/*
 *                    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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.util.ListIterator;

/**
 * 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 GeneIDGFF2Reader {

        private static final Logger logger = LoggerFactory.getLogger(GeneIDGFF2Reader.class);

        /**
         * 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) throws IOException {
                logger.info("Reading: {}", filename);

                FeatureList features = new FeatureList();
                BufferedReader br = new BufferedReader(new FileReader(filename));

                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
                                } else {

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

                }

                br.close();
                return features;
        }

        /**
         * 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

                int start = 0;
                int end = 0;

                start = end;
                end = s.indexOf('\t', start);
                String seqname = s.substring(start, end).trim();

                start = end + 1;
                end = s.indexOf('\t', start);
                String source = s.substring(start, end).trim();

                start = end + 1;
                end = s.indexOf('\t', start);
                String type = s.substring(start, end);

                start = end + 1;
                end = s.indexOf('\t', start);
                String locStart = s.substring(start, end);

                start = end + 1;
                end = s.indexOf('\t', start);
                String locEnd = s.substring(start, end);

                Double score;
                start = end + 1;
                end = s.indexOf('\t', start);
                try {
                        score = Double.parseDouble(s.substring(start, end));
                } catch (Exception e) {
                        score = 0.0;
                }

                start = end + 1;
                end = s.indexOf('\t', start);
                char strand = s.charAt(end - 1);

                Location location = Location.fromBio(Integer.parseInt(locStart), Integer.parseInt(locEnd), strand);

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

                int frame;
                start = end + 1;
                end = s.indexOf('\t', start);
                try {
                        frame = Integer.parseInt(s.substring(start, end));
                } catch (Exception e) {
                        frame = -1;
                }

                //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));
                }
                //need to add in attribute assignment for geneid where it just provides a gene name and will make it gtf like
                attributes = "gene_id " + '"' + attributes + '"' + ";";
                return new Feature(seqname, source, type, location, score, frame, attributes);

        }

        /**
         * Write features in FeatureList to file. Each Feature becomes one line in the file.
         * The userMap() data in the features is not written to file.
         *
         * @param features The list of features to write.
         * @param filename The path to the file.
         * @throws IOException Something went wrong -- check exception detail message.
         */
        public static void write(FeatureList features, String filename) throws IOException {
                logger.info("Writing: {}", filename);

                BufferedWriter bw = new BufferedWriter(new FileWriter(filename));

                ListIterator<FeatureI> iter = features.listIterator();
                while (iter.hasNext()) {
                        Feature feature = (Feature) iter.next();
                        writeLine(feature, bw);
                }

                bw.close();
        }

        private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
                String s = f.seqname() + '\t';
                s += f.source() + '\t';
                s += f.type() + '\t';

                s += f.location().bioStart() + "\t";
                s += f.location().bioEnd() + "\t";
                s += Double.toString(f.score()) + "\t";
                s += f.location().bioStrand() + "\t";

                if (f.frame() == -1) {
                        s += ".\t";
                } else {
                        s += f.frame() + "\t";
                }

                s += f.attributes();

                bw.write(s);
                bw.newLine();
        }


        public static void main(String[] args) throws Exception {

                FeatureList listGenes = GeneIDGFF2Reader.read("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gtf");

                for(FeatureI feature : listGenes){
                        logger.info("Gene Feature: {}", feature);
                }
//        logger.info(listGenes);
                //      GeneMarkGTF.write( list, args[1] );
        }
}