Package htsjdk.variant.variantcontext

Class LazyGenotypesContext

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:

  • Constructor Details

    • 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 Details

    • 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()