Package vcf

Class WindowIt<E extends GTRec>

java.lang.Object

vcf.WindowIt<E>

Type Parameters:

E - the type of elements in the window corresponding to this window iterator.

All Implemented Interfaces:

FileIt<Window<E>>, SampleFileIt<Window<E>>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<Window<E>>

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

Class WindowIt represents a sliding window of VCF recList.

Instances of class WindowIt are not thread-safe.

Method Summary

Modifier and Type	Method	Description
void	close()	Releases any I/O resources controlled by this object.
java.io.File	file()	Returns the file from which VCF recList are read, or returns null if the source is standard input.
GeneticMap	genMap()	Returns the genetic map.
boolean	hasNext()	Returns true if the sliding window of VCF recList can advance and returns false otherwise.
static <E extends GTRec> WindowIt<E>	newInstance(java.util.function.Supplier<SampleFileIt<E>> supplier, GeneticMap genMap, float windowCM, float overlapCM)	Constructs and returns a new WindowIt instance for the specified data.
Window<E>	next()	Advances the sliding window of VCF recList, and returns the advanced window as a RefGTRec[] object.
Samples	samples()	Returns the list of samples.
java.lang.String	toString()	Returns a string representation of this.

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Methods inherited from class java.lang.Object

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

Method Detail

newInstance

public static <E extends GTRec> WindowIt<E> newInstance(java.util.function.Supplier<SampleFileIt<E>> supplier,
                                                        GeneticMap genMap,
                                                        float windowCM,
                                                        float overlapCM)

Constructs and returns a new WindowIt instance for the specified data.

Type Parameters:

E - the type of elements in windows for the returned window iterator.

Parameters:

supplier - the object which supplies the SampleFileIt which reads input data

genMap - the genetic map

windowCM - the requested window length in cM

overlapCM - the requested overlap in cM between consecutive windows on the same chromosome

Returns:

a new WindowIt instance for the specified data

Throws:

java.lang.IllegalArgumentException - if a format error is detected in the input file

java.lang.IllegalArgumentException - if overlap < 0 || Float.isFinite(overlap) == false

java.lang.IllegalArgumentException - if window <= overlap || Float.isFinite(window) == false

java.lang.NullPointerException - if it == null || genMap == null

genMap

public GeneticMap genMap()

Returns the genetic map.

Returns:

the genetic map

hasNext

public boolean hasNext()

Returns true if the sliding window of VCF recList can advance and returns false otherwise.

Specified by:

hasNext in interface java.util.Iterator<E extends GTRec>

Returns:

true if the sliding window of VCF recList can advance

next

public Window<E> next()

Advances the sliding window of VCF recList, and returns the advanced window as a RefGTRec[] object.

Specified by:

next in interface java.util.Iterator<E extends GTRec>

Returns:

the advanced window of VCF recList

Throws:

java.lang.IllegalArgumentException - if a format error in the input data is detected

java.lang.IllegalArgumentException - if windowCm <= this.overlap() || Float.isFinite(windowCm) == false

java.lang.IllegalStateException - if this.canAdvanceWindow() == false

file

public java.io.File file()

Returns the file from which VCF recList are read, or returns null if the source is standard input.

Specified by:

file in interface FileIt<E extends GTRec>

Returns:

the file from which VCF recList are read, or null if the source is standard input

samples

public Samples samples()

Returns the list of samples.

Specified by:

samples in interface SampleFileIt<E extends GTRec>

Returns:

the list of samples

close

public void close()

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 FileIt<E extends GTRec>

toString

public java.lang.String toString()

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Specified by:

toString in interface FileIt<E extends GTRec>

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this