Package gorsat

Class BatchedReadSource

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>
    public class BatchedReadSource
extends org.gorpipe.model.gor.iterators.RowSource
    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.

    • Nested Class Summary

      • Nested classes/interfaces inherited from class org.gorpipe.gor.model.GenomicIterator

        org.gorpipe.gor.model.GenomicIterator.ChromoLookup

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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()  
      boolean hasNext()  
      boolean isBuffered()  
      boolean isCancelled()  
      org.gorpipe.gor.model.Row next()
      Make sure hasNext is called before this method
      void setPosition​(java.lang.String seekChr, int seekPos)  
      void updateTimeMeasurement​(long deltaTimeNs, RowBuffer current)  

      • Methods inherited from class org.gorpipe.model.gor.iterators.RowSource

        bufferSize, bufferSize_$eq, getBufferSize, getGorHeader, getParent, moveToPosition, moveToPosition$default$3, next, parent, parent_$eq, seek, setBufferSize, setParent, terminateReading

      • Methods inherited from class org.gorpipe.gor.model.GenomicIterator

        clone, decStat, filter, getColnum, getContext, getEx, getHeader, getLookup, getMonitor, getSourceName, incStat, init, initStats, isSourceAlreadyInserted, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select, selectHeader, setColnum, setContext, setEx, setHeader, setSourceAlreadyInserted, setSourceName

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.util.Iterator

        forEachRemaining, remove

    • Constructor Detail

      • BatchedReadSource

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

      • BatchedReadSource

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

    • Method Detail

      • updateTimeMeasurement

        public void updateTimeMeasurement​(long deltaTimeNs,
                                  RowBuffer current)

      • getAvgRowsPerMilliSecond

        public double getAvgRowsPerMilliSecond()
        Overrides:
        getAvgRowsPerMilliSecond in class org.gorpipe.model.gor.iterators.RowSource

      • getAvgBasesPerMilliSecond

        public double getAvgBasesPerMilliSecond()
        Overrides:
        getAvgBasesPerMilliSecond in class org.gorpipe.model.gor.iterators.RowSource

      • getAvgSeekTimeMilliSecond

        public double getAvgSeekTimeMilliSecond()
        Overrides:
        getAvgSeekTimeMilliSecond in class org.gorpipe.model.gor.iterators.RowSource

      • getAvgBatchSize

        public double getAvgBatchSize()
        Overrides:
        getAvgBatchSize in class org.gorpipe.model.gor.iterators.RowSource

      • getCurrentBatchSize

        public int getCurrentBatchSize()
        Overrides:
        getCurrentBatchSize in class org.gorpipe.model.gor.iterators.RowSource

      • getCurrentBatchLoc

        public int getCurrentBatchLoc()
        Overrides:
        getCurrentBatchLoc in class org.gorpipe.model.gor.iterators.RowSource

      • getCurrentBatchRow

        public org.gorpipe.gor.model.Row getCurrentBatchRow​(int i)
        Overrides:
        getCurrentBatchRow in class org.gorpipe.model.gor.iterators.RowSource

      • hasNext

        public boolean hasNext()
        Specified by:
        hasNext in interface java.util.Iterator<org.gorpipe.gor.model.Row>
        Overrides:
        hasNext in class org.gorpipe.gor.model.GenomicIterator
        Returns:
        true if rowSource has more rows

      • next

        public org.gorpipe.gor.model.Row next()
        Make sure hasNext is called before this method
        Specified by:
        next in interface java.util.Iterator<org.gorpipe.gor.model.Row>
        Overrides:
        next in class org.gorpipe.gor.model.GenomicIterator
        Returns:
        the next row in the iterator

      • setPosition

        public void setPosition​(java.lang.String seekChr,
                        int seekPos)
        Specified by:
        setPosition in class org.gorpipe.model.gor.iterators.RowSource

      • isCancelled

        public boolean isCancelled()

      • close

        public void close()
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in class org.gorpipe.model.gor.iterators.RowSource

      • isBuffered

        public boolean isBuffered()
        Overrides:
        isBuffered in class org.gorpipe.gor.model.GenomicIterator