/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.genome.parsers.gff;

import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;


/**
 * http://www.bioperl.org/wiki/GTF
 * Read and write FeatureLists as GFF/GTF formatted files.
 *<br><br>
 * The GFF moniker is applied to a variety of tab-delimited formats
 * that mock the notion of a standard. This class should parse most files
 * bearing at least a passing resemblance to any of the formats. You will, however, need
 * to research the semantics of the files you encounter. Generally,
 * the format consists of 9 tab-delimited fields:
 * <br>
 * <pre>
 * seqname   source   featureType   start   end   score   strand   frame   attributes
 * </pre>
 * The 9th field consists of key-value pairs separated by semicolons, the first of which JavaGene interprets
 * as the group id (as used in GFF1). It is the precise meaning of this 9th field that
 * varies from week to week. The Feature and FeatureList objects provide various utility methods to
 * ease the task of accessing and using the attributes. The proper interpretation of any
 * particular attribute, however, is left to you.
 *
 * @author Hanno Hinsch
 */
public class GFF3Reader {

	private static final Logger logger = LoggerFactory.getLogger(GFF3Reader.class);

	private static final  Pattern p = Pattern.compile("\t");

	/**
	 * Read a file into a FeatureList. Each line of the file becomes one Feature object.
	 *
	 * @param filename The path to the GFF file.
	 * @return A FeatureList.
	 * @throws IOException Something went wrong -- check exception detail message.
	 */
	public static FeatureList read(String filename, List<String> indexes) throws IOException {
		return read(Paths.get(filename), indexes);
	}

	/**
	 * Read a file into a FeatureList. Each line of the file becomes one Feature object.
	 *
	 * @param path The path to the GFF file.
	 * @return A FeatureList.
	 * @throws IOException Something went wrong -- check exception detail message.
	 */
	public static FeatureList read(Path path, List<String> indexes) throws IOException {
		logger.info("Reading: {}", path.toString());

		FeatureList features = new FeatureList();
		features.addIndexes(indexes);
		BufferedReader br = Files.newBufferedReader(path);

		String s;
		for (s = br.readLine(); null != s; s = br.readLine()) {
			s = s.trim();

			if (s.length() > 0) {
				if (s.charAt(0) == '#') {
					//ignore comment lines
					if(s.startsWith("##fasta"))
						break;
				} else {

					FeatureI f = parseLine(s);
					if (f != null) {
						features.add(f);

					}
				}
			}

		}

		br.close();
		return features;
	}


	public static FeatureList read(String filename) throws IOException {
	   return read(filename,new ArrayList<String>(0));
	}

	public static FeatureList read(Path path) throws IOException {
		return read(path,new ArrayList<String>(0));
	}


	/**
	 * create Feature from line of GFF file
	 */
	private static Feature parseLine(String s) {
		//FIXME update to use regex split on tabs
		//FIXME better errors on parse failures
		String[] line = p.split(s);
		String seqname =line[0].trim();

		String source =line[1].trim();

		String type =line[2].trim();


		String locStart =line[3].trim();

		String locEnd =line[4].trim();

		Double score;

		try {
			score = Double.parseDouble(line[5].trim());
		} catch (Exception e) {
			score = 0.0;
		}


		char strand = line[6].trim().charAt(0);
		//added by scooter willis to deal with glimmer predictions that
		//have the start after the end but is a negative strand
		int locationStart = Integer.parseInt(locStart);
		int locationEnd = Integer.parseInt(locEnd);
		if(locationStart > locationEnd){
			int temp = locationStart;
			locationStart = locationEnd;
			locationEnd = temp;

		}
		Location location = Location.fromBio(locationStart, locationEnd, strand);

		assert (strand == '-') == location.isNegative();

		int frame;
		try {
			frame = Integer.parseInt(line[7].trim());
		} catch (Exception e) {
			frame = -1;
		}
		String attributes=line[8];
	/*    //grab everything until end of line (or # comment)
		start = end + 1;
		end = s.indexOf('#', start);
		String attributes = null;
		if (end < 0) {
			attributes = new String(s.substring(start));
		} else {
			attributes = new String(s.substring(start, end));
		}
 */
		return new Feature(seqname, source, type, location, score, frame, attributes.split("#")[0]);

	}




	public static void main(String[] args) throws Exception {
		long start = System.currentTimeMillis();
		@SuppressWarnings("unused")
		FeatureList listGenes = GFF3Reader.read("/home/melo/workspace/release/stdout.combined.checked2.gtf");
		long stop = System.currentTimeMillis();
		logger.info("Loading = {}", stop-start);
//        logger.info(listGenes);
		//	GeneMarkGTF.write( list, args[1] );
	}
}

@@ -814,35 +814,8 @@
 er;%0A
-import java.io.FileReader;%0A
 impo

Remove unused import