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


import compbio.engine.client.CommandBuilder;

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

	// May not be necessary as defult is "<space>" but still dont know
	// How to deal with different key value separators for different params
	public static final String KEY_VALUE_SEPARATOR = " ";
	
	public RNAalifold() {
		super(KEY_VALUE_SEPARATOR);
	}
	
	@Override
	public RNAalifold setOutput(String outFile) {
		super.setOutput(outFile);
		return this;
	}
	
	@Override
	public RNAalifold setInput(String inFile) {
		cbuilder.setLast(inFile);
		super.setInput(inFile);
		return this;
	}
	
	@SuppressWarnings("unchecked")
	@Override
	public Class<RNAalifold> getType() {
		return (Class<RNAalifold>) this.getClass();
	}
	
	@SuppressWarnings("unchecked")
	@Override
	// PlaceHolder method
	public ScoreManager getResults(String workDirectory)
			throws ResultNotAvailableException {
		try {
			return Util.readRNAStruct(workDirectory, getOutput());
			
		} catch (FileNotFoundException e) {
			log.error(e.getMessage(), e.getCause());
			throw new ResultNotAvailableException(e);
		} catch (IOException e) {
			log.error(e.getMessage(), e.getCause());
			throw new ResultNotAvailableException(e);
		}
	}


	// the new currently used methods for reading are found in 
	// - compbio.data.sequence.SequenceUtil and 
	// - compbio.runner.Util
	
	// Simple and generic methods for reading a whole file
//	private static String readRNAStruct(String workDirectory,
//			String structFile) throws IOException, FileNotFoundException {
//		assert !compbio.util.Util.isEmpty(workDirectory);
//		assert !compbio.util.Util.isEmpty(structFile);
//		File sfile = new File(compbio.engine.client.Util.getFullPath(
//				workDirectory, structFile));
//		log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
//		if(!(sfile.exists() && sfile.length() > 0)) {
//			throw new FileNotFoundException("Result for the jobId "
//					+ workDirectory + "with file name " + structFile
//					+ " is not found!");
//		}
//		return readFile(sfile);
//	}
//	
//	private static BufferedReader input;
//	public static String readFile(File inputFile) throws 
//			FileNotFoundException, IOException {
//		
//		input	= new BufferedReader(new FileReader(inputFile));
//		
//		String file = new String();
//		String line = new String();
//		
//		while (true) {
//			line = input.readLine();
//			
//			if (line != null) {
//				file = file + line + "\r\n";
//			} else break;
//		}
//		// Close file
//		input.close();
//		return file;
//	}
	
}