AllData

java.lang.Object
- vcf.AllData

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, Data
```
public class AllData
extends java.lang.Object
implements Data
```
Class AllData represents a sliding window of reference and target VCF records.

Instances of class AllData are not thread-safe.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`advanceWindow(int overlap, int windowSize)` Advances the sliding window of VCF records, and returns the advanced window.
`static AllData`	`allData(SampleFileIt<VcfEmission> refIt, SampleFileIt<? extends VcfEmission> targetIt)` Constructs and returns a new `AllData` instance from VCF records returned by the specified `SampleFileIt` objects.
`Samples`	`allSamples()` Returns a list of all target and reference samples.
`boolean`	`canAdvanceWindow()` Returns `true` if the sliding window of VCF records can advance and returns `false` otherwise.
`void`	`close()` Releases any I/O resources controlled by this object.
`boolean`	`lastWindowOnChrom()` Returns `true` if the current window of VCF records is the last window for the chromosome and returns `false` otherwise.
`int`	`markerIndex(int nonRefIndex)` Returns the marker index corresponding to the specified target data marker.
`Markers`	`markers()` Returns the list of markers in the current window.
`int`	`nAllSamples()` Returns the total number of reference and target samples.
`int`	`nMarkers()` Returns the number of markers in the current window.
`int`	`nMarkersSoFar()` Returns the number of markers in the union of the current window and all previous windows.
`int`	`nRefSamples()` Returns the number of reference samples.
`int`	`nTargetMarkers()` Returns the number of target data markers in the current window.
`int`	`nTargetMarkersSoFar()` Returns the number of target VCF records in the union of the current window and all previous windows.
`int`	`nTargetSamples()` Returns the number of target samples.
`int`	`overlap()` Returns the number of VCF records in the overlap between the current window and the previous window.
`java.util.List<HapPair>`	`refHapPairs()` Returns a list of the reference haplotype pairs for the current window.
`SampleHapPairs`	`refSampleHapPairs()` Returns the reference haplotype pairs for the current window.
`Samples`	`refSamples()` Returns the list of reference samples, or `null` if there are no reference samples.
`java.util.List<HapPair>`	`restrictedRefHapPairs()` Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window.
`GL`	`targetGL()` Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window.
`int`	`targetMarkerIndex(int refIndex)` Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists.
`Markers`	`targetMarkers()` Returns the list of target data markers in the current window.
`int`	`targetOverlap()` Returns the number of target data markers in the overlap between the current marker window and the previous marker window.
`Samples`	`targetSamples()` Returns the list of target samples.
`java.lang.String`	`toString()` Returns a string representation of `this`.
`int`	`window()` Returns the current window index.

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

- Method Detail
  - allData
```
public static AllData allData(SampleFileIt<VcfEmission> refIt,
                              SampleFileIt<? extends VcfEmission> targetIt)
```
    Constructs and returns a new AllData instance from VCF records returned by the specified SampleFileIt objects.
    
    Parameters:
    
    refIt - an iterator that returns reference VCF records
    
    targetIt - an iterator that returns target VCF records
    
    Returns:
    
    a new AllData instance.
    
    Throws:
    
    java.lang.IllegalArgumentException - if either the reference data or target data contain no samples
    
    java.lang.IllegalArgumentException - if a format error is detected in a string VCF record
    
    java.lang.NullPointerException - if refIt == null || targetIt == null
  - lastWindowOnChrom
```
public boolean lastWindowOnChrom()
```
    Description copied from interface: Data
    
    Returns true if the current window of VCF records is the last window for the chromosome and returns false otherwise.
    
    Specified by:
    
    lastWindowOnChrom in interface Data
    
    Returns:
    
    true if the current window of VCF records is the last window for the chromosome
  - canAdvanceWindow
```
public boolean canAdvanceWindow()
```
    Description copied from interface: Data
    
    Returns true if the sliding window of VCF records can advance and returns false otherwise.
    
