Examples of RNASpecificTree

bgu.bio.adt.rna.RNASpecificTree
The Class RNASpecificTree is a tree representation of RNA secondary structure. in this representation each base-pair is a node and each interval bases (loops) are also nodes. the supported loops are hairpin, multi internal and external. This tree class is not Thread safe. multiple threads can read it but some methods (e.g. {@link #shuffle()}) may change the internal state of the tree.

Examples of bgu.bio.adt.rna.RNASpecificTree

        { 7, 9 }, { 8 }, { 5 }, { 5, 12 }, { 11, 13 }, { 12, 14 },
        { 13, 15 }, { 14 }, { 5 }, { 1 }, { 1, 19 }, { 18, 20 },
        { 19, 21 }, { 20, 22 }, { 21, 23 }, { 22, 24 }, { 23, 25 },
        { 24 } };


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


    int[][] ans = tree.getEdges();


    Assert.assertEquals("The structure is not the same as expected", true,
        MatrixUtils.equals(ans, correct));
  }

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Examples of bgu.bio.adt.rna.RNASpecificTree

        { 49, 52 }, { 51, 53 }, { 52, 54 }, { 53, 55 }, { 54, 56 },
        { 55, 57 }, { 56, 58 }, { 57 }, { 49 }, { 49, 61 }, { 60, 62 },
        { 61, 63 }, { 62, 64 }, { 63, 65 }, { 64 }, { 49 }, { 42 },
        { 8 } };


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


    int[][] ans = tree.getEdges();
    Assert.assertEquals("The structure is not the same as expected", true,
        MatrixUtils.equals(ans, correct));
  }

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Examples of bgu.bio.adt.rna.RNASpecificTree

  }


  @Test
  public void testShuffle1() {
    System.out.println("Test Shuffle");
    RNASpecificTree tree1 = new RNASpecificTree();
    tree1.buildFromViennaFormat(
        "aaaaaaAAAgggggggAAaaaaaAAAuuuuuAAuuuuAAAaaAaaAAccccAcccAAAAAAgggAAAgggggAAccccccAAAggggggAAaaaaAAAAAuuuuAAcccccAAAcccAAAAuuuuuu"
            .toCharArray(),
        "((((((...(((((((..(((((...)))))..((((...)).))..)))).)))......(((...(((((..((((((...))))))..((((.....))))..)))))...)))....))))))"
            .toCharArray());


    RNASpecificTree tree2 = new RNASpecificTree();
    tree2.buildFromViennaFormat(
        "aaaaaaAAAgggggggAAaaaaaAAAuuuuuAAuuuuAAAaaAaaAAccccAcccAAAAAAgggAAAgggggAAccccccAAAggggggAAaaaaAAAAAuuuuAAcccccAAAcccAAAAuuuuuu"
            .toCharArray(),
        "((((((...(((((((..(((((...)))))..((((...)).))..)))).)))......(((...(((((..((((((...))))))..((((.....))))..)))))...)))....))))))"
            .toCharArray());
    tree2.shuffle();
    tree2.shuffle();


    Assert.assertEquals(
        "The probabilty is slim!, can't get the same tree after the shuffle",
        false, tree1.equals(tree2));
  }

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Examples of bgu.bio.adt.rna.RNASpecificTree

