package compbio.runner.structure;


import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;

import org.apache.log4j.Logger;

import compbio.data.sequence.Alignment;
import compbio.data.sequence.UnknownFileFormatException;
import compbio.engine.client.PipedExecutable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.ResultNotAvailableException;
import compbio.runner.Util;

public class RNAalifold extends SkeletalExecutable<RNAalifold> 
		implements PipedExecutable<RNAalifold> {
	
	
	
	private static Logger log = Logger.getLogger(RNAalifold.class);

	
	@SuppressWarnings("unchecked")
	@Override
	// PlaceHolder method
	public String getResults(String resultFile)
			throws ResultNotAvailableException {
		return "null";
	}

	
	@Override
	public RNAalifold setOutput(String outFile) {
		log.info("Set ouput file: " + outFile.toString());
		super.setOutput(outFile);
		return this;
	}
	
	@Override
	public RNAalifold setInput(String inFile) {
		log.info("Set input file: " + inFile.toString());
		cbuilder.setLast(inFile);
		super.setInput(inFile);
		return this;
	}
	
	@SuppressWarnings("unchecked")
	@Override
	public Class<RNAalifold> getType() {
		return (Class<RNAalifold>) this.getClass();
	}
	
	
}