Package gorsat.process

Class ProcessRowSource

java.lang.Object
org.gorpipe.gor.model.GenomicIteratorBase
gorsat.process.ProcessSource
gorsat.process.ProcessRowSource
All Implemented Interfaces:
AutoCloseable, Iterator<org.gorpipe.gor.model.Row>, org.gorpipe.gor.model.GenomicIterator, org.gorpipe.gor.model.RowSourceStats
public class ProcessRowSource extends ProcessSource
Created by sigmar on 12/02/16.

  • Field Summary

    Fields inherited from class org.gorpipe.gor.model.GenomicIteratorBase

    statsSenderAnnotation, statsSenderName

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    Description
    static String
    checkNested(String cmd, org.gorpipe.gor.session.GorSession session, StringBuilder errorStr)
     
    void
    close()
     
    static org.gorpipe.gor.model.ChromoLookup
    createChromoLookup()
     
    static String
    filterCmd(String[] commands, String filter)
     
    boolean
    hasNext()
     
    boolean
    isBuffered()
     
    org.gorpipe.gor.model.Row
    next()
     
    boolean
    seek(String seekChr, int seekPos)
     
    InputStream
    setRange(String seekChr, int startPos, int endPos)
     

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

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

    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, setRequestedRange

    Methods inherited from interface java.util.Iterator

    forEachRemaining, remove

    Methods inherited from interface org.gorpipe.gor.model.RowSourceStats

    getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize

  • Constructor Details

    • ProcessRowSource

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

    • ProcessRowSource

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

  • Method Details

    • checkNested

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

    • hasNext

      public boolean hasNext()

    • next

      public org.gorpipe.gor.model.Row next()

    • filterCmd

      public static String filterCmd(String[] commands, String filter)

    • setRange

      public InputStream setRange(String seekChr, int startPos, int endPos)
      Specified by:
      setRange in class ProcessSource

    • seek

      public boolean seek(String seekChr, int seekPos)

    • close

      public void close()

    • isBuffered

      public boolean isBuffered()

    • createChromoLookup

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