Examples of parseKmersFromSequence()

Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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  /** Test for {@link ProteinKmerBitFeatureVectorTest#ProteinKmerFeatureVector(byte[])}. */
  public void testPrintKmers() {   
    ProteinKmerBitFeatureVector vector = new ProteinKmerBitFeatureVector(3, 20);
   
    vector.parseKmersFromSequence("AVAA");
   
    System.out.println(vector.printKmers());
   
    assertTrue(true);
  }
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Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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        vector.getKmerLength()) / ProteinKmerBitFeatureVector.BITS_IN_BYTE)];
   
    initializeBytes(testBytes);
    testBytes[0] = (byte) 0x1;
   
    vector.parseKmersFromSequence(sequence);
    byte[] bytes = vector.getFeatureVector();

    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
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Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AR";

    vector = new ProteinKmerBitFeatureVector(2, 20);
    vector.parseKmersFromSequence(sequence);
    bytes = vector.getFeatureVector();
   
    testBytes[0] = (byte) 0x2;
   
    System.out.println(vector.printByteVector());
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Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AV";
   
    vector = new ProteinKmerBitFeatureVector(2, 20);
    vector.parseKmersFromSequence(sequence);
    bytes = vector.getFeatureVector();
   
    testBytes[0] = (byte) 0x0;
    testBytes[2] = (byte) 0x8;
   
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Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "VV";
   
    vector = new ProteinKmerBitFeatureVector(2, 20);
    vector.parseKmersFromSequence(sequence);
    bytes = vector.getFeatureVector();
   
    testBytes[0] = (byte) 0x0;
    testBytes[2] = (byte) 0x0;
    testBytes[49] = (byte) 0x80;
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Examples of kmer.ProteinKmerBitFeatureVector.parseKmersFromSequence()

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      ProteinKmerBitFeatureVector featureVector = new ProteinKmerBitFeatureVector(
          context.getConfiguration().getInt(KMER_LENGTH, 3));
      // ProteinKmerCountFeatureVector featureVector = new ProteinKmerCountFeatureVector(
      //    context.getConfiguration().getInt(KMER_LENGTH, 3));
     
      featureVector.parseKmersFromSequence(line.substring(spaceIndex + 1).trim());
     
     
      LOG.info(featureVector.getFeatureVector().length);
      LOG.info(featureVector.printByteVector());
      LOG.info(featureVector.printKmers());
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Examples of kmer.ProteinKmerCountFeatureVector.parseKmersFromSequence()

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  /** Test for {@link ProteinKmerCountFeatureVectorTest#ProteinKmerFeatureVector(byte[])}. */
  public void testPrintKmers() {   
    ProteinKmerCountFeatureVector vector = new ProteinKmerCountFeatureVector(3, 20);
   
    vector.parseKmersFromSequence("AVAA");
   
    System.out.println(vector.printKmers());
   
    assertTrue(true);
  }
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Examples of kmer.ProteinKmerCountFeatureVector.parseKmersFromSequence()

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        vector.getKmerLength())];
   
    initializeBytes(testBytes);
    testBytes[0] = (byte) 0x1;
   
    vector.parseKmersFromSequence(sequence);
    byte[] bytes = vector.getFeatureVector();

    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
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Examples of kmer.ProteinKmerCountFeatureVector.parseKmersFromSequence()

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    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AR";

    vector = new ProteinKmerCountFeatureVector(2, 20);
    vector.parseKmersFromSequence(sequence);
    bytes = vector.getFeatureVector();
   
    testBytes[0] = (byte) 0x0;
    testBytes[1] = (byte) 0x1;
   
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Examples of kmer.ProteinKmerCountFeatureVector.parseKmersFromSequence()

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    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AV";
   
    vector = new ProteinKmerCountFeatureVector(2, 20);
    vector.parseKmersFromSequence(sequence);
    bytes = vector.getFeatureVector();
   
    testBytes[1] = (byte) 0x0;
    testBytes[19] = (byte) 0x1;
   
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