Package gorsat.process

Class ProcessRowSource

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.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​(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.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()  
      boolean seek​(java.lang.String seekChr, int seekPos)  
      java.io.InputStream setRange​(java.lang.String seekChr, int startPos, int endPos)  

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

        clone, decStat, getBufferSize, getContext, getHeader, getSourceName, incStat, init, initStats, isSourceAlreadyInserted, setBufferSize, 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 org.gorpipe.gor.model.GenomicIterator

        filter, getMonitor, moveToPosition, moveToPosition, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select

      • 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 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()

      • next

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

      • 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

      • seek

        public boolean seek​(java.lang.String seekChr,
                    int seekPos)

      • close

        public void close()

      • isBuffered

        public boolean isBuffered()

      • createChromoLookup

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