Package gorsat.process

Class ProcessRowSource

java.lang.Object
org.gorpipe.gor.model.GenomicIterator
org.gorpipe.model.gor.iterators.RowSource
gorsat.process.ProcessSource
gorsat.process.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

    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_$eq, clone, getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getBufferSize, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize, getEx, getGorHeader, getParent, moveToPosition, moveToPosition$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, 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, toString, wait, wait, wait

    Methods inherited from interface java.util.Iterator

    forEachRemaining, remove

  • Constructor Details

    • 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 Details

    • 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)
      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

    • createChromoLookup

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