Package gorsat

Class BatchedPipeStepIteratorAdaptor

java.lang.Object
org.gorpipe.gor.model.GenomicIterator
org.gorpipe.model.gor.iterators.RowSource
gorsat.BatchedPipeStepIteratorAdaptor
All Implemented Interfaces:
java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>, java.util.Spliterator<org.gorpipe.gor.model.Row>
public class BatchedPipeStepIteratorAdaptor
extends org.gorpipe.model.gor.iterators.RowSource
implements java.util.Spliterator<org.gorpipe.gor.model.Row>
Created by sigmar on 05/05/2017.

  • Nested Class Summary

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

    org.gorpipe.gor.model.GenomicIterator.ChromoLookup

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

    java.util.Spliterator.OfDouble, java.util.Spliterator.OfInt, java.util.Spliterator.OfLong, java.util.Spliterator.OfPrimitive<T extends java.lang.Object,​T_CONS extends java.lang.Object,​T_SPLITR extends java.util.Spliterator.OfPrimitive<T,​T_CONS,​T_SPLITR>>

  • Field Summary

    Fields inherited from interface java.util.Spliterator

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

  • Constructor Summary

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

  • Method Summary

    Modifier and Type Method Description
    int characteristics()  
    BatchedPipeStepIteratorAdaptor clone()  
    void close()  
    long estimateSize()  
    void forEachRemaining​(java.util.function.Consumer<? super org.gorpipe.gor.model.Row> action)  
    double getAvgBasesPerMilliSecond()  
    double getAvgBatchSize()  
    double getAvgRowsPerMilliSecond()  
    java.util.Comparator<org.gorpipe.gor.model.Row> getComparator()  
    int getCurrentBatchLoc()  
    org.gorpipe.gor.model.Row getCurrentBatchRow​(int i)  
    int getCurrentBatchSize()  
    java.util.stream.Stream<org.gorpipe.gor.model.Row> getStream()  
    java.util.stream.Stream<org.gorpipe.gor.model.Row> getStream​(boolean parallel)  
    boolean hasNext()  
    boolean isBuffered()  
    org.gorpipe.gor.model.Row next()  
    void remove()  
    void setCurrentChrom​(java.lang.String chrom)  
    void setPosition​(java.lang.String seekChr, int seekPos)  
    java.lang.String toString()  
    boolean tryAdvance​(java.util.function.Consumer<? super org.gorpipe.gor.model.Row> action)  
    java.util.Spliterator<org.gorpipe.gor.model.Row> trySplit()  
    void updateTimeMeasurement​(long deltaTimeNs, RowBuffer current)  

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

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

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

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

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface java.util.Spliterator

    getExactSizeIfKnown, hasCharacteristics

  • Constructor Details

  • Method Details

    • setCurrentChrom

      public void setCurrentChrom​(java.lang.String chrom)

    • 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

    • 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

    • updateTimeMeasurement

      public void updateTimeMeasurement​(long deltaTimeNs, RowBuffer current)

    • getStream

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

    • getStream

      public java.util.stream.Stream<org.gorpipe.gor.model.Row> getStream​(boolean parallel)

    • getComparator

      public java.util.Comparator<org.gorpipe.gor.model.Row> getComparator()
      Specified by:
      getComparator in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • tryAdvance

      public boolean tryAdvance​(java.util.function.Consumer<? super org.gorpipe.gor.model.Row> action)
      Specified by:
      tryAdvance in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • clone

      public BatchedPipeStepIteratorAdaptor clone()
      Overrides:
      clone in class org.gorpipe.model.gor.iterators.RowSource

    • trySplit

      public java.util.Spliterator<org.gorpipe.gor.model.Row> trySplit()
      Specified by:
      trySplit in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • estimateSize

      public long estimateSize()
      Specified by:
      estimateSize in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • characteristics

      public int characteristics()
      Specified by:
      characteristics in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • toString

      public java.lang.String toString()
      Overrides:
      toString in class java.lang.Object

    • 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

    • next

      public org.gorpipe.gor.model.Row next()
      Specified by:
      next in interface java.util.Iterator<org.gorpipe.gor.model.Row>
      Overrides:
      next in class org.gorpipe.gor.model.GenomicIterator

    • remove

      public void remove()
      Specified by:
      remove in interface java.util.Iterator<org.gorpipe.gor.model.Row>

    • forEachRemaining

      public void forEachRemaining​(java.util.function.Consumer<? super org.gorpipe.gor.model.Row> action)
      Specified by:
      forEachRemaining in interface java.util.Iterator<org.gorpipe.gor.model.Row>
      Specified by:
      forEachRemaining in interface java.util.Spliterator<org.gorpipe.gor.model.Row>

    • setPosition

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

    • 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.model.gor.iterators.RowSource