picard.fingerprint.Fingerprint

All Implemented Interfaces:: Serializable, Cloneable, Map<HaplotypeBlock,HaplotypeProbabilities>, NavigableMap<HaplotypeBlock,HaplotypeProbabilities>, SequencedMap<HaplotypeBlock,HaplotypeProbabilities>, SortedMap<HaplotypeBlock,HaplotypeProbabilities>

public class Fingerprint extends TreeMap<HaplotypeBlock,HaplotypeProbabilities>

class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.

See Also:

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap
AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>
Constructor Summary

Constructors

Constructor

Description

Fingerprint(String sample, Path source, String info)
Method Summary

Modifier and Type

Method

Description

void

add(HaplotypeProbabilities h)

static Function<FingerprintIdDetails,String>

getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY)

String

getInfo()

String

getPrintableId()

String

getSample()

Path

getSource()

Fingerprint

merge(Fingerprint other)

Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.

static Map<FingerprintIdDetails,Fingerprint>

mergeFingerprintsBy(Map<FingerprintIdDetails,Fingerprint> fingerprints, Function<FingerprintIdDetails,String> by)

Methods inherited from class java.util.TreeMap
ceilingEntry, ceilingKey, clear, clone, comparator, compute, computeIfAbsent, computeIfPresent, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, forEach, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, merge, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, putFirst, putIfAbsent, putLast, remove, replace, replace, replaceAll, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap
equals, hashCode, isEmpty, toString

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map
equals, getOrDefault, hashCode, isEmpty, remove

Methods inherited from interface java.util.NavigableMap
reversed

Methods inherited from interface java.util.SequencedMap
sequencedEntrySet, sequencedKeySet, sequencedValues

Constructor Details
- Fingerprint
  
  public Fingerprint(String sample, Path source, String info)
Method Details
- getSample
  
  public String getSample()
- getSource
  
  public Path getSource()
- getInfo
  
  public String getInfo()
- getPrintableId
  
  public String getPrintableId()
- add
  
  public void add(HaplotypeProbabilities h)
- merge
  
  public Fingerprint merge(Fingerprint other)
  
  Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
- getFingerprintIdDetailsStringFunction
  
  public static Function<FingerprintIdDetails,String> getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY)
- mergeFingerprintsBy
  
  public static Map<FingerprintIdDetails,Fingerprint> mergeFingerprintsBy(Map<FingerprintIdDetails,Fingerprint> fingerprints, Function<FingerprintIdDetails,String> by)

Class Fingerprint

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

Constructor Summary

Method Summary

Methods inherited from class java.util.TreeMap

Methods inherited from class java.util.AbstractMap

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Map

Methods inherited from interface java.util.NavigableMap

Methods inherited from interface java.util.SequencedMap

Constructor Details

Fingerprint

Method Details

getSample

getSource

getInfo

getPrintableId

add

merge

getFingerprintIdDetailsStringFunction

mergeFingerprintsBy