Package gorsat.process

Class ProcessIteratorAdaptor

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

    • 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
      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()  
      void setPosition​(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.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, pushdownCmd, 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 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,
                              io.kubernetes.client.openapi.ApiException
        Throws:
        java.io.IOException
        io.kubernetes.client.openapi.ApiException

    • Method Detail

      • 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

      • 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

      • subCommandSplit

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