Package gorsat

Class BatchedReadSource

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.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

    • 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()  
      java.lang.Throwable getEx()  
      boolean hasNext()  
      boolean isBuffered()  
      boolean isCancelled()  
      org.gorpipe.gor.model.Row next()
      Make sure hasNext is called before this method
      boolean seek​(java.lang.String seekChr, int seekPos)  
      void setEx​(java.lang.Throwable throwable)  
      void updateTimeMeasurement​(long deltaTimeNs, RowBuffer current)  

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

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

      • 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

      • 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

      • setEx

        public void setEx​(java.lang.Throwable throwable)

      • getEx

        public java.lang.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​(java.lang.String seekChr,
                    int seekPos)

      • isCancelled

        public boolean isCancelled()

      • close

        public void close()

      • isBuffered

        public boolean isBuffered()