Examples of buildFromViennaFormat()

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

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

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    /*t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
        */
   
    t.buildFromViennaFormat(
        "GCCUGAAGGGACGCCUGAAGGGA".toCharArray(),
        "(((.....))).(((.....)))".toCharArray());
   
    prune.calculateCost(t);
    smooth.calculateCost(t);
 
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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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        { 1, 4 }, { 3, 5 }, { 4, 6, 10, 11, 16 }, { 5, 7 }, { 6, 8 },
        { 7, 9 }, { 8 }, { 5 }, { 5, 12 }, { 11, 13 }, { 12, 14 },
        { 13, 15 }, { 14 }, { 5 }, { 1 } };

    RNASpecificTree tree = new RNASpecificTree();
    tree.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());

    int[][] ans = tree.getEdges();
    Assert.assertEquals("The structure is not the same as expected", true,
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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  @Test
  public void testGroups() {

    RNASpecificTree tree = new RNASpecificTree();
    tree.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
    tree.groupByStructure();
    try {
      tree.toDotFile("/home/milon/tmp/1.dot", true);
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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  }

  @Test
  public void testEquals() {
    RNASpecificTree tree1 = new RNASpecificTree();
    tree1.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree2 = new RNASpecificTree();
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Examples of bgu.bio.adt.rna.RNASpecificTree.buildFromViennaFormat()

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        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree2 = new RNASpecificTree();
    tree2.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree3 = new RNASpecificTree();
View Full Code Here

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

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        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree3 = new RNASpecificTree();
    tree3.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUAUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree4 = new RNASpecificTree();
View Full Code Here

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

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        "CGACAGGAAACUGACAAACCCUAUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree4 = new RNASpecificTree();
    tree4.buildFromViennaFormat("CGACAGGAAACUGACAA".toCharArray(),
        "...((((...))))...".toCharArray());

    Assert.assertEquals("Trees should be the same", true,
        tree1.equals(tree2));
    Assert.assertEquals("Trees should not be the same", false,
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