Package gorsat

Class BatchedPipeStepIteratorAdaptor

java.lang.Object

org.gorpipe.gor.model.GenomicIteratorBase

gorsat.BatchedPipeStepIteratorAdaptor

All Implemented Interfaces:

AutoCloseable, Iterator<org.gorpipe.gor.model.Row>, Spliterator<org.gorpipe.gor.model.Row>, org.gorpipe.gor.model.GenomicIterator, org.gorpipe.gor.model.RowSourceStats

public class BatchedPipeStepIteratorAdaptor
extends org.gorpipe.gor.model.GenomicIteratorBase
implements Spliterator<org.gorpipe.gor.model.Row>

Created by sigmar on 05/05/2017.

Nested Class Summary

Nested classes/interfaces inherited from interface java.util.Spliterator

Spliterator.OfDouble, Spliterator.OfInt, Spliterator.OfLong, Spliterator.OfPrimitive<T extends Object,T_CONS extends Object,T_SPLITR extends Spliterator.OfPrimitive<T,T_CONS,T_SPLITR>>

Field Summary

Fields inherited from class org.gorpipe.gor.model.GenomicIteratorBase

statsSenderAnnotation, statsSenderName

Fields inherited from interface java.util.Spliterator

CONCURRENT, DISTINCT, IMMUTABLE, NONNULL, ORDERED, SIZED, SORTED, SUBSIZED

Constructor Summary

Constructors

Constructor	Description
BatchedPipeStepIteratorAdaptor(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator, gorsat.Commands.Analysis pipeStep, boolean autoclose, String theHeader, BatchedReadSourceConfig brsConfig)
BatchedPipeStepIteratorAdaptor(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator, gorsat.Commands.Analysis pipeStep, String theHeader, BatchedReadSourceConfig brsConfig)

Method Summary

Modifier and Type	Method	Description
int	characteristics()
BatchedPipeStepIteratorAdaptor	clone()
void	close()
long	estimateSize()
void	forEachRemaining(Consumer<? super org.gorpipe.gor.model.Row> action)
double	getAvgBasesPerMilliSecond()
double	getAvgBatchSize()
double	getAvgRowsPerMilliSecond()
Comparator<org.gorpipe.gor.model.Row>	getComparator()
int	getCurrentBatchLoc()
org.gorpipe.gor.model.Row	getCurrentBatchRow(int i)
int	getCurrentBatchSize()
Throwable	getEx()
Stream<org.gorpipe.gor.model.Row>	getStream()
Stream<org.gorpipe.gor.model.Row>	getStream(boolean parallel)
boolean	hasNext()
boolean	isBuffered()
org.gorpipe.gor.model.Row	next()
void	remove()
boolean	seek(String seekChr, int seekPos)
boolean	seek(String seekChr, int seekPos, int endPos)
void	setCurrentChrom(String chrom)
void	setEx(Throwable throwable)
String	toString()
boolean	tryAdvance(Consumer<? super org.gorpipe.gor.model.Row> action)
Spliterator<org.gorpipe.gor.model.Row>	trySplit()

Methods inherited from class org.gorpipe.gor.model.GenomicIteratorBase

decStat, getBufferSize, getContext, getHeader, getSourceName, getTypes, incStat, init, initStats, isSourceAlreadyInserted, setBufferSize, setContext, setHeader, setSourceAlreadyInserted, setSourceName, setTypes

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.gorpipe.gor.model.GenomicIterator

filter, getMonitor, moveToPosition, moveToPosition, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, select, setRequestedRange

Methods inherited from interface org.gorpipe.gor.model.RowSourceStats

getAvgSeekTimeMilliSecond

Methods inherited from interface java.util.Spliterator

getExactSizeIfKnown, hasCharacteristics

Constructor Details

BatchedPipeStepIteratorAdaptor

public BatchedPipeStepIteratorAdaptor(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator,
 gorsat.Commands.Analysis pipeStep,
 String theHeader,
 BatchedReadSourceConfig brsConfig)

