Package main
Class CurrentData
- java.lang.Object
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- main.CurrentData
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public class CurrentData extends java.lang.Object
Class
CurrentData
represents input data for the current marker window. All marker indices returned my methods of classCurrentData
are indexed with respect to the current marker window.Instances of class
CurrentData
are immutable.
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Constructor Summary
Constructors Constructor Description CurrentData(Par par, GeneticMap genMap, Data data, GT overlapHaps)
Constructs a newCurrentData
instance from the specified data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<HapPair>
addRestrictedRefHapPairs(java.util.List<BitHapPair> list)
Returns a list with the specified haplotypes following by the reference haplotype pairs that are restricted to the target data markers.Samples
allSamples()
Returns a list of all target and reference samples.FloatArray
genDist()
Return aFloatArray
of sizethis.nTargMarkers()
whosek
-th element is the genetic distance between thek
-th target marker and the previous marker, or0.0
if(k == 0)
.float
intensity()
Returns the intensity used to generate the pRecomb values.MarkerMap
map()
Returns the genetic map.int
markerIndex(int targetMarker)
Returns the index of the specified marker in the reference data markers.int[]
markerIndices()
Returns an array of lengththis.nTargMarkers()
which maps thek
-th marker in the list of target data markers to the index of the marker in the list of reference data markers.Markers
markers()
Returns the list of reference data markers.int
nAllSamples()
Returns the number of reference and target samples.int
nextOverlapStart()
Returns the first marker index in the overlap between this marker window and the next marker window, or returnsthis.nMarkers()
the next marker window is from a different chromosome.int
nextSpliceStart()
Returns the first marker index after the splice point between this marker window and the next marker window, or returnsthis.nMarkers()
if there is no overlap or if there are no markers after the splice point.int
nextTargetOverlapStart()
Returns the first target marker index in the overlap between this marker window and the next marker window, or returnsthis.nMarkers()
if there is no overlap or if there are no target markers in the overlap.int
nextTargetSpliceStart()
Returns the first target marker index after the splice point between this marker window and the next marker window, or returnsthis.nTargMarkers()
if there is no overlap or if there are no target markers after the splice pointint
nHaps()
int
nMarkers()
Returns the number of reference data markers.int
nRefHaps()
Returns the number of reference haplotypes.int
nRefSamples()
Returns the number of reference samples.int
nTargetSamples()
Returns the number of target samples.int
nTargHaps()
Returns the number of target haplotypes.int
nTargMarkers()
Returns the number of target data markers.Par
par()
Return the analysis parameters.Pedigree
ped()
Returns the parent-offspring relationships.int
prevSpliceStart()
Returns the first marker index after the splice point with the previous marker window.int
prevTargetSpliceStart()
Returns the first target marker index after the splice point with the previous marker window.RefGT
refGT()
Returns the phased, nonmissing reference genotype data ornull
if there are no reference data.Samples
refSamples()
Returns the list of reference samples, ornull
if there are no reference samples.RefGT
restrictRefGT()
Returns the phased, nonmissing reference genotype data for the target data markers ornull
if there are no reference data.GT
targGT()
Returns the genotype likelihoods for the target samples at the target data markers.int
targMarkerIndex(int marker)
Returns the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data.int[]
targMarkerIndices()
Returns an array of lengththis.nMarkers()
whosek
-th element is the index of thek
-th marker in the list of target markers or is -1 if the marker is not present in the target data.Markers
targMarkers()
Returns the list of target data markers.Samples
targSamples()
Returns the list of target samples.int
window()
Returns the marker window index.
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Constructor Detail
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CurrentData
public CurrentData(Par par, GeneticMap genMap, Data data, GT overlapHaps)
Constructs a newCurrentData
instance from the specified data.- Parameters:
par
- the analysis parametersgenMap
- the genetic map ornull
if no genetic map is specifieddata
- input data for the current marker windowoverlapHaps
- haplotype constraints in the overlap with previous window ornull
if no such constraints exist- Throws:
java.lang.IllegalArgumentException
- if(overlapHaps != null && data.targetSamples().equals(overlapHaps.samples()) == false)
java.lang.IllegalArgumentException
- if(overlapHaps != null && overlapHaps.marker(j).equals(data.targGT().marker(j) == false)
for somej
satisfying(0 <= j && j <= overlapHaps.nMarkers())
java.lang.IllegalArgumentException
- ifoverlapHaps != null && overlapHaps.isPhased() == false
java.lang.NullPointerException
- if any parameter isnull
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Method Detail
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par
public Par par()
Return the analysis parameters.- Returns:
- the analysis parameters
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window
public int window()
Returns the marker window index.- Returns:
- the marker window index
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nextOverlapStart
public int nextOverlapStart()
Returns the first marker index in the overlap between this marker window and the next marker window, or returnsthis.nMarkers()
the next marker window is from a different chromosome.- Returns:
- the first marker index in the overlap between this marker window and the next marker window
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nextTargetOverlapStart
public int nextTargetOverlapStart()
Returns the first target marker index in the overlap between this marker window and the next marker window, or returnsthis.nMarkers()
if there is no overlap or if there are no target markers in the overlap.- Returns:
- the first target marker index in the overlap between this marker window and the next marker window
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prevSpliceStart
public int prevSpliceStart()
Returns the first marker index after the splice point with the previous marker window. Returns 0 if the current marker window is the first marker window.- Returns:
- the first marker index after the splice point with the previous marker window
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nextSpliceStart
public int nextSpliceStart()
Returns the first marker index after the splice point between this marker window and the next marker window, or returnsthis.nMarkers()
if there is no overlap or if there are no markers after the splice point.- Returns:
- the first marker index after the next splice point
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prevTargetSpliceStart
