Examples of computeHSA()


Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    TIntArrayList[] alignment = new TIntArrayList[3];

    UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory,false);

    System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    double ans1 = 0,ans2 = 0;
   
    //reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    double temp = hsaEngine2.computeHSA(t, s);
    ans1 = hsaEngine2.computeHSA(t, sR);
   
    //no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

   
    //reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    double temp = hsaEngine2.computeHSA(t, s);
    ans1 = hsaEngine2.computeHSA(t, sR);
   
    //no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
   
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

   
    //no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
   
    temp = hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    if (!MathOperations.equals(ans1, ans2)){
      System.out.println("Got problem with matchers");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
   
    temp = hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    if (!MathOperations.equals(ans1, ans2)){
      System.out.println("Got problem with matchers");
    }
  }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    TIntArrayList[] alignment = new TIntArrayList[3];

    UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory);

    System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }

    System.out.println("\nCost s-t: " + hsa.computeHSA(s, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }

    System.out.println("\nCost t-t: " + hsa.computeHSA(t, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }

    System.out.println("\nCost s-s: " + hsa.computeHSA(s, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

    }

    long start = System.currentTimeMillis();
    int iters = 10000;
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, s);
    }
    System.out.println("\nTime of " + iters + " iterations for t-s: "
        + (System.currentTimeMillis() - start));

    start = System.currentTimeMillis();
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