Package gorsat.process

Class ProcessIteratorAdaptor

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>, org.gorpipe.gor.model.GenomicIterator, org.gorpipe.gor.model.RowSourceStats
    public class ProcessIteratorAdaptor
extends org.gorpipe.gor.model.GenomicIteratorBase
implements java.io.Serializable
    Created by sigmar on 03/11/15.
    See Also:
    Serialized Form

    • Field Summary

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

        statsSenderAnnotation, statsSenderName

    • Constructor Summary

      Constructors 
      Constructor Description
      ProcessIteratorAdaptor​(org.gorpipe.gor.session.GorContext context, java.lang.String cmd, java.lang.String alias, java.util.Iterator<org.gorpipe.gor.model.Row> rs, gorsat.Commands.Analysis an, java.lang.String header, boolean skipheader, java.util.Optional<java.lang.String> skip, boolean allowerror, boolean nor)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      boolean hasNext()  
      boolean isBuffered()  
      org.gorpipe.gor.model.Row next()  
      boolean seek​(java.lang.String seekChr, int seekPos)  
      static void subCommandSplit​(java.nio.file.Path fileRoot, java.lang.String subCommand, java.util.List<java.lang.String> split)  

      • 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

      • ProcessIteratorAdaptor

        public ProcessIteratorAdaptor​(org.gorpipe.gor.session.GorContext context,
                              java.lang.String cmd,
                              java.lang.String alias,
                              java.util.Iterator<org.gorpipe.gor.model.Row> rs,
                              gorsat.Commands.Analysis an,
                              java.lang.String header,
                              boolean skipheader,
                              java.util.Optional<java.lang.String> skip,
                              boolean allowerror,
                              boolean nor)
                       throws java.io.IOException
        Throws:
        java.io.IOException

    • Method Detail

      • hasNext

        public boolean hasNext()
        Specified by:
        hasNext in interface java.util.Iterator<org.gorpipe.gor.model.Row>

      • next

        public org.gorpipe.gor.model.Row next()
        Specified by:
        next in interface java.util.Iterator<org.gorpipe.gor.model.Row>

      • seek

        public boolean seek​(java.lang.String seekChr,
                    int seekPos)
        Specified by:
        seek in interface org.gorpipe.gor.model.GenomicIterator

      • close

        public void close()
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface org.gorpipe.gor.model.GenomicIterator

      • isBuffered

        public boolean isBuffered()
        Specified by:
        isBuffered in interface org.gorpipe.gor.model.GenomicIterator

      • subCommandSplit

        public static void subCommandSplit​(java.nio.file.Path fileRoot,
                                   java.lang.String subCommand,
                                   java.util.List<java.lang.String> split)