htsjdk.samtools.util.Histogram.keySet()方法的使用及代码示例

x33g5p2x  于2022-01-20 转载在 其他  
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本文整理了Java中htsjdk.samtools.util.Histogram.keySet()方法的一些代码示例，展示了Histogram.keySet()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Histogram.keySet()方法的具体详情如下：
包路径：htsjdk.samtools.util.Histogram
类名称：Histogram
方法名：keySet

Histogram.keySet介绍

[英]Returns the set of keys for this histogram.
[中]

代码示例

代码示例来源：origin: com.github.samtools/htsjdk

/***
 * Immutable method that divides the current Histogram by an input Histogram and generates a new one
 * Throws an exception if the bins don't match up exactly
 * @param divisorHistogram
 * @return
 * @throws IllegalArgumentException if the keySet of this histogram is not equal to the keySet of the given divisorHistogram
 */
public Histogram<K> divideByHistogram(final Histogram<K> divisorHistogram) {
  final Histogram<K> output = new Histogram<K>();
  if (!this.keySet().equals(divisorHistogram.keySet())) throw new IllegalArgumentException("Attempting to divide Histograms with non-identical bins");
  for (final K key : this.keySet()){
    final Bin<K> dividend = this.get(key);
    final Bin<K> divisor = divisorHistogram.get(key);
    output.increment(key, dividend.getValue()/divisor.getValue());
  }
  return output;
}

代码示例来源：origin: samtools/htsjdk

/***
 * Immutable method that divides the current Histogram by an input Histogram and generates a new one
 * Throws an exception if the bins don't match up exactly
 * @param divisorHistogram
 * @return
 * @throws IllegalArgumentException if the keySet of this histogram is not equal to the keySet of the given divisorHistogram
 */
public Histogram<K> divideByHistogram(final Histogram<K> divisorHistogram) {
  final Histogram<K> output = new Histogram<K>();
  if (!this.keySet().equals(divisorHistogram.keySet())) throw new IllegalArgumentException("Attempting to divide Histograms with non-identical bins");
  for (final K key : this.keySet()){
    final Bin<K> dividend = this.get(key);
    final Bin<K> divisor = divisorHistogram.get(key);
    output.increment(key, dividend.getValue()/divisor.getValue());
  }
  return output;
}

代码示例来源：origin: org.seqdoop/htsjdk

/***
 * Immutable method that divides the current Histogram by an input Histogram and generates a new one
 * Throws an exception if the bins don't match up exactly
 * @param divisorHistogram
 * @return
 * @throws IllegalArgumentException
 */
public Histogram<K> divideByHistogram(final Histogram<K> divisorHistogram) throws IllegalArgumentException{
  Histogram<K> output = new Histogram<K>();
  if (!this.keySet().equals(divisorHistogram.keySet()))  throw new IllegalArgumentException("Attempting to divide Histograms with non-identical bins");
  for (final K key : this.keySet()){
    Bin dividend = this.get(key);
    Bin divisor = divisorHistogram.get(key);
    output.increment(key, dividend.getValue()/divisor.getValue());
  }
  return output;
}

代码示例来源：origin: com.github.samtools/htsjdk

/***
 * Mutable method that allows the addition of a Histogram into the current one.
 * @param addHistogram
 */
public void addHistogram(final Histogram<K> addHistogram) {
  for (final K key : addHistogram.keySet()){
    this.increment(key, addHistogram.get(key).getValue());
  }
}

代码示例来源：origin: samtools/htsjdk

if (histo != null) keys.addAll(histo.keySet());
out.append(HISTO_HEADER + nonEmptyHistograms.get(0).keySet().iterator().next().getClass().getName());
out.newLine();

代码示例来源：origin: com.github.samtools/htsjdk

if (histo != null) keys.addAll(histo.keySet());
out.append(HISTO_HEADER + nonEmptyHistograms.get(0).keySet().iterator().next().getClass().getName());
out.newLine();

代码示例来源：origin: org.seqdoop/htsjdk

if (histo != null) keys.addAll(histo.keySet());
out.append(HISTO_HEADER + nonEmptyHistograms.get(0).keySet().iterator().next().getClass().getName());
out.newLine();

