Run RNAfold from Java. Based on this code: http://csbi.ltdk.helsinki.fi/meap/anduril/doc/components/RNAFold/RNAFold.java

gistfile1.txt

protected String execute(Sequence aSequence, String[] commands)
		throws InvalidSequenceException, IOException {
	String returnMe = "";
	if (aSequence.getLength() == 0) {
		throw new InvalidSequenceException(
				"The sequence provided to execute RNAFold was empty!");
	}
	
	String[] cmdArr = new String[commands.length + 1];
	System.arraycopy(new String[] { "RNAfold" }, 0, cmdArr, 0, 1);
	System.arraycopy(commands, 0, cmdArr, 1, commands.length);
	
	Process p = Runtime.getRuntime().exec(cmdArr);
	InputStream output_stream = p.getInputStream();
	InputStream seq_stream = PdbHelper.makeInputStreamFromString(aSequence
			.getSequenceString());
	OutputStream out_stream = p.getOutputStream();
	InputStream error_stream = p.getErrorStream();

	ByteArrayOutputStream out_baos = new ByteArrayOutputStream();
	ByteArrayOutputStream error_baos = new ByteArrayOutputStream();

	try {
		// A thread for handling the input to RNAFold
		Thread stdInThread = ProcessRunner.bindStreams(seq_stream,
				out_stream, seq_stream + " feed", true);
		// A thread for handling the output of RNAFold
		Thread stdOutThread = ProcessRunner.bindStreams(output_stream,
				out_baos, "writer", false);

		try {
			int status = p.waitFor();
			if (status != 0) {
				log.error("Something bad happened!\n!");
				System.exit(-1);
			}
		} catch (InterruptedException e) {
			log.error("wating problem\n", e);
			System.exit(-1);
		}
		returnMe = out_baos.toString();
		if (returnMe.length() > 0) {
			return returnMe;
		}
		stdInThread.join(10*1000);
		stdOutThread.join(10*1000);
	} catch (InterruptedException e) {
		log.error("problem\n", e);
	} finally {
		try {
			output_stream.close();
			seq_stream.close();
			out_stream.close();
			out_baos.close();
		} catch (IOException e) {
			log.error("io problem\n", e);
		}
		p.destroy();
	}

	return returnMe;
}