        false, tree1.equals(tree2));
  }


  @Test
  public void testToViennaFormat() {
    RNASpecificTree tree = new RNASpecificTree();
    char[] sequence = "GGGGCAGAGAACCUAAGCCGUCUGGUGGAUGGCUCGGCUCGGGGCGCCGACGAAGGGCGUGGCAAGCUGCGAUAAGCCCCGGCGAGGCGCAGGCAGCCGUCGAACCGGGGAUUCCCGAAUGGGACCUCCCGCGGCUUUUGCCGCACUCCCAGUCGGGAGGGGGAACGCGGGGAAUUGAAACAUCUUAGUACCCGCAGGAAAAGAAAGCAAAAGCGAUGCCGUUAGUAGGGGCGACCGAAAGCGGCACAGGGCAAACUGAACCCUCCGGGGAAACCCGGAGGGGAUGUGGUGUAGUAGGGCCCUGCACUGGAGCCUCGAGGGUGAAGCCGAAGUCCGCUGGAACGCGGCGCCGUAGAGGGUGAAAGCCCCGUAGGCGUAAGCCCUCAGGCUCCUGCAGGGUUCCUGAGUACCGUCGGUCGGAUAUCCGGCGGGAAGCUGGGAGGCAUCGGCUCCCAACCCUAAAUACGUCCCGAGACCGAUAGCGAACUAGUACCGUGAGGGAAAGCUGAAAAGCACCCCUGGCAGGGGGUGAAAAGAGCCUGAAACCAGACGGCGAUAGGUGGGUGCGGCCCGAAAGGGUUGACCCUCCCCGAAGGAAACACGGGCGACCGUGGAGUACGAGGGGAGGCGACCGGGGUUGCACCGUCCGUCUUGGAUCACGGGGCAGGGAGUUCACGGCCGUGGCGAGGUUAAGGGGGUUAACCCCGAAGCCACAGGGAAACCGACAGGUCCGCAGCCCGUAAGGGUGAGGGACGGGGUGUGAAAGCGCCCGGAGUCACGGCCGUGAGACCCGAAGCCGGUCGAUCUAGCCCGGGGCAGGGUGAAGUCCCUCAACAGAGGGAUGGAGGCCCGAUAGGGGUGCUGACGUGCAAUUCGCUCCCGUGACCCCGGGCUAGGGGUGAAAGGCCAAUCGAGGCCGGCGAUAGCUGGUUCCCGCCGAAUUAUCCCUCAGGAUAGCCCGGCCGGAGGUAGGUGGUGGGGUAGAGCACUGAUUGGGGGUUUAGGGGGAGAAAUCCCCCGGCUCCCUGUCAAACUCCGAACCCACUGCCGCCGUAGAAGGCCGGAGUAGGGUGACGGUGUAAGCCGUCAACCGAGAGGGGAACAACCCAGACCGGGGUUAAGGCCCCUAAAUGCCGGCUAAGUGUUACUCCAAAGGGCGUCCCUGGCCUUAGACAGCGGGGAGGUAGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGCUCACCCGUCGAGGUCAGGGGCCCCGAAAAUGGACGGGGCUUAAGCCGGCUGCCGAGACCCCGGCGCACGGACCGAUUGGUCCGUGAUCGGGUAGGCGGGCGUGCCGGUGGGGUGGAAGCCGGGCCGUAAGGUCCGGUGGACCCGUCGGUAUUGUGGAUCCUGCCGGGAGUAGCAGCAUAGCCGGGUGAGAAUCCCGGCCGCCGAAGGGGCCAGGGUUCCACGGCAAUGUUCAUCAGCCGUGGGUUAGUCGGUCCUAAGCCAGUCCGUAACUCGGCGCUGGCGAAAGGGAAACGGGUUUAUAUUCCCGUACCGCGGUGGUAGGUGCGGCAACGCAAGCCCGAGGGGUGACGCCUCGGGGUAGGCGGACCGGCCCACAAGGCCGGCUAAGCGUAUAAGUCCGGGGAGUGCCGUAAUGGCGAGAACCGGAUGAAAGCGCGAAUGGCCUCCCGUAAGGGGGGUUCCGCCGAUCCCUGGGGCCCGUGAAAAGCCCUCGGGAACGAUCCACCGCGACCGUACCGAGAACCGACACAGGUGCCCCUGGGUGAGAAGCCUAAGGCGUGUCGGGGGAAACCCAGCCGAGGGAACUCGGCAAAUUGGCCCCGUAACUUCGGGAUAAGGGGUGCCUGCGGGUGCGUAACCCGCAGGUCGCAGUGACUCGGGGGACCCGACUGUUUAGUAAAAACACAGGUCCCAGCUAGCCCGAAAGGGUUUGUACUGGGGCCGACGCCUGCCCAGUGCCGGUAUGUGAAGCCCGGGUCCAACCGGGUGAAGCACCGGUAAACGGCGGGGGUAACUAUAACCCUCUUAAGGUAGCGAAAUUCCUUGUCGGUUAAAUGCCGACCUGCAUGAAUGGCGUAACGAGGUCCCCACUGUCCCCGGCUGGGGCCCGGCGAAACCACUGCCAGGCGCAUAUGCCUGGGACCUCCGGUGGGAAGCGAAGACCCCAUGGAGCUUUACUGCAGCCUGCCGUUGCCGUACGGCGGGGGGUGCGCAGCGUAGGCGGGAGGCGUCGAAGCCCGCCUUCCGGGGCGGGUGGAGCCGUCCAUGAGACACCGCCCACCCUCUGCCGUACGGCUAACCCCCGACGGGGGGACAGCGGUAGGUGGGCAGUUUGGCUGGGGCGGCACACCCUCGAAAAGGUAUCGAGGGUGCCCUAAGGUCGGCUCAGGCGGGUCAGGAAUCCGCCGUAGAGUGCAAGGGCAAAAGCCGGCCUGACUGGACCCGUAACAGAGGCGGGUCCAGCCGCGAAAGCGUGGCCUAGCGAACCCCUGUGCCUCCCCGGUGGGGGCCAGGGAUGACAGAAAAGCUACCCUGGGGAUAACAGAGUCGUCUCGGGCGAGAGCCCAUAUCGACCCCGAGGCUUGCUACCUCGCUGUCGGCUCUUCCCAUCCUGGCCCUGCAGCAGGGGCCAAGGGUGGGGGUGUUCACCCAUUAAAGGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUCGGAUGCUAUCUACCGGAGGUGUUGGCCGCCUGAGGGGAAGGCUCCCCCAGUACGAGAGGAACAGGGAGCCGCGGCCUCUGGUCUACCGGUUGUCCUACAGGGCACAGCCGGGCAGCUACGCCGUGUCCGAUAAGGCCUGAAAGCAUCUAAGGCCGAAGCGGUCCCCGAAAAUAGGCGGCCACUCCCAGGCGCAGGGGGUCGGGCGACCGGUCCUUUGCCUGGGACGAGGGCUCGGGAAGAAGACCCGUUUGAUGGGGCGGGGAUGUAAGCGGGAAGGGAAACCGACCCGUUCAGUCUGCCGCUCCCAAUCGCCCGAGGUUUCUGCCUC"
        .toCharArray();
