Package vcf

Class TargSlidingWindow

  • All Implemented Interfaces:
    java.io.Closeable, java.lang.AutoCloseable, SlidingWindow
    public class TargSlidingWindow
extends java.lang.Object
implements SlidingWindow

    Class TargSlidingWindow represents a sliding window of target VCF records.

    Instances of class TargSlidingWindow are not thread-safe.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Releases any I/O resources controlled by this object.
      int cumMarkers()
      Returns the number of distinct markers returned in preceding this.nextWindow() method calls.
      int cumTargMarkers()
      Returns the number of distinct target markers returned in preceding this.nextWindow() method calls.
      GeneticMap genMap()
      Returns the genetic map.
      static TargSlidingWindow instance​(Par par)
      Constructs and returns a new TargSlidingWindow instance for the specified target data.
      java.util.Optional<Window> nextWindow()
      Returns the next sliding window of VCF records.
      Pedigree ped()
      Returns the target sample pedigree data.
      Samples targSamples()
      Returns the target samples.
      java.lang.String toString()
      Returns a string representation of this.

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • instance

        public static TargSlidingWindow instance​(Par par)
        Constructs and returns a new TargSlidingWindow instance for the specified target data.
        Parameters:
        par - the command line parameters
        Returns:
        a new TargSlidingWindow instance for the specified target data
        Throws:
        java.lang.IllegalArgumentException - if par.ref() != null
        java.lang.IllegalArgumentException - if a VCF record format error is detected or if there is no data remaining after sample and marker filtering
        java.lang.NullPointerException - if par == null

      • ped

        public Pedigree ped()
        Description copied from interface: SlidingWindow
        Returns the target sample pedigree data.
        Specified by:
        ped in interface SlidingWindow
        Returns:
        the target sample pedigree data

      • cumTargMarkers

        public int cumTargMarkers()
        Description copied from interface: SlidingWindow
        Returns the number of distinct target markers returned in preceding this.nextWindow() method calls.
        Specified by:
        cumTargMarkers in interface SlidingWindow
        Returns:
        the number of distinct target markers returned in preceding this.nextWindow() method calls

      • cumMarkers

        public int cumMarkers()
        Description copied from interface: SlidingWindow
        Returns the number of distinct markers returned in preceding this.nextWindow() method calls.
        Specified by:
        cumMarkers in interface SlidingWindow
        Returns:
        the number of distinct markers returned in preceding this.nextWindow() method calls

      • nextWindow

        public java.util.Optional<Window> nextWindow()
        Description copied from interface: SlidingWindow
        Returns the next sliding window of VCF records.
        Specified by:
        nextWindow in interface SlidingWindow
        Returns:
        the next sliding window of VCF records or Optional.empty() if there are no additional windows.

      • close

        public void close()
        Description copied from interface: SlidingWindow
        Releases any I/O resources controlled by this object.
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface java.io.Closeable
        Specified by:
        close in interface SlidingWindow

      • 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.