Package kmer

Examples of kmer.ProteinKmerCountFeatureVector.printByteVector()

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

    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AR";
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    bytes = vector.getFeatureVector();
   
    testBytes[0] = (byte) 0x0;
    testBytes[1] = (byte) 0x1;
   
    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "AV";
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    bytes = vector.getFeatureVector();
   
    testBytes[1] = (byte) 0x0;
    testBytes[19] = (byte) 0x1;
   
    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
    assertTrue(equalBytes(bytes, testBytes));
   
    sequence = "VV";
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    bytes = vector.getFeatureVector();
   
    testBytes[19] = (byte) 0x0;
    testBytes[399] = (byte) 0x1;
   
    System.out.println(vector.printByteVector());
    System.out.println(printByteVector(testBytes));
   
    assertTrue(equalBytes(bytes, testBytes));
  }
 
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    int item = new Random().nextInt(closestCenters.size());   
    closestCenter = closestCenters.get(item);
   
    if (debug) {
      ProteinKmerCountFeatureVector featureVector = new ProteinKmerCountFeatureVector(value.getBytes() /*vector*/, kmerLength);
      LOG.info("Closest Center: " + closestCenter + ", Distance: " + minDistance + ", FeatureVector: " + featureVector.printByteVector());
    }
   
    if (closestCenter == -1) {
     
    } else {
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        distances[position] += (int) featureVector.getFeatureVector()[position];
      }
     
      if (debug) {
        LOG.info(featureVector.printByteVector());
        LOG.info(featureVector.printKmers());
      }
     
      featureVector = null;     
      ++numOfSequences;     
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      clusterFeatureVector.getFeatureVector()[i] = distance;
    }
   

    if (debug) {
      LOG.info("New cluster center feature vector: " + clusterFeatureVector.printByteVector());
      LOG.info("New cluster center kmers: " + clusterFeatureVector.printKmers());
    }
   
    context.write(key, new BytesWritable(clusterFeatureVector.getFeatureVector()));
  }
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