Package gorsat

Class 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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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_$eq, getAvgSeekTimeMilliSecond, getBufferSize, getGorHeader, getParent, moveToPosition, moveToPosition$default$3, next, parent, parent_$eq, seek, setBufferSize, setParent, terminateReading

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

        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, wait, wait, wait

      • Methods inherited from interface java.util.Spliterator

        getExactSizeIfKnown, hasCharacteristics

    • Constructor Detail

      • BatchedPipeStepIteratorAdaptor

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

      • BatchedPipeStepIteratorAdaptor

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

    • Method Detail

      • 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()
                                     throws java.lang.CloneNotSupportedException
        Overrides:
        clone in class org.gorpipe.gor.model.GenomicIterator
        Throws:
        java.lang.CloneNotSupportedException

      • 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)
        Specified by:
        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.gor.model.GenomicIterator