ProcessTools (biojava-legacy 1.9.5 API)

    • Method Detail

      • exec

        public static int exec​(String[] args,
                               Reader input,
                               Writer stdout,
                               Writer stderr)
                        throws IOException

        Deprecated.

        Execute the specified command and wait for it to return.

        Parameters:
        args - the command line to execute.
        input - data to present to the process' standard input, or null if the process does not require input.
        stdout - a Writer which will be filled with data from the process' output stream, or null to ignore output.
        stderr - a Writer which will be filled with data from the process' error stream, or null to ignore output.
        Returns:
        the process' return code.
        Throws:
        IOException
      • exec

        public static int exec​(String[] args,
                               String[] envp,
                               File dir,
                               Reader input,
                               Writer stdout,
                               Writer stderr,
                               long timeout)
                        throws IOException,
                               ProcessTimeoutException

        Deprecated.

        Execute the specified command and wait for it to return, or kill it if the specified timeout expires first.

        Parameters:
        args - the command line to execute.
        envp - environment variables for the child process, or null to inherit the current set.
        dir - working directory for the child process, or null to inherit the current directory.
        input - data to present to the process' standard input, or null if the process does not require input.
        stdout - a Writer which will be filled with data from the process' output stream, or null to ignore output.
        stderr - a Writer which will be filled with data from the process' error stream, or null to ignore output.
        timeout - maximum run-time (in milliseconds) for the child process. A value of 0 indicates no limit.
        Returns:
        the process' return code.
        Throws:
        IOException - if an error occurs while starting or communicating with the process
        ProcessTimeoutException - if the child process was killed because its timeout had expired.
      • exec

        public static int exec​(String command,
                               Reader input,
                               Writer stdout,
                               Writer stderr)
                        throws IOException

        Deprecated.

        Execute the specified command and wait for it to return. This is the simplified version that tries to be nice and make your life easier. If you know exactly what you want, you might want to use exec(String[],...) instead.

        Parameters:
        command - the command line to execute.
        input - data to present to the process' standard input, or null if the process does not require input.
        stdout - a Writer which will be filled with data from the process' output stream, or null to ignore output.
        stderr - a Writer which will be filled with data from the process' error stream, or null to ignore output.
        Returns:
        the process' return code.
        Throws:
        IOException - if an error occurs while starting or communicating with the process
      • exec

        public static int exec​(String command,
                               String[] envp,
                               File dir,
                               Reader input,
                               Writer stdout,
                               Writer stderr,
                               long timeout)
                        throws IOException,
                               ProcessTimeoutException

        Deprecated.

        Execute the specified command and wait for it to return. This is the simplified version that tries to be nice and make your life easier. If you know exactly what you want, you might want to use exec(String[],...) instead.

        Parameters:
        command - the command line to execute.
        input - data to present to the process' standard input, or null if the process does not require input.
        stdout - a Writer which will be filled with data from the process' output stream, or null to ignore output.
        stderr - a Writer which will be filled with data from the process' error stream, or null to ignore output.
        timeout - maximum run-time (in milliseconds) for the child process. A value of 0 indicates no limit.
        Returns:
        the process' return code.
        Throws:
        IOException - if an error occurs while starting or communicating with the process
        ProcessTimeoutException - if the child process was killed because its timeout had expired.