Package gorsat

Class BatchedReadSource

java.lang.Object

org.gorpipe.gor.model.GenomicIteratorBase

gorsat.BatchedReadSource

All Implemented Interfaces:

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

public class BatchedReadSource
extends org.gorpipe.gor.model.GenomicIteratorBase

A wrapper rowSource reading the child rowSource in a thread into a buffer and offering to the main thread in batches

Created by sigmar on 21/11/2016.

Field Summary

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

statsSenderAnnotation, statsSenderName

Constructor Summary

Constructors

Constructor	Description
BatchedReadSource(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator, BatchedReadSourceConfig brsConfig, String header, org.gorpipe.gor.monitor.GorMonitor gorMonitor)
BatchedReadSource(org.gorpipe.gor.model.GenomicIterator sourceIterator, BatchedReadSourceConfig brsConfig)

Method Summary

Modifier and Type	Method	Description
void	close()
double	getAvgBasesPerMilliSecond()
double	getAvgBatchSize()
double	getAvgRowsPerMilliSecond()
double	getAvgSeekTimeMilliSecond()
int	getCurrentBatchLoc()
org.gorpipe.gor.model.Row	getCurrentBatchRow(int i)
int	getCurrentBatchSize()
Throwable	getEx()
boolean	hasNext()
boolean	isBuffered()
boolean	isCancelled()
org.gorpipe.gor.model.Row	next()	Make sure hasNext is called before this method
boolean	seek(String seekChr, int seekPos)
void	setEx(Throwable throwable)
void	updateTimeMeasurement(long deltaTimeNs, RowBuffer current)

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

clone, 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, toString, wait, wait, wait

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

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

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Constructor Details

BatchedReadSource

public BatchedReadSource(org.gorpipe.gor.model.GenomicIterator sourceIterator,
 BatchedReadSourceConfig brsConfig)

BatchedReadSource

public BatchedReadSource(Iterator<? extends org.gorpipe.gor.model.Row> sourceIterator,
 BatchedReadSourceConfig brsConfig,
 String header,
 org.gorpipe.gor.monitor.GorMonitor gorMonitor)

Method Details

setEx

public void setEx(Throwable throwable)

getEx

public Throwable getEx()

updateTimeMeasurement

public void updateTimeMeasurement(long deltaTimeNs,
 RowBuffer current)

getAvgRowsPerMilliSecond

public double getAvgRowsPerMilliSecond()

getAvgBasesPerMilliSecond

public double getAvgBasesPerMilliSecond()

getAvgSeekTimeMilliSecond

public double getAvgSeekTimeMilliSecond()

getAvgBatchSize

public double getAvgBatchSize()

getCurrentBatchSize

public int getCurrentBatchSize()

getCurrentBatchLoc

public int getCurrentBatchLoc()

getCurrentBatchRow

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

hasNext

public boolean hasNext()

Returns:

true if rowSource has more rows

next

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

Make sure hasNext is called before this method

Returns:

the next row in the iterator

seek

public boolean seek(String seekChr,
 int seekPos)

isCancelled

public boolean isCancelled()

close

public void close()

isBuffered

public boolean isBuffered()