Package vcf

Class MarkerIndices

java.lang.Object
vcf.MarkerIndices
public class MarkerIndices extends Object

Class MarkerIndices stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.

Instances of class MarkerIndices are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    MarkerIndices(boolean[] inTarg, int overlapEnd, int overlapStart)
    Constructs a MarkerIndices instance from the specified data.
    MarkerIndices(int overlapEnd, int overlapStart, int nMarkers)
    Constructs a MarkerIndices instance from the specified data

  • Method Summary

    Modifier and Type
    Method
    Description
    int[]
    markerToTargMarker()
    Returns an array of length this.nMarkers() whose k-th element is the index of the k-th marker in the list of target markers or is -1 if the marker is not present in the target data.
    int
    markerToTargMarker(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
    nextSplice()
    Returns the first marker index after the splice point between this marker window and the next marker window, or returns this.nMarkers() if there is no overlap or if there are no markers after the splice point.
    int
    nextTargSplice()
    Returns the first target marker index after the splice point between this marker window and the next marker window, or returns this.nTargMarkers() if there is no overlap or if there are no target markers after the splice point
    int
    nMarkers()
    Returns the number of markers
    int
    nTargMarkers()
    Returns the number of target markers
    int
    overlapEnd()
    Returns the end marker index (exclusive) of the overlap with the previous window.
    int
    overlapStart()
    Returns the first marker index in the overlap between this marker window and the next marker window.
    int
    prevSplice()
    Returns the first marker index after the splice point with the previous marker window.
    int
    prevTargSplice()
    Returns the first target marker index after the splice point with the previous marker window.
    int[]
    targMarkerToMarker()
    Returns an array of length this.nTargMarkers() which maps the k-th marker in the list of target data markers to the index of the marker in the list of reference data markers.
    int
    targMarkerToMarker(int targetMarker)
    Returns the index of the specified marker in the reference data markers.
    int
    targOverlapEnd()
    Returns the end marker index (exclusive) of the overlap with the previous window in the target data.
    int
    targOverlapStart()
    Returns the first marker index of the overlap between this marker window and the next marker window in the target data.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • MarkerIndices

      public MarkerIndices(boolean[] inTarg, int overlapEnd, int overlapStart)
      Constructs a MarkerIndices instance from the specified data.
      Parameters:
      inTarg - an array whose k-th element is true if the k-th marker is present in the target genotype data
      overlapEnd - the end marker index (exclusive) of the overlap with the previous window
      overlapStart - the start marker index (inclusive) of the overlap with the next window
      Throws:
      IndexOutOfBoundsException - if overlapEnd < 0 || overlapEnd > inTarg.length
      IndexOutOfBoundsException - if overlapStart < 0 || overlapStart > inTarg.length
      NullPointerException - if inTarg==null

    • MarkerIndices

      public MarkerIndices(int overlapEnd, int overlapStart, int nMarkers)
      Constructs a MarkerIndices instance from the specified data
      Parameters:
      overlapEnd - the ending marker index (exclusive) for the overlap with the previous window
      overlapStart - the starting marker index (inclusive) for the overlap with the next window
      nMarkers - the number of markers
      Throws:
      IllegalArgumentException - if nMarkers < 0
      IndexOutOfBoundsException - if overlapEnd < 0 || overlapEnd > nMarkers
      IndexOutOfBoundsException - if overlapStart < 0 || overlapStart > nMarkers

  • Method Details

    • nMarkers

      public int nMarkers()
      Returns the number of markers
      Returns:
      the number of markers

    • nTargMarkers

      public int nTargMarkers()
      Returns the number of target markers
      Returns:
      the number of target markers

    • prevSplice

      public int prevSplice()
      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

    • overlapEnd

      public int overlapEnd()
      Returns the end marker index (exclusive) of the overlap with the previous window.
      Returns:
      the end marker index (exclusive) of the overlap with the previous window

    • overlapStart

      public int overlapStart()
      Returns the first marker index in the overlap between this marker window and the next marker window. Returns this.nMarkers() if this marker window is the last on its chromosome.
      Returns:
      the first marker index in the overlap between this marker window and the next marker window

    • prevTargSplice

      public int prevTargSplice()
      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

    • nextSplice

      public int nextSplice()
      Returns the first marker index after the splice point between this marker window and the next marker window, or returns this.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

    • targOverlapEnd

      public int targOverlapEnd()
      Returns the end marker index (exclusive) of the overlap with the previous window in the target data.
      Returns:
      the end marker index (exclusive) of the overlap with the previous window in the target data

    • targOverlapStart

      public int targOverlapStart()
      Returns the first marker index of the overlap between this marker window and the next marker window in the target data. Returns this.nMarkers() if there is no overlap or if there are no target markers in the overlap.
      Returns:
      the first marker index of the overlap between this marker window and the next marker window in the target data

    • nextTargSplice

      public int nextTargSplice()
      Returns the first target marker index after the splice point between this marker window and the next marker window, or returns this.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

    • targMarkerToMarker

      public int targMarkerToMarker(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:
      IndexOutOfBoundsException - if targetMarker < 0 || targetMarker >= this.nTargMarkers()

    • targMarkerToMarker

      public int[] targMarkerToMarker()
      Returns an array of length this.nTargMarkers() which maps the k-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 the k-th marker in the list of target data markers to the index of the marker in the list of reference data markers

    • markerToTargMarker

      public int markerToTargMarker(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:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers().

    • markerToTargMarker

      public int[] markerToTargMarker()
      Returns an array of length this.nMarkers() whose k-th element is the index of the k-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() whose k-th element is the index of the k-th marker in the list of target markers or is -1 if the marker is not present in the target data