E
- the type of elements in the window corresponding to this
window iterator.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.
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> |
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 . |
public static <E extends GTRec> WindowIt<E> newInstance(java.util.function.Supplier<SampleFileIt<E>> supplier, GeneticMap genMap, float windowCM, float overlapCM)
WindowIt
instance for
the specified data.E
- the type of elements in windows for the returned
window iterator.supplier
- the object which supplies the SampleFileIt
which
reads input datagenMap
- the genetic mapwindowCM
- the requested window length in cMoverlapCM
- the requested overlap in cM between consecutive
windows on the same chromosomeWindowIt
instance for the specified datajava.lang.IllegalArgumentException
- if a format error is detected in the
input filejava.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
public GeneticMap genMap()
public boolean hasNext()
true
if the sliding window of VCF recList can advance
and returns false
otherwise.public Window<E> next()
RefGTRec[]
object.next
in interface java.util.Iterator<E extends GTRec>
java.lang.IllegalArgumentException
- if a format error in the input data
is detectedjava.lang.IllegalArgumentException
- if
windowCm <= this.overlap() || Float.isFinite(windowCm) == false
java.lang.IllegalStateException
- if
this.canAdvanceWindow() == false
public java.io.File file()
null
if the source is standard input.public Samples samples()
samples
in interface SampleFileIt<E extends GTRec>
public void close()
public java.lang.String toString()
this
. The exact
details of the representation are unspecified and subject to change.