Examples of RnaSpecificTypeRelatedTreePruning

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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    testOrderedBipartiteMatching();   
  }

  private static void testRNAShuffleExample() throws IOException {
    RnaSpecificTypeRelatedTreePruning prune2 = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        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"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
    final RNASpecificTree sR = new RNASpecificTree("S-Random");
//    sR.buildFromViennaFormat(
//        "GGGAGUAUGUACCGAUAGGGUGAUUCCGGGCCCUUCGACNGGCUCCAUC"
//            .toCharArray(),
//        "(((((............((......))(((.))).(.....)))))).."
//            .toCharArray());
    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);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
   
    smooth.calculateCost(t);
    smooth.calculateCost(s);
    smooth.calculateCost(sR);
   
View Full Code Here

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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    Tree tree = new Tree(neighbors, null, null, null);
  }

  public static void testRNAExample() {

    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();
    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

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

    RNASpecificTree t = new RNASpecificTree();
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    t.buildFromViennaFormat(
        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

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

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
    // "(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))".toCharArray());
    // s.buildFromViennaFormat("CCGGgGGAUCACCACGGCGGgGGAUCACCACGG".toCharArray(),
    // "((((.((....))))))(((.((....))))).".toCharArray());
    s.buildFromViennaFormat(
        "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

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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public class TestHSA {

  @Test
  public void testRNAShuffleExample() {
    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        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"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
    final RNASpecificTree sR = new RNASpecificTree("S-Random");
    sR.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .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

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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        MathOperations.equals(ans1, ans2));
  }

  @Test
  public void testUnrootedExample() {
    RnaSpecificTypeRelatedTreePruning pruneRooted = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificTypeRelatedTreePruning pruneUnrooted = new RnaSpecificTypeRelatedTreePruning(
        false, false);

    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        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");
    s.buildFromViennaFormat(
        "UUUUUUUUUUuuuGGGGGGcccUUUUUUuuuCCCCCCCCcccGGGGGGGGuuuAAAAAAAAAA"
            .toCharArray(),
        "((((((((((...((((((...))))))...((((((((...))))))))...))))))))))"
            .toCharArray());

    smooth.calculateCost(t);
    smooth.calculateCost(s);

    double ans1 = 0, ans2 = 0;

    // reuse
    HSA hsaEngine = new HSA(1, 1, cost, new OrderedMatcherFactory(), true);

    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

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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    isSame(ans, exp);
  }

  @Test
  public void testSelfSim() {
    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        true, false);
   
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();

    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

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

    final RNASpecificTree t = new RNASpecificTree("T");
    /*t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
        */
   
    t.buildFromViennaFormat(
        "GCCUGAAGGGACGCCUGAAGGGA".toCharArray(),
        "(((.....))).(((.....)))".toCharArray());
   
    prune.calculateCost(t);
    smooth.calculateCost(t);
   
    try {
      t.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
View Full Code Here

Examples of bgu.bio.adt.rna.costs.RnaSpecificTypeRelatedTreePruning

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    Tree tree = new Tree(neighbors, null, null, null);
  }

  public static void testRNAExample() {

    RnaSpecificTypeRelatedTreePruning prune = new RnaSpecificTypeRelatedTreePruning(
        false, true);
    RnaSpecificSmoothCost smooth = new RnaSpecificSmoothCost();
    SequenceAlignment aligner = new AffineGapGlobalSequenceAlignmentNoMatrix(
        10, 10, RnaAlphabet.getInstance(), new AffineGapScoringMatrix(
            "matrix" + File.separator
                + "interval-RIBOSUM85-60.matrix",
            RnaAlphabet.getInstance()));

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

    RNASpecificTree t = new RNASpecificTree();
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    t.buildFromViennaFormat(
        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

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

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
    // "(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))".toCharArray());
    // s.buildFromViennaFormat("CCGGgGGAUCACCACGGCGGgGGAUCACCACGG".toCharArray(),
    // "((((.((....))))))(((.((....))))).".toCharArray());
    s.buildFromViennaFormat(
        "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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