List of computeHSA() Examples

Examples of computeHSA()

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

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

    System.out.println("\nTime of " + iters + " iterations for t-s: "
        + (System.currentTimeMillis() - start));


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


    start = System.currentTimeMillis();

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

    System.out.println("\nTime of " + iters + " iterations for s-t: "
        + (System.currentTimeMillis() - start));


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


    start = System.currentTimeMillis();

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

    System.out.println("\nTime of " + iters + " iterations for t-t: "
        + (System.currentTimeMillis() - start));


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


    String flowType;

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

  private static void checkTrees(Tree t, CostFunction w, Tree s) {
    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory);


    double cost = hsa.computeHSA(t, s, alignment);
    System.out.println("Cost: " + cost);
    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()

    int i = 0;
    int iters = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(t, s);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }

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

    }


    // checking for symmetry problems:


    alignment = new TIntArrayList[3];
    currCost = hsa.computeHSA(s, t, alignment);
    System.out.println("Cost: " + cost);
    for (int j = 0; j < alignment[0].size(); ++j) {
      System.out.print("(" + alignment[0].get(j) + ","
          + alignment[1].get(j) + "), ");
    }

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

    // checking for pooling problems:
    i = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(s, t);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }

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

    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    // MatcherFactory matcherFactory = new OrderedMatcherFactory();
    HSA hsa = new HSA(cost, matcherFactory);


    System.out.println("Cost: " + 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()

          + alignment[1].get(i) + "), ");
    }


    // System.out.println("\nCost: " + hsa.computeHSA(s, t,alignment));


    System.out.println("\nCost: " + 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()

    }


    long start = System.currentTimeMillis();
    int iters = 30;
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, s);
    }
    System.out.println("\nTime of " + iters + " iterations: "
        + (System.currentTimeMillis() - start));
    String flowType;
//    if (matcherFactory.make(3, 3) instanceof UnorderedBipartiteCavityMatcherMinCostMaxFlow) {

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