/* Copyright (c) 2011 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.pipeline._jpred;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.SequenceUtil;

public class Pairwise {

	private final List<FastaSequence> sequences; 
	final Set<PScore> pscores; 
	
	public Pairwise(List<FastaSequence> sequences) {
		this.sequences = sequences;
		pscores = new HashSet<PScore>(); 
	}

	void compare() {
		for (int i = 0; i < sequences.size(); i++) {
			FastaSequence seq1 = sequences.get(i); 
			System.out.println(seq1.getId());
			for (int j = i+1; j < sequences.size(); j++) {
				FastaSequence seq2 = sequences.get(j);
				PScore pscore = new PScore();
				pscore.name = seq1.getId();
				pscore.otherName = seq2.getId();
				pscores.add(pscore);
				compare(pscore, seq1.getSequence(), seq2.getSequence());
			}
		}
	}

	void compare(PScore pscore, String seq1, String seq2) { 
		char[] chars1 = seq1.trim().toUpperCase().toCharArray(); 
		char[] chars2 = seq2.trim().toUpperCase().toCharArray();
		if(chars1.length != chars2.length) { 
			throw new IllegalArgumentException("Different lenght sequence are provided but same expected! \n Sequence 1: \n" + pscore.name+ 
					"\n Length:"+chars1.length +"\n "+ 
					"Sequence 2: \n " + pscore.otherName + 
					" \n Lenght: " + chars2.length ); 
		}
		compare(pscore, chars1, chars2); 
	}
	
	void compare(PScore pscore, char[] seq1, char[] seq2) { 
		int sameResedue = 0; 
		for (int i = 0; i < seq1.length; i++) {
			if(seq1[i]==seq2[i]) { 
				sameResedue++;
			}
		}
		pscore.score = (double)sameResedue /seq1.length;
		System.out.println(pscore.score*100);
	}
	
	public static final void main(String[]  args) throws FileNotFoundException, IOException {
		File in = new File(args[0]);
		List<FastaSequence> fslist = SequenceUtil.readFasta(new BufferedInputStream(new FileInputStream(in)));
		Pairwise pair = new Pairwise(fslist);
		pair.compare(); 
		System.out.println(pair.pscores);
	}
}