LazyGenotypesContext (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.variant.variantcontext.GenotypesContext
- - htsjdk.variant.variantcontext.LazyGenotypesContext

All Implemented Interfaces:

Serializable, Iterable<Genotype>, Collection<Genotype>, List<Genotype>
```
public class LazyGenotypesContext
extends GenotypesContext
```
Lazy-loading GenotypesContext. A lazy-loading context has access to the VCFParser and a unparsed string of genotype data. If the user attempts to manipulate the genotypes contained in this context, we decode the data and become a full blown GenotypesContext. However, if the user never does this we are spared a lot of expense decoding the genotypes unnecessarily.

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`LazyGenotypesContext.LazyData`	Returns the data used in the full GenotypesContext constructor `GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)`
`static interface`	`LazyGenotypesContext.LazyParser`	Simple lazy parser interface.

Field Summary
- Fields inherited from class htsjdk.variant.variantcontext.GenotypesContext
  NO_GENOTYPES, notToBeDirectlyAccessedGenotypes, sampleNamesInOrder, sampleNameToOffset, serialVersionUID

Constructor Summary

Constructors
Constructor	Description
`LazyGenotypesContext(LazyGenotypesContext.LazyParser parser, Object unparsedGenotypeData, int nUnparsedGenotypes)`	Creates a new lazy loading genotypes context using the LazyParser to create genotypes data on demand.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`decode()`	Force us to decode the genotypes, if not already done
`protected void`	`ensureSampleNameMap()`	Overrides the ensure* functionality.
`protected void`	`ensureSampleOrdering()`
`protected ArrayList<Genotype>`	`getGenotypes()`	Overrides the genotypes accessor.
`Object`	`getUnparsedGenotypeData()`
`protected void`	`invalidateSampleNameMap()`
`protected void`	`invalidateSampleOrdering()`
`boolean`	`isEmpty()`
`int`	`size()`

Methods inherited from interface java.util.Collection
parallelStream, removeIf, stream

Methods inherited from class htsjdk.variant.variantcontext.GenotypesContext
add, add, addAll, addAll, checkImmutability, clear, contains, containsAll, containsSample, containsSamples, copy, copy, create, create, create, create, create, get, get, getMaxPloidy, getSampleNames, getSampleNamesOrderedByName, immutable, indexOf, isLazyWithData, isMutable, iterateInSampleNameOrder, iterateInSampleNameOrder, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, replace, retainAll, set, subList, subsetToSamples, toArray, toArray, toString

Methods inherited from interface java.lang.Iterable
forEach

Methods inherited from interface java.util.List
equals, hashCode, replaceAll, sort, spliterator

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

- Constructor Detail
  - LazyGenotypesContext
```
public LazyGenotypesContext(LazyGenotypesContext.LazyParser parser,
                            Object unparsedGenotypeData,
                            int nUnparsedGenotypes)
```
    Creates a new lazy loading genotypes context using the LazyParser to create genotypes data on demand.
    
    Parameters:
    
    parser - the parser to be used to load on-demand genotypes data
    
    unparsedGenotypeData - the encoded genotypes data that we will decode if necessary
    
    nUnparsedGenotypes - the number of genotypes that will be produced if / when we actually decode the genotypes data
- Method Detail
  - getGenotypes
```
protected ArrayList<Genotype> getGenotypes()
```
    Overrides the genotypes accessor. If we haven't already, decode the genotypes data and store the decoded results in the appropriate variables. Otherwise we just returned the decoded result directly. Note some care needs to be taken here as the value in notToBeDirectlyAccessedGenotypes may diverge from what would be produced by decode, if after the first decode the genotypes themselves are replaced
    
    Overrides:
    
    getGenotypes in class GenotypesContext
    
    Returns:
  - decode
```
public void decode()
```
    Force us to decode the genotypes, if not already done
  - ensureSampleNameMap
```
protected void ensureSampleNameMap()
```
    Overrides the ensure* functionality. If the data hasn't been loaded yet and we want to build the cache, just decode it and we're done. If we've already decoded the data, though, go through the super class
    
    Overrides:
    
    ensureSampleNameMap in class GenotypesContext
  - ensureSampleOrdering
```
protected void ensureSampleOrdering()
```
    Overrides:
    
    ensureSampleOrdering in class GenotypesContext
  - invalidateSampleNameMap
```
protected void invalidateSampleNameMap()
```
    Overrides:
    
    invalidateSampleNameMap in class GenotypesContext
  - invalidateSampleOrdering
```
protected void invalidateSampleOrdering()
```
    Overrides:
    
    invalidateSampleOrdering in class GenotypesContext
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface Collection<Genotype>
    
    Specified by:
    
    isEmpty in interface List<Genotype>
    
    Overrides:
    
    isEmpty in class GenotypesContext
  - size
```
public int size()
```
    Specified by:
    
    size in interface Collection<Genotype>
    
    Specified by:
    
    size in interface List<Genotype>
    
    Overrides:
    
    size in class GenotypesContext
  - getUnparsedGenotypeData
```
public Object getUnparsedGenotypeData()
```

Class LazyGenotypesContext

Nested Class Summary

Field Summary

Fields inherited from class htsjdk.variant.variantcontext.GenotypesContext

Constructor Summary

Method Summary

Methods inherited from interface java.util.Collection

Methods inherited from class htsjdk.variant.variantcontext.GenotypesContext

Methods inherited from interface java.lang.Iterable

Methods inherited from interface java.util.List

Methods inherited from class java.lang.Object

Constructor Detail

LazyGenotypesContext

Method Detail

getGenotypes

decode

ensureSampleNameMap

ensureSampleOrdering

invalidateSampleNameMap

invalidateSampleOrdering

isEmpty

size

getUnparsedGenotypeData