);

    TIntArrayList ans = maximalWeightedClique
View Full Code Here
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Related Classes of bgu.bio.adt.graphs.FlexibleUndirectedGraph

  • bgu.bio.algorithms.graphs.MaximalWeightedClique
  • bgu.bio.algorithms.graphs.TestFlexibleGraphs
  • bgu.bio.algorithms.graphs.TestMaximalWeightedClique
  • bgu.bio.algorithms.graphs.TestWeightedClique
  • bgu.bio.io.file.json.JSONArray
  • bgu.bio.io.file.json.JSONObject
  • gnu.trove.list.array.TIntArrayList
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