Package vcf

Class IntervalVcfIt<E extends MarkerContainer>

java.lang.Object
vcf.IntervalVcfIt<E>
Type Parameters:
E - the type parameter
All Implemented Interfaces:
FileIt<E>, SampleFileIt<E>, Closeable, AutoCloseable, Iterator<E>
public final class IntervalVcfIt<E extends MarkerContainer> extends Object implements SampleFileIt<E>

Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.

  • Constructor Summary

    Constructors
    Constructor
    Description
    IntervalVcfIt(SampleFileIt<E> it, ChromInterval chromInt)
    Constructs a new IntervalVcfIterator instance.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    Stops reading data elements and releases any system resources that are held by this object.
    File
    file()
    Returns the file from which the data are read, or null if the data are read from standard input or if the data source is unknown.
    boolean
    hasNext()
    Returns true if the iteration has more elements.
    E
    next()
    Returns the next element in the iteration.
    void
    remove()
    The remove method is not supported by this iterator.
    Samples
    samples()
    Returns the list of samples.

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface blbutil.FileIt

    toString

    Methods inherited from interface java.util.Iterator

    forEachRemaining

  • Constructor Details

    • IntervalVcfIt

      public IntervalVcfIt(SampleFileIt<E> it, ChromInterval chromInt)
      Constructs a new IntervalVcfIterator instance.
      Parameters:
      it - an iterator whose next() method returns a marker container
      chromInt - a chromosome interval
      Throws:
      NullPointerException - if it == null || interval == null

  • Method Details

    • file

      public File file()
      Description copied from interface: FileIt
      Returns the file from which the data are read, or null if the data are read from standard input or if the data source is unknown.
      Specified by:
      file in interface FileIt<E extends MarkerContainer>
      Returns:
      the file from which the data are read, or null if the data are read from standard input or if the data source is unknown

    • samples

      public Samples samples()
      Description copied from interface: SampleFileIt
      Returns the list of samples.
      Specified by:
      samples in interface SampleFileIt<E extends MarkerContainer>
      Returns:
      the list of samples

    • hasNext

      public boolean hasNext()
      Returns true if the iteration has more elements.
      Specified by:
      hasNext in interface Iterator<E extends MarkerContainer>
      Returns:
      true if the iteration has more elements.

    • next

      public E next()
      Returns the next element in the iteration.
      Specified by:
      next in interface Iterator<E extends MarkerContainer>
      Returns:
      the next element in the iteration.
      Throws:
      NoSuchElementException - if the iteration has no more elements.

    • remove

      public void remove()
      The remove method is not supported by this iterator.
      Specified by:
      remove in interface Iterator<E extends MarkerContainer>
      Throws:
      UnsupportedOperationException - if this method is invoked

    • close

      public void close()
      Description copied from interface: FileIt
      Stops reading data elements and releases any system resources that are held by this object. Buffered data elements may remain accessible via the hasNext() and next() methods after invoking close(). After invoking close(), further invocations of close() have no effect.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface FileIt<E extends MarkerContainer>