Examples of buildFromViennaFormat()

Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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public class TestSizeRelatedCostCalculator {
  @Test
  public void testSimple1(){
    RNASpecificTree t = new RNASpecificTree();
    t.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
   
    SizeRelatedTreePruning cost = new SizeRelatedTreePruning(1);
    cost.calculateCost(t);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA"
            .toCharArray(),
        "((..((........))(((.....)))....(.......)))...."
            .toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA"
            .toCharArray(),
        "((..((........))(((.....)))....(.......)))...."
            .toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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//    sR.buildFromViennaFormat(
//        "GGGAGUAUGUACCGAUAGGGUGAUUCCGGGCCCUUCGACNGGCUCCAUC"
//            .toCharArray(),
//        "(((((............((......))(((.))).(.....)))))).."
//            .toCharArray());
    sR.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    t.buildFromViennaFormat(
        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
    // "(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))".toCharArray());
    // s.buildFromViennaFormat("CCGGgGGAUCACCACGGCGGgGGAUCACCACGG".toCharArray(),
    // "((((.((....))))))(((.((....))))).".toCharArray());
    s.buildFromViennaFormat(
        "GGCGACACGGAUUCCAGUGCAUAUCUUAGUGAUACUCCAGUUAACUCCAUACUUUCCCUGCAAUACGCUAUUCGCCUCAGAUGUAUUUGGGUGGUUGCUCCACUAAAGCCCAGGAAUAUCCAGCCAGUUACAUUUGAGGCCAUUUGGGCUUAAGCGUAUUCCAUGGAAAGUUUUCUCCCCACAUUUCGGAAAUUAAAUUCCGAGCCAGCAAGAAAAUCUUCUCUGUUACAAUUUGACAUGGCUAAAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGGCGUAAUCUCAUACAAUGAUUACCCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAAAGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCAAGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUGCAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACUUAUAAAAACCCACAUUCUAUUUACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC"
            .toCharArray(),
        "((((..(((((((.((((((...((((((((((.................(((((((.((.((((((((....((((((((((((.((((...((((.(((...........))).)).))..)))).))))))))))))............)))))))).)).)))))))........................(((((((...((((((((((.((((.((((..((((((((.((((((((.(((.((.....((((((.....((((((((.(((((((.(((((...........))))))))..))))..))))))))...........))))))..........)).))).)).)))))).))))(.(((((.(((.........((((((((((((.......))))).))..)))))...............)))))))))..))))..))))....)))))))))))))).....)))))))..........................))))))))))...)))))).)))))))..))))"
            .toCharArray());
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
    final RNASpecificTree sR = new RNASpecificTree("S-Random");
    sR.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "GGGGGGGGuuuAAAAAAAAAAcccUUUUUUUUUUuuuGGGGGGcccUUUUUUuuuCCCCCCCC"
            .toCharArray(),
        "((((((((...((((((((((...))))))))))...((((((...))))))...))))))))"
            .toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
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