Package gorsat.process

Class ProcessIteratorAdaptor

java.lang.Object

org.gorpipe.gor.model.GenomicIteratorBase

gorsat.process.ProcessIteratorAdaptor

All Implemented Interfaces:

Serializable, AutoCloseable, 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 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, String cmd, String alias, Iterator<org.gorpipe.gor.model.Row> rs, gorsat.Commands.Analysis an, String header, boolean skipheader, Optional<String> skip, boolean allowerror, boolean nor)

Method Summary

Modifier and Type	Method	Description
void	close()
boolean	hasNext()
boolean	isBuffered()
org.gorpipe.gor.model.Row	next()
boolean	seek(String seekChr, int seekPos)
static void	subCommandSplit(Path fileRoot, String subCommand, List<String> split)

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

ProcessIteratorAdaptor

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

Throws:

IOException

Method Details

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<org.gorpipe.gor.model.Row>

next

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

Specified by:

next in interface Iterator<org.gorpipe.gor.model.Row>

seek

public boolean seek(String seekChr,
 int seekPos)

Specified by:

seek in interface org.gorpipe.gor.model.GenomicIterator

close

public void close()

Specified by:

close in interface 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(Path fileRoot,
 String subCommand,
 List<String> split)