public class LazyGenotypesContext extends GenotypesContext
| Modifier and Type | Class and Description |
|---|---|
static class |
LazyGenotypesContext.LazyData
Returns the data used in the full GenotypesContext constructor
GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List) |
static interface |
LazyGenotypesContext.LazyParser
Simple lazy parser interface.
|
NO_GENOTYPES, notToBeDirectlyAccessedGenotypes, sampleNamesInOrder, sampleNameToOffset, serialVersionUID| Constructor and Description |
|---|
LazyGenotypesContext(LazyGenotypesContext.LazyParser parser,
java.lang.Object unparsedGenotypeData,
int nUnparsedGenotypes)
Creates a new lazy loading genotypes context using the LazyParser to create
genotypes data on demand.
|
| Modifier and Type | Method and Description |
|---|---|
void |
decode()
Force us to decode the genotypes, if not already done
|
protected void |
ensureSampleNameMap()
Overrides the ensure* functionality.
|
protected void |
ensureSampleOrdering() |
protected java.util.ArrayList<Genotype> |
getGenotypes()
Overrides the genotypes accessor.
|
java.lang.Object |
getUnparsedGenotypeData() |
protected void |
invalidateSampleNameMap() |
protected void |
invalidateSampleOrdering() |
boolean |
isEmpty() |
int |
size() |
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, toStringpublic LazyGenotypesContext(LazyGenotypesContext.LazyParser parser, java.lang.Object unparsedGenotypeData, int nUnparsedGenotypes)
parser - the parser to be used to load on-demand genotypes dataunparsedGenotypeData - the encoded genotypes data that we will decode if necessarynUnparsedGenotypes - the number of genotypes that will be produced if / when we actually decode the genotypes dataprotected java.util.ArrayList<Genotype> getGenotypes()
getGenotypes in class GenotypesContextpublic void decode()
protected void ensureSampleNameMap()
ensureSampleNameMap in class GenotypesContextprotected void ensureSampleOrdering()
ensureSampleOrdering in class GenotypesContextprotected void invalidateSampleNameMap()
invalidateSampleNameMap in class GenotypesContextprotected void invalidateSampleOrdering()
invalidateSampleOrdering in class GenotypesContextpublic boolean isEmpty()
isEmpty in interface java.util.Collection<Genotype>isEmpty in interface java.util.List<Genotype>isEmpty in class GenotypesContextpublic int size()
size in interface java.util.Collection<Genotype>size in interface java.util.List<Genotype>size in class GenotypesContextpublic java.lang.Object getUnparsedGenotypeData()