/*
 *                    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.phosphosite;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.GZIPInputStream;

/**
 * Created by ap3 on 31/10/2014.
 */
public class Site {

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

        public Site(){


        }

        public static List<Site> parseSites(File f) throws IOException {

                InputStream gzipStream;
                try (InputStream inStream = new FileInputStream(f)) {
                        gzipStream = new GZIPInputStream(inStream);
                }

                Reader decoder = new InputStreamReader(gzipStream);
                BufferedReader buf = new BufferedReader(decoder);

                String line = null;

                List<Site > data = new ArrayList<>();

                List<String> headerFields = null;

                int proteinIndex = -1;
                int uniprotIndex = -1;
                int residueIndex = -1;
                int orgIndex     = -1;
                int groupIndex   = -1;
                int geneIndex    = -1;

                boolean inHeader = true;


                while ((line = buf.readLine()) != null){
                        if ( line.startsWith("GENE") ||
                                        line.startsWith("PROTEIN")) {

                                headerFields = parseHeaderFields(line);

                                proteinIndex = headerFields.indexOf("PROTEIN");
                                uniprotIndex = headerFields.indexOf("ACC_ID");
                                residueIndex = headerFields.indexOf("MOD_RSD");
                                orgIndex     = headerFields.indexOf("ORGANISM");
                                groupIndex   = headerFields.indexOf("SITE_GRP_ID");
                                geneIndex        = headerFields.indexOf("GENE");

                                inHeader = false;
                                continue;
                        }
                        if ( inHeader)
                                continue;

                        if ( line.trim().length() == 0)
                                continue;

                        // fields are:
                        String[] spl = line.split("\t");
                        if ( spl.length  < 5){
                                logger.info("Found wrong line length: " + line);
                                continue;

                        }

                        String protein = spl[proteinIndex];
                        String uniprot = spl[uniprotIndex];

                        String residue = spl[residueIndex];

                        String[] resSpl = residue.split("-");
                        String modType = null;
                        if ( resSpl.length == 2) {

                                 modType = resSpl[1];
                        }
                        String group    = spl[groupIndex];

                        String organism = spl[orgIndex];

                        String geneSymb = spl[geneIndex];

                        Site s = new Site();
                        s.setProtein(protein);
                        s.setUniprot(uniprot);
                        s.setGeneSymb(geneSymb);
                        s.setModType(modType);
                        s.setResidue(residue);
                        s.setGroup(group);
                        s.setOrganism(organism);
                        data.add(s);

                }
                buf.close();

                return data;

        }

        private static List<String> parseHeaderFields(String line) {
                String[] spl = line.split("\t");

                List<String> h = new ArrayList<>();
                for (String s: spl){
                        h.add(s);

                }

                return h;
        }

        String protein;
        String uniprot;
        String geneSymb;
        String chrLoc;
        String modType;
        String residue ;
        String group;
        String organism;

        public String getProtein() {
                return protein;
        }

        public void setProtein(String protein) {
                this.protein = protein;
        }

        public String getUniprot() {
                return uniprot;
        }

        public void setUniprot(String uniprot) {
                this.uniprot = uniprot;
        }

        public String getGeneSymb() {
                return geneSymb;
        }

        public void setGeneSymb(String geneSymb) {
                this.geneSymb = geneSymb;
        }

        public String getChrLoc() {
                return chrLoc;
        }

        public void setChrLoc(String chrLoc) {
                this.chrLoc = chrLoc;
        }

        public String getModType() {
                return modType;
        }

        public void setModType(String modType) {
                this.modType = modType;
        }

        public String getResidue() {
                return residue;
        }

        public void setResidue(String residue) {
                this.residue = residue;
        }

        public String getGroup() {
                return group;
        }

        public void setGroup(String group) {
                this.group = group;
        }

        public String getOrganism() {
                return organism;
        }

        public void setOrganism(String organism) {
                this.organism = organism;
        }

        @Override
        public String toString() {
                StringBuffer s = new StringBuffer();

                s.append("Site{" +
                                "protein='" + protein + '\'');
                if ( uniprot != null)
                                s.append(", uniprot='" + uniprot + '\'' );
                if ( geneSymb != null)
                        s.append(
                                ", geneSymb='" + geneSymb + '\'' );
                if (chrLoc != null)
                                s.append(", chrLoc='" + chrLoc + '\'' );
                if (modType != null)
                        s.append(", modType='" + modType + '\'' );

                if (residue != null)
                        s.append(        ", residue='" + residue + '\'' );
                if ( group != null)
                                s.append(", group='" + group + '\'' );
                if (organism != null)
                        s.append(", organism='" + organism + '\'' );

                  s.append(      '}');

                return s.toString();
        }
}