Class OsCmdRunner

java.lang.Object
java.lang.Thread
org.snpeff.osCmd.OsCmdRunner
All Implemented Interfaces:
Runnable
public class OsCmdRunner extends Thread
Run an OS command as a thread
Author:
pcingola

  • Constructor Details

    • OsCmdRunner

      public OsCmdRunner(String jobId, String[] osCmdStr)

  • Method Details

    • runIfNotExists

      public static boolean runIfNotExists(String[] opts, 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 String getError()

    • getExitValue

      public int getExitValue()

    • getHead

      public String getHead()

    • getHeadStderr

      public String getHeadStderr()

    • getJobId

      public String getJobId()

    • getOsCmd

      public ExecuteOsCommand getOsCmd()

    • getProgress

      public int getProgress()

    • getStderr

      public String getStderr()

    • getStdout

      public String getStdout()

    • isDone

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

    • isExecuting

      public boolean isExecuting()

    • run

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

    • runIfNotExists

      public boolean runIfNotExists(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 String toString()
      Overrides:
      toString in class Thread