package compbio.runner.structure;


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

//imports for filereader method
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.File;

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;


import compbio.engine.client.CommandBuilder;

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

	
	@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();
	}
	
	@SuppressWarnings("unchecked")
	@Override
	// PlaceHolder method
	public String getResults(String workDirectory)
			throws ResultNotAvailableException {
		try {
			// System.out.print(readRNAStruct(workDirectory, getOutput()));
			return 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);
		}
	}

	
	// Simple and generic methods for reading a whole file
	// Should surfice until a more detailed datamodel and parser are developed
	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;
	}
	
}