    char[] structrue = "(((((((((......((((((((((.....(((..(((((((((((.......(((((((........))).....((((((...(((.......)))......))))))...))))...(((....)))(((((....))))).(((((....)))))......((((((.....((....))......))))).).........((....))...(((((.....((.....))....)))))..((((....(((..(((((((((....)))))))))....))).......((((((((((..(((((((.((((((...(((...(.((((......)))))..(...).(((.......)))...)))....)))))))))))))))))))).)))......(((((((........)))))))......(((((.......)))))..)))).....))))))))).))...............((....))....)).........((((.....))))...........).....)))))))))).......((((((((((....((......(((((((...(....(((((....))))).....)..)))))))...)).))))))))))..((((........))))((((((....(((((((((((((..((((..((((.....))))..))))...((....)).....((((...((((....))))...))))..(((((....)))))....)))))))))))))..((.(...((((((...((((((((((((.((((...(((((((....)))))))....))))....((((.((.((........))))))))..).))))))))))).(((.....)))......))))))......).))..((((((....(((((....))))).(((((((...(((.((((((((....(((...((((((((((((..((((((....))))))))))))))))))..)).)....)))))))))))......)))))).)..(((((((((......)))))))))....(((......)))...(((((((...(((......(.((((((................(((.((((((((((.......(((((.(((..(((.........)))..)))(...)(...((......)).).)))))...)))))))))))))...................))))))))))...)))))))((((((((((....))))))))..))....))))))(.((((((((((......((((((((....))))))))...))))))))))..).....))))))...............((((((.......))))))((((....((((..((...((((((...((.....)).))))))......((((((...(((((((((.....))).))))))....))...(((((........)))))..(((((((((((.((((....))))..(((((.((((...(((((((((..((((((((((((.....)))))))...((((....((((((((((((((.....))))))))))))))....)))).....(((((((....))))))).)))))...))))))))).........)))))))))..))).))))))))))))..)).....((......)).)))).((((.......)))).))))...((((.....((((((((((((..............(((((...((....))....)))))((((((((((.....))))))))))(...).......(((((((((..(((.........)))..(((((((((..((((....))))..)..))))))))..((((.(((..(((((((..(((....(((((......)))))....))))))))..)))))((((((.......))))))(...)...............((((((.....))))))..........))))...)).)))))))....)))))))))))).))))............(((((........)))))..((((((((.(((.((......((((.(((((((.((((...(((((((..((((((((((((((((((.........(((((..(((......((((((((....))))))))...)))............)))))))))))))))))))))))...(((((...))))).....)))))))....))))..((((.....))).)((((((...........))))))..((....((((((((.((((((.......))))))...))((......))....))))))....(((((((((.........))))))))).(((....))).))..........(((((.(((((.......)))))))))).........)))))..))))))........(((.((((((((...((.......))...)))))))..))))..........(((((((((((..((.((((((......))))))...)).(((((.....))))).....)))))..)..)))).).....(((((((....))).))))....))..)))))))))))....((((((((..((((..((((((((...............))))))))(((((...(((....((((((((((....)))))..)))))....))).)))))..(((....(((((...........)))))....))).))))......))))))))..((((((((..((((((((((....))))))))))))))))))...(((((((((.......)))))....(((((((((((..(..(((((((((....))))))))))...))).))))).)))...)))).....)))))))))"
        .toCharArray();
    tree.buildFromViennaFormat(sequence, structrue);
    char[][] ans = tree.toViennaFormat();
    Assert.assertArrayEquals(sequence, ans[0]);
    Assert.assertArrayEquals(structrue, ans[1]);
  }

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