Package org.snpeff.osCmd

Class ExecuteOsCommand

java.lang.Object

java.lang.Thread

org.snpeff.osCmd.ExecuteOsCommand

All Implemented Interfaces:

java.lang.Runnable, Progress

public class ExecuteOsCommand
extends java.lang.Thread
implements Progress

Launches an 'OS command' (e.g. "ls", "dir") Note: Launching a system command in Java is not trivial, we need to start 2 threads that read STDOUT and STDERR of the process, otherwise it will block (actually it may even cause a deadlock) References: http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html?page=1

Author:

pcingola

Nested Class Summary

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

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

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
ExecuteOsCommand(java.lang.String command)
ExecuteOsCommand(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
int	exec()
java.lang.String[]	getCommandArgs()
int	getExitValue()
java.lang.String	getHead()	First lines of stdout
java.lang.String	getHeadStderr()	First lines of stderr
int	getProgress()
java.lang.String	getPwd()
java.lang.String	getRedirectStderr()
java.lang.String	getRedirectStdout()
java.lang.String	getStderr()
java.io.OutputStream	getStdin()
java.lang.String	getStdout()
LineFilter	getStdOutFilter()
boolean	isAlertDone()
boolean	isBinaryStderr()
boolean	isBinaryStdout()
boolean	isExecuting()
boolean	isQuiet()
boolean	isSaveStd()
boolean	isStarted()
void	kill()
void	progress()	Report progress
void	resetBuffers()
void	run()
void	setBinaryStderr(boolean binaryStderr)
void	setBinaryStdout(boolean binaryStdout)
void	setCommandArgs(java.lang.String[] commandArgs)
void	setObjetcToNotify(java.lang.Object objetcToNotify)
void	setPwd(java.lang.String pwd)
void	setQuiet(boolean quietStdout, boolean quietStderr)
void	setRedirectStderr(java.lang.String redirectStderr)
void	setRedirectStdout(java.lang.String redirectStdout)
void	setSaveStd(boolean saveStd)
void	setShowExceptions(boolean showExceptions)
void	setStdoutAlert(java.lang.String alert)
void	setStdoutAlertNotify(java.lang.Object toBeNotified)
void	setStdOutFilter(LineFilter stdOutFilter)
java.lang.String	toString()

Methods inherited from class java.lang.Thread

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

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static boolean debug

Constructor Detail

ExecuteOsCommand

public ExecuteOsCommand(java.lang.String[] args)

ExecuteOsCommand

public ExecuteOsCommand(java.lang.String command)

Method Detail

exec

public int exec()

getCommandArgs

public java.lang.String[] getCommandArgs()

getExitValue

public int getExitValue()

getHead

public java.lang.String getHead()

First lines of stdout

getHeadStderr

public java.lang.String getHeadStderr()

First lines of stderr

getProgress

public int getProgress()

Specified by:

getProgress in interface Progress

getPwd

public java.lang.String getPwd()

getRedirectStderr

public java.lang.String getRedirectStderr()

getRedirectStdout

public java.lang.String getRedirectStdout()

getStderr

public java.lang.String getStderr()

getStdin

public java.io.OutputStream getStdin()

getStdout

public java.lang.String getStdout()

getStdOutFilter

public LineFilter getStdOutFilter()

isAlertDone

public boolean isAlertDone()

isBinaryStderr

public boolean isBinaryStderr()

isBinaryStdout

public boolean isBinaryStdout()

isExecuting

public boolean isExecuting()

isQuiet

public boolean isQuiet()

isSaveStd

public boolean isSaveStd()

isStarted

public boolean isStarted()

kill

public void kill()

progress

public void progress()

Report progress

Specified by:

progress in interface Progress

resetBuffers

public void resetBuffers()

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread

setBinaryStderr

public void setBinaryStderr(boolean binaryStderr)

setBinaryStdout

public void setBinaryStdout(boolean binaryStdout)

setCommandArgs

public void setCommandArgs(java.lang.String[] commandArgs)

setObjetcToNotify

public void setObjetcToNotify(java.lang.Object objetcToNotify)

setPwd

public void setPwd(java.lang.String pwd)

setQuiet

public void setQuiet(boolean quietStdout,
                     boolean quietStderr)

setRedirectStderr

public void setRedirectStderr(java.lang.String redirectStderr)

setRedirectStdout

public void setRedirectStdout(java.lang.String redirectStdout)

setSaveStd

public void setSaveStd(boolean saveStd)

setShowExceptions

public void setShowExceptions(boolean showExceptions)

setStdoutAlert

public void setStdoutAlert(java.lang.String alert)

setStdoutAlertNotify

public void setStdoutAlertNotify(java.lang.Object toBeNotified)

setStdOutFilter

public void setStdOutFilter(LineFilter stdOutFilter)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Thread