Examples of vertexSet()

Examples of org._3pq.jgrapht.UndirectedGraph.vertexSet()

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  {
    List models = TestInference.createTestModels ();
    for (Iterator mdlIt = models.iterator (); mdlIt.hasNext ();) {
      UndirectedModel mdl = (UndirectedModel) mdlIt.next ();
      UndirectedGraph g = Graphs.mdlToGraph (mdl);
      Set vertices = g.vertexSet ();

      // check the number of vertices
      assertEquals (mdl.numVariables (), vertices.size ());

      // check the number of edges
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeRoute.vertexSet()

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                }
            } else {
                if (haplotype.isReference()) {
                    referenceHaplotype = haplotype;
                    referenceRoute = haplotypeRoute;
                    referenceVertices = haplotypeRoute.vertexSet();
                    referenceBases = haplotypeRoute.getBases();
                }
                haplotypeRouteByHaplotype.put(haplotype, haplotypeRoute);
            }
        }
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph.vertexSet()

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   @Test(dataProvider="buildByStringDataProvider")
   public void testBuildByString(final String string, final int kmerSize, final int vertexCount, final int edgeCount) {
       final HaplotypeGraph g = new HaplotypeGraph(string);
       Assert.assertEquals(g.getKmerSize(),kmerSize,g.toString());
       Assert.assertEquals(g.vertexSet().size(),vertexCount,g.toString());
       Assert.assertEquals(g.edgeSet().size(),edgeCount,g.toString());
   }

   @Test(dataProvider="equalTestDataProvider")
   public void testEquals(final HaplotypeGraph one, final HaplotypeGraph two, final boolean expected) {
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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        // System.out.println("r:"+ bnodeRain.getName() + ":\n" +
        // cpf2string(VE.queryMarginal(bnodeRain)));
        // System.out.println("r:"+ bnodeWetGrass.getName() + ":\n" +
        // cpf2string(VE.queryMarginal(bnodeWetGrass)));
   
        Set<BNNode> nodes1 = bn.vertexSet();

        for (BNNode node : nodes1) {
            System.out.println(
                    node.getName() + ":\n" + node.getMarginal().toString()
                    + "\n");
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            // deb.doAll();
     
            inference.initialize(network, new JoinTreeCompiler());
            inference.run();
      
            Set<BNNode> nodes = network.vertexSet();

            for (BNNode node : nodes) {
        
                System.out.println(
                        node.getName() + ":\n" + node.getMarginal().toString()
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            // deb.doAll();

            inference.initialize(network, new JoinTreeCompiler());
            inference.run();

            Set<BNNode> nodes = network.vertexSet();

            for (BNNode node : nodes) {
                System.out.println(
                        node.getName() + ":\n" + node.getMarginal().toString()
                        + "\n");
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            inference.initialize(bn, new JoinTreeCompiler());
            // inference.setObservation("Cloudy", "true");
            inference.run();
       
            for (BNNode n : bn.vertexSet()) {
                System.out.println(n.getName() + ": " + n.getMarginal());
            }
       
        } catch (Exception e) {
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            if (network == null) {
                System.out.println("Problems with loading the  network");
                return;
            }

            Set<BNNode> nodes = network.vertexSet();

            System.out.println("CPTs of original network\n");
     
            for (BNNode node : nodes) {
                System.out.println(
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            inference.initialize(network, new JoinTreeCompiler());
            inference.run();
            // now, show the probabilities again
            // nodes = network.vertexSet();
            System.out.println("CPTs after learning\n");
            nodes = network.vertexSet();
            for (BNNode node : nodes) {
                System.out.println(
                        node.getName() + ":\n" + node.getFunction().toString()
                        + "\n");
            }
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Examples of org.integratedmodelling.riskwiz.bn.BeliefNetwork.vertexSet()

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            if (network == null) {
                System.out.println("Problems with loading the  network");
                return;
            }

            Set<BNNode> nodes = network.vertexSet();

            System.out.println("CPTs of original network\n");
     
            for (BNNode node : nodes) {
                System.out.println(
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