Package org.snpeff.osCmd

Class OsCmdRunner

  • All Implemented Interfaces:
    java.lang.Runnable
    public class OsCmdRunner
extends java.lang.Thread
    Run an OS command as a thread
    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 inherited from class java.lang.Thread

        MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

    • Constructor Summary

      Constructors 
      Constructor Description
      OsCmdRunner​(java.lang.String jobId, java.lang.String[] osCmdStr)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Close (kill) command
      void finish()
      Stop execution of this thread
      long getDefaultWaitTime()  
      java.lang.String getError()  
      int getExitValue()  
      java.lang.String getHead()  
      java.lang.String getHeadStderr()  
      java.lang.String getJobId()  
      ExecuteOsCommand getOsCmd()  
      int getProgress()  
      java.lang.String getStderr()  
      java.lang.String getStdout()  
      boolean isDone()
      Has this runner finished?
      boolean isExecuting()  
      void run()  
      static boolean runIfNotExists​(java.lang.String[] opts, java.lang.String outputFile, boolean redirectToOutput)
      Run an OS command only if the output files does not exists.
      boolean runIfNotExists​(java.lang.String outputFile, boolean redirectToOutput)
      Run a command only if 'outputFile' does not exist
      void setDefaultWaitTime​(long defaultWaitTime)  
      void setSaveStd​(boolean save)  
      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

    • Constructor Detail

      • OsCmdRunner

        public OsCmdRunner​(java.lang.String jobId,
                   java.lang.String[] osCmdStr)

    • Method Detail

      • runIfNotExists

        public static boolean runIfNotExists​(java.lang.String[] opts,
                                     java.lang.String outputFile,
                                     boolean redirectToOutput)
        Run an OS command only if the output files does not exists. opts[0] : OS Command opts[1] ... opts[N] : Command line options outputFile : Where the results are stored (if the file exists, the command is NOT run) redirect : If 'redirect=true' then run "command > outputFile" (i.e. redirect STDOUT to 'outputFile'). Output is assumed to be binary.
        Parameters:
        opts -
        outputFile -
        redirectToOutput -
        Returns:
        true if command executed OK or outputFile exists

      • close

        public void close()
        Close (kill) command

      • finish

        public void finish()
        Stop execution of this thread

      • getDefaultWaitTime

        public long getDefaultWaitTime()

      • getError

        public java.lang.String getError()

      • getExitValue

        public int getExitValue()

      • getHead

        public java.lang.String getHead()

      • getHeadStderr

        public java.lang.String getHeadStderr()

      • getJobId

        public java.lang.String getJobId()

      • getProgress

        public int getProgress()

      • getStderr

        public java.lang.String getStderr()

      • getStdout

        public java.lang.String getStdout()

      • isDone

        public boolean isDone()
        Has this runner finished?
        Returns:

      • isExecuting

        public boolean isExecuting()

      • run

        public void run()
        Specified by:
        run in interface java.lang.Runnable
        Overrides:
        run in class java.lang.Thread

      • runIfNotExists

        public boolean runIfNotExists​(java.lang.String outputFile,
                              boolean redirectToOutput)
        Run a command only if 'outputFile' does not exist
        Parameters:
        outputFile -
        redirectToOutput -
        Returns:

      • setDefaultWaitTime

        public void setDefaultWaitTime​(long defaultWaitTime)

      • setSaveStd

        public void setSaveStd​(boolean save)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Thread