/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 *  
 * Jalview 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 GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.io;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import jalview.analysis.SecStrConsensus;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.SecondaryStructureAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;

import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
import fr.orsay.lri.varna.models.rna.RNA;
import fr.orsay.lri.varna.utils.RNAMLParser;

public class RnamlFile extends AlignFile {
	public int id;
	public String namefile;
	public String name;
	protected ArrayList<RNA> result;

	public RnamlFile() {
		super();

	}

	public RnamlFile(String inFile, String type) throws Exception {
		super(inFile, type);

	}

	public RnamlFile(FileParse source) throws Exception {
		super(source);

	}

	public BufferedReader CreateReader() throws FileNotFoundException {
		FileReader fr = null;
		fr = new FileReader(inFile);

		BufferedReader r = new BufferedReader(fr);
		return r;
	}

	@SuppressWarnings("unchecked")
	public void parse() throws FileNotFoundException,
			ExceptionPermissionDenied, ExceptionLoadingFailed,
			ExceptionFileFormatOrSyntax {

		result = RNAFactory.loadSecStrRNAML(getReader());

		ArrayList<ArrayList> allarray = new ArrayList();
		ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
		ArrayList strucinarray = new ArrayList();
		SequenceI[] seqs = new SequenceI[result.size()];
		namefile = inFile.getName();

		for (int i = 0; i < result.size(); i++) {

			RNA current = result.get(i);
			String rna = current.getStructDBN(true);
			String seq = current.getSeq();
			int begin = 1;
			int end = 1000;
			id = i;
			System.out.println("id=" + i);
			name = this.safeName(namefile, i);
			seqs[i] = new Sequence(name, seq, begin, end);

			seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
			String[] annot = new String[rna.length()];
			Annotation[] ann = new Annotation[rna.length()];

			for (int j = 0; j < rna.length(); j++) {
				annot[j] = "" + rna.charAt(j);

			}
			for (int k = 0; k < rna.length(); k++) {
				ann[k] = new Annotation(annot[k], "",
						jalview.schemes.ResidueProperties.getRNASecStrucState(
								annot[k]).charAt(0), 0f);
			}

			AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
					current.getID(), ann);

			seqs[i].addAlignmentAnnotation(align);
			seqs[i].setRNA(result.get(i));

			char[] struc = align.getRNAStruc().toCharArray();

			allarray.add(strucinarray);

			this.annotations.addElement(align);
			BP.add(align.bps);
			
		}
		this.setSeqs(seqs);
		int[] tab = SecStrConsensus.extractConsensus(BP);


	}

	public void parse(BufferedReader r) throws ExceptionPermissionDenied,
			ExceptionLoadingFailed, ExceptionFileFormatOrSyntax {

		result = RNAFactory.loadSecStrRNAML(r);

		ArrayList<ArrayList> allarray = new ArrayList();
		ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
		ArrayList strucinarray = new ArrayList();
		SequenceI[] seqs = new SequenceI[result.size()];
		namefile = inFile.getName();

		for (int i = 0; i < result.size(); i++) {

			RNA current = result.get(i);
			String rna = current.getStructDBN(true);

			String seq = current.getSeq();
			int begin = 1;
			int end = 1000;
			id = i;
			name = this.safeName(namefile, i);
			seqs[i] = new Sequence(name, seq, begin, end);

			seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
			String[] annot = new String[rna.length()];
			Annotation[] ann = new Annotation[rna.length()];

			for (int j = 0; j < rna.length(); j++) {
				annot[j] = "" + rna.charAt(j);

			}
			for (int k = 0; k < rna.length(); k++) {
				ann[k] = new Annotation(annot[k], "",
						jalview.schemes.ResidueProperties.getRNASecStrucState(
								annot[k]).charAt(0), 0f);
			}

			AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
					current.getID(), ann);

			seqs[i].addAlignmentAnnotation(align);
			seqs[i].setRNA(result.get(i));

			char[] struc = align.getRNAStruc().toCharArray();
			for (int y = 0; y < struc.length; y++) {
				strucinarray.add(struc[y]);
				// System.out.println("structy"+struc[y]);
			}
			// System.out.println("Sequence"+i+"\t : "+strucinarray.toString());
			allarray.add(strucinarray);

			this.annotations.addElement(align);
			System.out.println(rna);
			BP.add(align.bps);
			System.out.println(align.bps.size());
		}
		this.setSeqs(seqs);
		int[] tab = SecStrConsensus.extractConsensus(BP);

	
	}

	

	public static String print(SequenceI[] s) {
		return "not yet implemented";
	}

	public String print() {
		System.out.print("print :");
		return print(getSeqsAsArray());
	}

	public ArrayList getRNA() {
		return result;
	}

	public Vector getAnnot() {
		return annotations;
	}

	// public static void main(String[] args) {
	// Pattern p= Pattern.compile("(.+)[.][^.]+");
	// Matcher m = p.matcher("toto.xml.zip");
	// System.out.println(m.matches());
	// System.out.println(m.group(1));
	// }
	public String safeName(String namefile, int id) {

		Pattern p = Pattern.compile("(.*)[.][^.]+");
		Matcher m = p.matcher(namefile);
		name = m.group(1) + "_" + id;

		return name;

	}

}