Package bgu.bio.adt.rna

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

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

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