Package bgu.bio.adt.rna.costs

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

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    sR.shuffle(rand);
    sR.toFASTAFile("sR.fasta");
    sR.toDotFile("sR.dot", false);
    s.toDotFile("s.dot", false);
    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
View Full Code Here
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    sR.toFASTAFile("sR.fasta");
    sR.toDotFile("sR.dot", false);
    s.toDotFile("s.dot", false);
    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
View Full Code Here
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    sR.toDotFile("sR.dot", false);
    s.toDotFile("s.dot", false);
    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
   
View Full Code Here
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        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

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

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
View Full Code Here
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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();
View Full Code Here
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        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
    prune.calculateCost(t);
    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
    smooth.calculateCost(s);
View Full Code Here
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            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
    prune.calculateCost(t);
    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
View Full Code Here
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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);
View Full Code Here
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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));
View Full Code Here
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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));
    }
View Full Code Here
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