public int prevTargetSpliceStart()
Returns the first target marker index after the splice point with the previous marker window. Returns 0 if the current marker window is the first marker window.- Returns:
- the first target marker index after the splice point with the previous marker window
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nextTargetSpliceStart
public int nextTargetSpliceStart()
Returns the first target marker index after the splice point between this marker window and the next marker window, or returnsthis.nTargMarkers()
if there is no overlap or if there are no target markers after the splice point- Returns:
- the first target marker index after the next splice point
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ped
public Pedigree ped()
Returns the parent-offspring relationships.- Returns:
- the parent-offspring relationships
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nRefHaps
public int nRefHaps()
Returns the number of reference haplotypes.- Returns:
- the number of reference haplotypes
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nRefSamples
public int nRefSamples()
Returns the number of reference samples.- Returns:
- the number of reference samples
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refSamples
public Samples refSamples()
Returns the list of reference samples, ornull
if there are no reference samples.- Returns:
- the list of reference samples, or
null
if there are no reference samples
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nTargHaps
public int nTargHaps()
Returns the number of target haplotypes.- Returns:
- the number of target haplotypes
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nTargetSamples
public int nTargetSamples()
Returns the number of target samples.- Returns:
- the number of target samples
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targSamples
public Samples targSamples()
Returns the list of target samples.- Returns:
- the list of target samples
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nHaps
public int nHaps()
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nAllSamples
public int nAllSamples()
Returns the number of reference and target samples.- Returns:
- the number of reference and target samples
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allSamples
public Samples allSamples()
Returns a list of all target and reference samples. Target samples are listed first in the same order as the list returned bythis.targetSamples()
. Reference samples are listed last in the same order as the list returned bythis.refSamples()
.- Returns:
- a list of all target and reference samples
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nTargMarkers
public int nTargMarkers()
Returns the number of target data markers.- Returns:
- the number of target data markers
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targMarkers
public Markers targMarkers()
Returns the list of target data markers.- Returns:
- the list of target data markers
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nMarkers
public int nMarkers()
Returns the number of reference data markers.- Returns:
- the number of reference data markers
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markers
public Markers markers()
Returns the list of reference data markers.- Returns:
- the list of reference data markers
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markerIndex
public int markerIndex(int targetMarker)
Returns the index of the specified marker in the reference data markers.- Parameters:
targetMarker
- index of a marker in the list of target data markers- Returns:
- the index of the specified marker in the reference data markers
- Throws:
java.lang.IndexOutOfBoundsException
- iftargetMarker < 0 || targetMarker >= this.nTargMarkers()
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markerIndices
public int[] markerIndices()
Returns an array of lengththis.nTargMarkers()
which maps thek
-th marker in the list of target data markers to the index of the marker in the list of reference data markers.- Returns:
- an array of length
this.nTargMarkers()
which maps thek
-th marker in the list of target data markers to the index of the marker in the list of reference data markers
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targMarkerIndex
public int targMarkerIndex(int marker)
Returns the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data.- Parameters:
marker
- index of a marker in the reference data- Returns:
- the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
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targMarkerIndices
public int[] targMarkerIndices()
Returns an array of lengththis.nMarkers()
whosek
-th element is the index of thek
-th marker in the list of target markers or is -1 if the marker is not present in the target data.- Returns:
- an array of length
this.nMarkers()
whosek
-th element is the index of thek
-th marker in the list of target markers or is -1 if the marker is not present in the target data
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addRestrictedRefHapPairs
public java.util.List<HapPair> addRestrictedRefHapPairs(java.util.List<BitHapPair> list)
Returns a list with the specified haplotypes following by the reference haplotype pairs that are restricted to the target data markers.- Parameters:
list
- a list of haplotype pairs for target data markers- Returns:
- a list with the specified haplotypes following by the reference haplotype pairs that are restricted to the target data markers
- Throws:
java.lang.NullPointerException
- iflist == null
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refGT
public RefGT refGT()
Returns the phased, nonmissing reference genotype data ornull
if there are no reference data.- Returns:
- the reference genotype data or
null
if there are no reference data
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restrictRefGT
public RefGT restrictRefGT()
Returns the phased, nonmissing reference genotype data for the target data markers ornull
if there are no reference data.- Returns:
- the reference genotype data for the target data markers or
null
if there are no reference data
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targGT
public GT targGT()
Returns the genotype likelihoods for the target samples at the target data markers.- Returns:
- the genotype likelihoods for the target samples at the target data markers.
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intensity
public float intensity()
Returns the intensity used to generate the pRecomb values.- Returns:
- the intensity used to generate the pRecomb values
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map
public MarkerMap map()
Returns the genetic map.- Returns:
- the genetic map
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genDist
public FloatArray genDist()
Return aFloatArray
of sizethis.nTargMarkers()
whosek
-th element is the genetic distance between thek
-th target marker and the previous marker, or0.0
if(k == 0)
.- Returns:
- a
FloatArray
of sizethis.nTargMarkers()
whosek
-th element is the genetic distance between thek
-th target marker and the previous marker,
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