    Specified by:
    
    canAdvanceWindow in interface Data
    
    Returns:
    
    true if the sliding window of VCF records can advance
  - advanceWindow
```
public void advanceWindow(int overlap,
                          int windowSize)
```
    Description copied from interface: Data
    
    Advances the sliding window of VCF records, and returns the advanced window. The size of the advanced window may differ from the requested value. If the advanced window size is less than the requested value, the actual value will be as large as possible.
    
    Specified by:
    
    advanceWindow in interface Data
    
    Parameters:
    
    overlap - the number of markers of overlap
    
    windowSize - the requested number of the markers in the window immediately after the method returns
  - window
```
public int window()
```
    Description copied from interface: Data
    
    Returns the current window index. The window index is the number of previous invocations of the advanceWindow() method.
    
    Specified by:
    
    window in interface Data
    
    Returns:
    
    the window index
  - targetOverlap
```
public int targetOverlap()
```
    Description copied from interface: Data
    
    Returns the number of target data markers in the overlap between the current marker window and the previous marker window. Returns 0 if the current marker window is the first marker window.
    
    Specified by:
    
    targetOverlap in interface Data
    
    Returns:
    
    the number of target data markers in the overlap between the current marker window and the previous marker window
  - overlap
```
public int overlap()
```
    Description copied from interface: Data
    
    Returns the number of VCF records in the overlap between the current window and the previous window. Returns 0 if the current window is the first window.
    
    Specified by:
    
    overlap in interface Data
    
    Returns:
    
    the number of VCF records in the overlap between the current window and the previous window
  - nTargetMarkers
```
public int nTargetMarkers()
```
    Description copied from interface: Data
    
    Returns the number of target data markers in the current window.
    
    Specified by:
    
    nTargetMarkers in interface Data
    
    Returns:
    
    the number of target data markers in the current window
  - nTargetMarkersSoFar
```
public int nTargetMarkersSoFar()
```
    Description copied from interface: Data
    
    Returns the number of target VCF records in the union of the current window and all previous windows.
    
    Specified by:
    
    nTargetMarkersSoFar in interface Data
    
    Returns:
    
    the number of target VCF records in the union of the current window and all previous windows
  - targetMarkers
```
public Markers targetMarkers()
```
    Description copied from interface: Data
    
    Returns the list of target data markers in the current window.
    
    Specified by:
    
    targetMarkers in interface Data
    
    Returns:
    
    the list of target data markers in the current window
  - nMarkers
```
public int nMarkers()
```
    Description copied from interface: Data
    
    Returns the number of markers in the current window.
    
    Specified by:
    
    nMarkers in interface Data
    
    Returns:
    
    the number of markers in the current window
  - nMarkersSoFar
```
public int nMarkersSoFar()
```
    Description copied from interface: Data
    
    Returns the number of markers in the union of the current window and all previous windows.
    
    Specified by:
    
    nMarkersSoFar in interface Data
    
    Returns:
    
    the number of markers in the union of the current window and all previous windows
  - markers
```
public Markers markers()
```
    Description copied from interface: Data
    
    Returns the list of markers in the current window.
    
    Specified by:
    
    markers in interface Data
    
    Returns:
    
    the list of markers in the current window
  - targetMarkerIndex
```
public int targetMarkerIndex(int refIndex)
```
    Description copied from interface: Data
    
    Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists. Indices are with respect to the current window.
    
    Specified by:
    
    targetMarkerIndex in interface Data
    
    Parameters:
    
    refIndex - a marker index
    
    Returns:
    
    the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists
  - markerIndex
```
public int markerIndex(int nonRefIndex)
```
    Description copied from interface: Data
    
    Returns the marker index corresponding to the specified target data marker. Indices are with respect to the current window.
    
    Specified by:
    
    markerIndex in interface Data
    
    Parameters:
    
    nonRefIndex - a target data marker index
    
    Returns:
    
    the marker index corresponding to the specified target data marker
  - nTargetSamples
```
public int nTargetSamples()
```
    Description copied from interface: Data
    
    Returns the number of target samples.
    
