org.fhcrc.cpl.toolbox.statistics
Class RInterface.RErrorReaderThread

java.lang.Object
  java.lang.Thread
      org.fhcrc.cpl.toolbox.statistics.RInterface.RErrorReaderThread

All Implemented Interfaces:

java.lang.Runnable

Enclosing class:

RInterface

public static class RInterface.RErrorReaderThread
extends java.lang.Thread

Manages the R error inputstream. On some systems, the error inputstream must be read periodically or writing to the outputstream will hang. In particular, I've seen output writing hang after 8kb are written; apparently something gets written to the error outputstream during that write, and unless it's written, nothing doing.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

protected java.lang.StringBuffer	accumulatedResponse
java.io.IOException	exception
protected boolean	hasNewData
protected java.io.InputStream	inputStream
protected boolean	keepReading
protected java.lang.StringBuffer	newDataBuf
int	status
static int	STATUS_ERROR
static int	STATUS_READING

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

RInterface.RErrorReaderThread(java.lang.Process p)

Method Summary

java.lang.String	getNewData()
java.lang.String	getReadString()
boolean	hasNewData()
void	run()
void	shutdown()

Methods inherited from class java.lang.Thread

activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

inputStream

protected java.io.InputStream inputStream

accumulatedResponse

protected java.lang.StringBuffer accumulatedResponse

newDataBuf

protected java.lang.StringBuffer newDataBuf

keepReading

protected boolean keepReading

exception

public java.io.IOException exception

status

public int status

STATUS_READING

public static final int STATUS_READING

See Also:

Constant Field Values

STATUS_ERROR

public static final int STATUS_ERROR

See Also:

Constant Field Values

hasNewData

protected boolean hasNewData

Constructor Detail

RInterface.RErrorReaderThread

public RInterface.RErrorReaderThread(java.lang.Process p)

Method Detail

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread

shutdown

public void shutdown()

getReadString

public java.lang.String getReadString()

hasNewData

public boolean hasNewData()

getNewData

public java.lang.String getNewData()