BatchedPipeStepIteratorAdaptor

public BatchedPipeStepIteratorAdaptor(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator,
 gorsat.Commands.Analysis pipeStep,
 boolean autoclose,
 String theHeader,
 BatchedReadSourceConfig brsConfig)

Method Details

setEx

public void setEx(Throwable throwable)

getEx

public Throwable getEx()

setCurrentChrom

public void setCurrentChrom(String chrom)

getAvgRowsPerMilliSecond

public double getAvgRowsPerMilliSecond()

Specified by:

getAvgRowsPerMilliSecond in interface org.gorpipe.gor.model.RowSourceStats

getAvgBasesPerMilliSecond

public double getAvgBasesPerMilliSecond()

Specified by:

getAvgBasesPerMilliSecond in interface org.gorpipe.gor.model.RowSourceStats

getAvgBatchSize

public double getAvgBatchSize()

Specified by:

getAvgBatchSize in interface org.gorpipe.gor.model.RowSourceStats

getCurrentBatchSize

public int getCurrentBatchSize()

Specified by:

getCurrentBatchSize in interface org.gorpipe.gor.model.RowSourceStats

getCurrentBatchLoc

public int getCurrentBatchLoc()

Specified by:

getCurrentBatchLoc in interface org.gorpipe.gor.model.RowSourceStats

getCurrentBatchRow

public org.gorpipe.gor.model.Row getCurrentBatchRow(int i)

Specified by:

getCurrentBatchRow in interface org.gorpipe.gor.model.RowSourceStats

getStream

public Stream<org.gorpipe.gor.model.Row> getStream()

getStream

public Stream<org.gorpipe.gor.model.Row> getStream(boolean parallel)

getComparator

public Comparator<org.gorpipe.gor.model.Row> getComparator()

Specified by:

getComparator in interface Spliterator<org.gorpipe.gor.model.Row>

tryAdvance

public boolean tryAdvance(Consumer<? super org.gorpipe.gor.model.Row> action)

Specified by:

tryAdvance in interface Spliterator<org.gorpipe.gor.model.Row>

clone

public BatchedPipeStepIteratorAdaptor clone()
                                     throws CloneNotSupportedException

Overrides:

clone in class org.gorpipe.gor.model.GenomicIteratorBase

Throws:

CloneNotSupportedException

trySplit

public Spliterator<org.gorpipe.gor.model.Row> trySplit()

Specified by:

trySplit in interface Spliterator<org.gorpipe.gor.model.Row>

estimateSize

public long estimateSize()

Specified by:

estimateSize in interface Spliterator<org.gorpipe.gor.model.Row>

characteristics

public int characteristics()

Specified by:

characteristics in interface Spliterator<org.gorpipe.gor.model.Row>

toString

public String toString()

Overrides:

toString in class Object

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<org.gorpipe.gor.model.Row>

next

public org.gorpipe.gor.model.Row next()

Specified by:

next in interface Iterator<org.gorpipe.gor.model.Row>

remove

public void remove()

Specified by:

remove in interface Iterator<org.gorpipe.gor.model.Row>

forEachRemaining

public void forEachRemaining(Consumer<? super org.gorpipe.gor.model.Row> action)

Specified by:

forEachRemaining in interface Iterator<org.gorpipe.gor.model.Row>

Specified by:

forEachRemaining in interface Spliterator<org.gorpipe.gor.model.Row>

seek

public boolean seek(String seekChr,
 int seekPos)

Specified by:

seek in interface org.gorpipe.gor.model.GenomicIterator

seek

public boolean seek(String seekChr,
 int seekPos,
 int endPos)

Specified by:

seek in interface org.gorpipe.gor.model.GenomicIterator

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface org.gorpipe.gor.model.GenomicIterator

isBuffered

public boolean isBuffered()

Specified by:

isBuffered in interface org.gorpipe.gor.model.GenomicIterator