Package gorsat.process

Class ProcessRowSource

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>
    public class ProcessRowSource
extends ProcessSource
    Created by sigmar on 12/02/16.

    • Nested Class Summary

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

        org.gorpipe.gor.model.GenomicIterator.ChromoLookup

    • Constructor Summary

      Constructors 
      Constructor Description
      ProcessRowSource​(java.lang.String cmd, java.lang.String type, boolean nor, org.gorpipe.gor.session.GorSession session, gorsat.Commands.GenomicRange.Range range, java.lang.String filter)  
      ProcessRowSource​(java.lang.String cmd, java.lang.String type, boolean nor, org.gorpipe.gor.session.GorSession session, gorsat.Commands.GenomicRange.Range range, java.lang.String filter, int bs)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String checkNested​(java.lang.String cmd, org.gorpipe.gor.session.GorSession session, java.lang.StringBuilder errorStr)  
      void close()  
      static org.gorpipe.gor.model.GenomicIterator.ChromoLookup createChromoLookup()  
      static java.lang.String filterCmd​(java.lang.String[] commands, java.lang.String filter)  
      boolean hasNext()  
      boolean isBuffered()  
      org.gorpipe.gor.model.Row next()  
      void setPosition​(java.lang.String seekChr, int seekPos)  
      java.io.InputStream setRange​(java.lang.String seekChr, int startPos, int endPos)  

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

        bufferSize, bufferSize_$eq, getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getBufferSize, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize, getGorHeader, getParent, moveToPosition, moveToPosition$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

      • ProcessRowSource

        public ProcessRowSource​(java.lang.String cmd,
                        java.lang.String type,
                        boolean nor,
                        org.gorpipe.gor.session.GorSession session,
                        gorsat.Commands.GenomicRange.Range range,
                        java.lang.String filter)

      • ProcessRowSource

        public ProcessRowSource​(java.lang.String cmd,
                        java.lang.String type,
                        boolean nor,
                        org.gorpipe.gor.session.GorSession session,
                        gorsat.Commands.GenomicRange.Range range,
                        java.lang.String filter,
                        int bs)

    • Method Detail

      • checkNested

        public static java.lang.String checkNested​(java.lang.String cmd,
                                           org.gorpipe.gor.session.GorSession session,
                                           java.lang.StringBuilder errorStr)

      • 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

      • filterCmd

        public static java.lang.String filterCmd​(java.lang.String[] commands,
                                         java.lang.String filter)

      • setRange

        public java.io.InputStream setRange​(java.lang.String seekChr,
                                    int startPos,
                                    int endPos)
        Specified by:
        setRange in class ProcessSource

      • 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

      • createChromoLookup

        public static org.gorpipe.gor.model.GenomicIterator.ChromoLookup createChromoLookup()