代码示例来源：origin: org.seqdoop/htsjdk

/***
   * Mutable method that allows the addition of a Histogram into the current one.
   * @param addHistogram
   */
  public void addHistogram(final Histogram<K> addHistogram) {
    for (final K key : addHistogram.keySet()){
      this.increment(key, addHistogram.get(key).getValue());
    }
  }
}

代码示例来源：origin: samtools/htsjdk

/***
 * Mutable method that allows the addition of a Histogram into the current one.
 * @param addHistogram
 */
public void addHistogram(final Histogram<K> addHistogram) {
  for (final K key : addHistogram.keySet()){
    this.increment(key, addHistogram.get(key).getValue());
  }
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testGetKeySet() {
  final int[] is = {4,4,5,5,5};
  final Histogram<Integer> histo = new Histogram<>();
  for (final int i : is) histo.increment(i);
  Assert.assertEquals(histo.keySet(), new HashSet<>(Arrays.asList(4,5)));
}

代码示例来源：origin: com.github.broadinstitute/picard

private List<RrbsCpgDetailMetrics> buildDetailMetrics() {
    final List<RrbsCpgDetailMetrics> detailMetrics = new ArrayList<RrbsCpgDetailMetrics>();
    for (final CpgLocation key : cpgTotal.keySet()) {
      final RrbsCpgDetailMetrics cpgMetric = new RrbsCpgDetailMetrics();
      cpgMetric.SAMPLE = sample;
      cpgMetric.READ_GROUP = readGroup;
      cpgMetric.LIBRARY = library;
      cpgMetric.SEQUENCE_NAME = key.getSequence();
      cpgMetric.POSITION = key.getPosition();
      cpgMetric.TOTAL_SITES = (int)cpgTotal.get(key).getValue();
      cpgMetric.CONVERTED_SITES = cpgConverted.containsKey(key) ? (int)cpgConverted.get(key).getValue() : 0;
      cpgMetric.PCT_CONVERTED = cpgMetric.CONVERTED_SITES == 0 ? 0 : cpgMetric.CONVERTED_SITES / (double)cpgMetric.TOTAL_SITES;
      detailMetrics.add(cpgMetric);
    }
    return detailMetrics;
  }
}

代码示例来源：origin: samtools/htsjdk

final Object keys[] = keySet().toArray();
for (Object binId : keys) {
  if (!binsToKeep.contains(binId)) {

代码示例来源：origin: com.github.samtools/htsjdk

final Object keys[] = keySet().toArray();
for (Object binId : keys) {
  if (!binsToKeep.contains(binId)) {

代码示例来源：origin: broadinstitute/picard

private List<RrbsCpgDetailMetrics> buildDetailMetrics() {
    final List<RrbsCpgDetailMetrics> detailMetrics = new ArrayList<RrbsCpgDetailMetrics>();
    for (final CpgLocation key : cpgTotal.keySet()) {
      final RrbsCpgDetailMetrics cpgMetric = new RrbsCpgDetailMetrics();
      cpgMetric.SAMPLE = sample;
      cpgMetric.READ_GROUP = readGroup;
      cpgMetric.LIBRARY = library;
      cpgMetric.SEQUENCE_NAME = key.getSequence();
      cpgMetric.POSITION = key.getPosition();
      cpgMetric.TOTAL_SITES = (int)cpgTotal.get(key).getValue();
      cpgMetric.CONVERTED_SITES = cpgConverted.containsKey(key) ? (int)cpgConverted.get(key).getValue() : 0;
      cpgMetric.PCT_CONVERTED = cpgMetric.CONVERTED_SITES == 0 ? 0 : cpgMetric.CONVERTED_SITES / (double)cpgMetric.TOTAL_SITES;
      detailMetrics.add(cpgMetric);
    }
    return detailMetrics;
  }
}

代码示例来源：origin: org.seqdoop/htsjdk

final Object keys[] = keySet().toArray();
for (Object binId : keys) {
  if (!binsToKeep.contains((K)binId)) {

