Examples of calculateCost()

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

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

    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
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Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning.calculateCost()

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    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);
    for (int i = 0; i < tb[0].size(); i++) {
      System.out.println(tb[0].getQuick(i) + " -> " + tb[1].getQuick(i));
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Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning.calculateCost()

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    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);
    for (int i = 0; i < tb[0].size(); i++) {
      System.out.println(tb[0].getQuick(i) + " -> " + tb[1].getQuick(i));
    }
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Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning.calculateCost()

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    t.buildFromViennaFormat(
        "GCCUGAAGGGACGCCUGAAGGGA".toCharArray(),
        "(((.....))).(((.....)))".toCharArray());
   
    prune.calculateCost(t);
    smooth.calculateCost(t);
   
    try {
      t.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
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Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning.calculateCost()

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

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

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

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

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

    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    // MatcherFactory matcherFactory = new OrderedMatcherFactory();
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Examples of bgu.bio.algorithms.graphs.costs.SizeRelatedTreePruning.calculateCost()

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    t.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
   
    SizeRelatedTreePruning cost = new SizeRelatedTreePruning(1);
    cost.calculateCost(t);
   
    Assert.assertEquals(17, t.getWeight(10, t.getNeighborIx(10, 5)),0.01);
    Assert.assertEquals(3, t.getWeight(6, t.getNeighborIx(6, 7)),0.01);
  }
}
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Examples of org.h2.table.Plan.calculateCost()

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                            bestPart = j;
                            break;
                        }
                        list[i] = filters[j];
                        Plan part = new Plan(list, i+1, condition);
                        double costNow = part.calculateCost(session);
                        if (costPart < 0 || costNow < costPart) {
                            costPart = costNow;
                            bestPart = j;
                        }
                    }
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Examples of org.h2.table.Plan.calculateCost()

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        }
    }

    private boolean testPlan(TableFilter[] list) {
        Plan p = new Plan(list, list.length, condition);
        double costNow = p.calculateCost(session);
        if (cost < 0 || costNow < cost) {
            cost = costNow;
            bestPlan = p;
            return true;
        }
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Examples of org.h2.table.Plan.calculateCost()

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                            bestPart = j;
                            break;
                        }
                        list[i] = filters[j];
                        Plan part = new Plan(list, i+1, condition);
                        double costNow = part.calculateCost(session);
                        if (costPart < 0 || costNow < costPart) {
                            costPart = costNow;
                            bestPart = j;
                        }
                    }
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