    Specified by:
    
    nTargetSamples in interface Data
    
    Returns:
    
    the number of target samples
  - targetSamples
```
public Samples targetSamples()
```
    Description copied from interface: Data
    
    Returns the list of target samples.
    
    Specified by:
    
    targetSamples in interface Data
    
    Returns:
    
    the list of target samples
  - nRefSamples
```
public int nRefSamples()
```
    Description copied from interface: Data
    
    Returns the number of reference samples.
    
    Specified by:
    
    nRefSamples in interface Data
    
    Returns:
    
    the number of reference samples
  - refSamples
```
public Samples refSamples()
```
    Description copied from interface: Data
    
    Returns the list of reference samples, or null if there are no reference samples.
    
    Specified by:
    
    refSamples in interface Data
    
    Returns:
    
    the list of reference samples, or null if there are no reference samples
  - nAllSamples
```
public int nAllSamples()
```
    Description copied from interface: Data
    
    Returns the total number of reference and target samples.
    
    Specified by:
    
    nAllSamples in interface Data
    
    Returns:
    
    the total number of reference and target samples
  - allSamples
```
public Samples allSamples()
```
    Description copied from interface: Data
    
    Returns a list of all target and reference samples. Target samples are listed first in the same order as the list returned by this.targetSamples(). Reference samples are listed last in the same order as the list returned by this.refSamples().
    
    Specified by:
    
    allSamples in interface Data
    
    Returns:
    
    a list of all target and reference samples
  - targetGL
```
public GL targetGL()
```
    Description copied from interface: Data
    
    Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window. The returned GL instance will contain no markers if this.advanceWindow() has not yet been invoked.
    
    Specified by:
    
    targetGL in interface Data
    
    Returns:
    
    the genotype likelihoods for the target samples restricted to the target data markers in the current window
  - restrictedRefHapPairs
```
public java.util.List<HapPair> restrictedRefHapPairs()
```
    Description copied from interface: Data
    
    Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window. The returned list will be empty if there are no reference samples or if this.advanceWindow() has not yet been invoked.
    
    Specified by:
    
    restrictedRefHapPairs in interface Data
    
    Returns:
    
    a list of reference haplotype pairs that are restricted to the target data markers
  - refHapPairs
```
public java.util.List<HapPair> refHapPairs()
```
    Description copied from interface: Data
    
    Returns a list of the reference haplotype pairs for the current window. The returned list will be empty if there are no reference samples or if this.advanceWindow() has not yet been invoked.
    
    Specified by:
    
    refHapPairs in interface Data
    
    Returns:
    
    a list of the reference haplotype pairs
  - refSampleHapPairs
```
public SampleHapPairs refSampleHapPairs()
```
    Description copied from interface: Data
    
    Returns the reference haplotype pairs for the current window. Returns null if there are no reference samples or if this.advanceWindow() has not yet been invoked.
    
    Specified by:
    
    refSampleHapPairs in interface Data
    
    Returns:
    
    the reference haplotype pairs or null if there are no reference haplotype pairs
  - close
```
public void close()
```
    Description copied from interface: Data
    
    Releases any I/O resources controlled by this object.
    
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
    
    Specified by:
    
    close in interface Data
  - toString
```
public java.lang.String toString()
```
    Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string representation of this

Class AllData

Method Summary

Methods inherited from class java.lang.Object

Method Detail

allData

lastWindowOnChrom

canAdvanceWindow

advanceWindow

window

targetOverlap

overlap

nTargetMarkers

nTargetMarkersSoFar

targetMarkers

nMarkers

nMarkersSoFar

markers

targetMarkerIndex

markerIndex

nTargetSamples

targetSamples

nRefSamples

refSamples

nAllSamples

allSamples

targetGL

restrictedRefHapPairs

refHapPairs

refSampleHapPairs

close

toString