Examples of computeHSA()

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

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          + 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()

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    }

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

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    double ans1 = 0, ans2 = 0;

    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    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()

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    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    hsaEngine2.computeHSA(t, s);
    ans1 = hsaEngine2.computeHSA(t, sR);

    // no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(), true);

    hsaEngine2.computeHSA(t, s);
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

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    ans1 = hsaEngine2.computeHSA(t, sR);

    // no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(), true);

    hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    Assert.assertEquals("Got a problem with the matchers", true,
        MathOperations.equals(ans1, ans2));
  }
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

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    // no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(), true);

    hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    Assert.assertEquals("Got a problem with the matchers", true,
        MathOperations.equals(ans1, ans2));
  }

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

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    // reuse
    HSA hsaEngine = new HSA(1, 1, cost, new OrderedMatcherFactory(), true);

    pruneRooted.calculateCost(t);
    pruneRooted.calculateCost(s);
    ans1 = hsaEngine.computeHSA(t, s);

    pruneUnrooted.calculateCost(t);
    pruneUnrooted.calculateCost(s);
    TIntArrayList[] tb = new TIntArrayList[3];
    ans2 = hsaEngine.computeHSA(t, s, tb);
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

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    ans1 = hsaEngine.computeHSA(t, s);

    pruneUnrooted.calculateCost(t);
    pruneUnrooted.calculateCost(s);
    TIntArrayList[] tb = new TIntArrayList[3];
    ans2 = hsaEngine.computeHSA(t, s, tb);
    for (int i = 0; i < tb[0].size(); i++) {
      System.out.println(tb[0].getQuick(i) + " -> " + tb[1].getQuick(i));
    }
    Assert.assertEquals("Should be unrooted alignment", false,
        MathOperations.equals(ans1, ans2));
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

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    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new OrderedMatcherFactory(),
        true);
    TIntArrayList[] trace = new TIntArrayList[3];
    ans1 = hsaEngine2.computeHSA(t, t, trace);

    Assert.assertEquals("trace should be the same", trace[0], trace[1]);
    ans2 = hsaEngine2.computeHSA(t, trace);
   
    System.out.println(ans1);
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Examples of bgu.bio.algorithms.graphs.hsa.HSA.computeHSA()

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        true);
    TIntArrayList[] trace = new TIntArrayList[3];
    ans1 = hsaEngine2.computeHSA(t, t, trace);

    Assert.assertEquals("trace should be the same", trace[0], trace[1]);
    ans2 = hsaEngine2.computeHSA(t, trace);
   
    System.out.println(ans1);
    System.out.println(ans2);

    Assert.assertEquals(
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