Package vcf

Class Window<E extends GTRec>

java.lang.Object

vcf.Window<E>

Type Parameters:

E - the type of elements in this window

public class Window<E extends GTRec>
extends java.lang.Object

Class Window represents a window of VCF recList.

Constructor Summary

Constructors

Constructor	Description
Window(java.util.List<E> recList, int overlapEnd, int overlapStart, boolean lastWindowOnChrom, boolean lastWindow)	Constructs a new Window instance from the specified data.

Method Summary

Modifier and Type	Method	Description
void	addRecords(java.util.List<E> list, int start, int end)	Adds the specified records to he specified list.
int	chromIndex()	Returns the chromosome index of the first maker in the window.
boolean	lastWindow()	Returns true if the sliding window of genotype records is the last window and returns false otherwise.
boolean	lastWindowOnChrom()	Returns true if the sliding window of genotype records is the last window for its chromosome and returns false otherwise.
int	nMarkers()	Returns the number of markers in this window.
int	overlapEnd()	Returns the index of the first marker after the overlap with the preceding marker window.
int	overlapStart()	Returns the index of the first marker in the overlap with the next marker window.
E	rec(int marker)	Returns the specified record.
java.util.List<E>	recList()	Returns the list of recList in this window.

Methods inherited from class java.lang.Object

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

Constructor Detail

Window

public Window(java.util.List<E> recList,
              int overlapEnd,
              int overlapStart,
              boolean lastWindowOnChrom,
              boolean lastWindow)

Constructs a new Window instance from the specified data. The contract for the constructed instance is undefined if any element of the specified recList is null.

Parameters:

recList - a list of marker recList

overlapEnd - the index of the first marker after the overlap with the preceding marker window

overlapStart - the index of the first marker in the overlap with the next marker window

lastWindowOnChrom - true if the sliding window of VCF Records is the last window for its chromosome

lastWindow - true if the sliding window of VCF Records is the last window

Throws:

java.lang.IllegalArgumentException - if recList.isEmpty()

java.lang.IllegalArgumentException - if lastWindowOnChrom && overlapStart != recList.size()

java.lang.NullPointerException - if recList==null

Method Detail

nMarkers

public int nMarkers()

Returns the number of markers in this window.

Returns:

the number of markers in this window

recList

public java.util.List<E> recList()

Returns the list of recList in this window.

Returns:

the list of recList in this window

rec

public E rec(int marker)

Returns the specified record.

Parameters:

marker - a marker index

Returns:

the specified record

Throws:

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMarkers()

addRecords

public void addRecords(java.util.List<E> list,
                       int start,
                       int end)

Adds the specified records to he specified list.

Parameters:

list - the list to be added to

start - the start record index (inclusive)

end - the end record index (exclusive)

Throws:

java.lang.IndexOutOfBoundsException - if start < 0 || end > this.nMarkers() || start > end

java.lang.NullPointerException - if list == null

overlapEnd

public int overlapEnd()

Returns the index of the first marker after the overlap with the preceding marker window. Returns 0 if the current window is the first window.

Returns:

the index of the first marker after the overlap with the preceding marker window

overlapStart

public int overlapStart()

Returns the index of the first marker in the overlap with the next marker window. Returns this.size() if the next marker window does not exist or is from a different chromosome.

Returns:

the first marker index in the overlap between this marker window and the next marker window

chromIndex

public int chromIndex()

Returns the chromosome index of the first maker in the window.

Returns:

the chromosome index of the first maker in the window

lastWindowOnChrom

public boolean lastWindowOnChrom()

Returns true if the sliding window of genotype records is the last window for its chromosome and returns false otherwise.

Returns:

true if the sliding window of genotype records is the last window for its chromosome

lastWindow

public boolean lastWindow()

Returns true if the sliding window of genotype records is the last window and returns false otherwise.

Returns:

true if the sliding window of genotype records is the last window