Examples of calculateCost()

Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
   
   
   
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
   
   
   
    double ans1 = 0,ans2 = 0;
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
   
   
   
    double ans1 = 0,ans2 = 0;
   
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

    prune.calculateCost(t);
    smooth.calculateCost(t);

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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            .toCharArray(),
        "((((..(((((((.((((((...((((((((((.................(((((((.((.((((((((....((((((((((((.((((...((((.(((...........))).)).))..)))).))))))))))))............)))))))).)).)))))))........................(((((((...((((((((((.((((.((((..((((((((.((((((((.(((.((.....((((((.....((((((((.(((((((.(((((...........))))))))..))))..))))))))...........))))))..........)).))).)).)))))).))))(.(((((.(((.........((((((((((((.......))))).))..)))))...............)))))))))..))))..))))....)))))))))))))).....)))))))..........................))))))))))...)))))).)))))))..))))"
            .toCharArray());

    prune.calculateCost(s);
    smooth.calculateCost(s);

    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    // MatcherFactory matcherFactory = new OrderedMatcherFactory();
    HSA hsa = new HSA(cost, matcherFactory);
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    sR.shuffle(rand);
    prune.calculateCost(t);
    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);

    double ans1 = 0, ans2 = 0;
View Full Code Here

Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    prune.calculateCost(t);
    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);

    double ans1 = 0, ans2 = 0;

    // reuse
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);

    double ans1 = 0, ans2 = 0;

    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
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Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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        "UUUUUUUUUUuuuGGGGGGcccUUUUUUuuuCCCCCCCCcccGGGGGGGGuuuAAAAAAAAAA"
            .toCharArray(),
        "((((((((((...((((((...))))))...((((((((...))))))))...))))))))))"
            .toCharArray());

    smooth.calculateCost(t);
    smooth.calculateCost(s);

    double ans1 = 0, ans2 = 0;

    // reuse
View Full Code Here

Examples of bgu.bio.adt.rna.costs.RnaSpecificSmoothCost.calculateCost()

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            .toCharArray(),
        "((((((((((...((((((...))))))...((((((((...))))))))...))))))))))"
            .toCharArray());

    smooth.calculateCost(t);
    smooth.calculateCost(s);

    double ans1 = 0, ans2 = 0;

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