代码示例来源：origin: PapenfussLab/gridss

public void addMetricsToFile(final MetricsFile<GcMetrics,Integer> file) {
    final GcMetrics metrics = new GcMetrics();
    metrics.SAMPLE             = this.sample;
    metrics.LIBRARY            = this.library;
    metrics.READ_GROUP         = this.readGroup;
    double totalGc = 0;
    int totalReads = 0;
    for (Integer gcBin : histogram.keySet()) {
      int count = (int)histogram.get(gcBin).getValue();
      totalReads += count;
      totalGc += gcBin * count;
    }
    metrics.MEAN_GC_CONTENT = totalGc;
    metrics.READ_COUNT = totalReads;
    file.addHistogram(histogram);
    file.addMetric(metrics);       
  }
}

代码示例来源：origin: broadinstitute/picard

@Override
public void test() throws IOException {
  final MetricsFile<DuplicationMetrics, Double> metricsOutput = testMetrics();
  // Check contents of set size bin against expected values
  if (!expectedSetSizeMap.isEmpty()) {
    boolean checked = false;
    for (final Histogram<Double> histo : metricsOutput.getAllHistograms()) {
      final String label = histo.getValueLabel();
      for (final Double bin : histo.keySet()) {
        final String binStr = String.valueOf(bin);
        final List<String> labelBinStr = Arrays.asList(label, binStr);
        if (expectedSetSizeMap.containsKey(labelBinStr)) {
          checked = true;
          Histogram.Bin<Double> binValue = histo.get(bin);
          final double actual = binValue.getValue();
          final double expected = expectedSetSizeMap.get(labelBinStr);
          Assert.assertEquals(actual, expected);
        }
      }
    }
    if (!checked) {
      Assert.fail("Could not not find matching entry for expectedSetSizeMap in metrics.");
    }
  }
}

代码示例来源：origin: PapenfussLab/gridss

public static InsertSizeDistribution create(Histogram<Integer> insertSizeHistogram) {
  if (insertSizeHistogram == null) return null;
  int[] insertSize = new int[insertSizeHistogram.size()];
  double[] count = new double[insertSizeHistogram.size()];
  double total = insertSizeHistogram.getSumOfValues();
  int i = 0;
  Set<Integer> keys = insertSizeHistogram.keySet();
  for (Integer key : keys) {
    insertSize[i] = key;
    count[i] = insertSizeHistogram.get(key).getValue();
    i++;
  }
  return new InsertSizeDistribution(insertSize, count, (long)total);
}
public InsertSizeDistribution(int[] singletons, double[] readCounts) {

代码示例来源：origin: PapenfussLab/gridss

public void addMetricsToFile(final MetricsFile<MapqMetrics,Integer> file) {
    final MapqMetrics metrics = new MapqMetrics();
    metrics.SAMPLE             = this.sample;
    metrics.LIBRARY            = this.library;
    metrics.READ_GROUP         = this.readGroup;
    metrics.MAPPED_READS       = (long) histogram.getCount();
    metrics.MIN_MAPQ           = SAMRecord.UNKNOWN_MAPPING_QUALITY;
    metrics.MAX_MAPQ           = 0;
    for (int key : histogram.keySet()) {
      if (key != SAMRecord.UNKNOWN_MAPPING_QUALITY) {
        if (histogram.get(key).getValue() > 0) {
          metrics.MIN_MAPQ = Math.min(metrics.MIN_MAPQ, key);
          metrics.MAX_MAPQ = Math.max(metrics.MAX_MAPQ, key);
        }
      }
    }
    if (histogram.get(SAMRecord.NO_MAPPING_QUALITY) != null) {
      metrics.ZERO_MAPQ      = (long) histogram.get(SAMRecord.NO_MAPPING_QUALITY).getValue();
    }
    if (histogram.get(SAMRecord.UNKNOWN_MAPPING_QUALITY) != null) {
      metrics.UNKNOWN_MAPQ   = (long) histogram.get(SAMRecord.UNKNOWN_MAPPING_QUALITY).getValue();
    }
    file.addHistogram(histogram);
    file.addMetric(metrics);       
  }
}

代码示例来源：origin: broadinstitute/picard

for (final Integer bin : duplicationHisto.keySet()) {
  final double duplicateGroups = duplicationHisto.get(bin).getValue();
  final double opticalDuplicates = opticalHisto.get(bin) == null ? 0 : opticalHisto.get(bin).getValue();

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