/*
 *                    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.core.search.io.blast;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Scanner;
import java.util.logging.Logger;
import org.biojava.nbio.core.search.io.Hit;
import org.biojava.nbio.core.search.io.Hsp;
import org.biojava.nbio.core.search.io.Result;
import org.biojava.nbio.core.search.io.ResultFactory;
import org.biojava.nbio.core.sequence.template.Sequence;

/**
 * Designed by Paolo Pavan.
 * You may want to find my contacts on Github and LinkedIn for code info
 * or discuss major changes.
 * https://github.com/paolopavan
 *
 * @author Paolo Pavan
 */

public class BlastTabularParser implements ResultFactory {
        private final String blastReference =
                        "Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.";
        /**
         * Tries to define a different level of consistency during parsing.
         * LITERAL is intended a strict parsing much tight to the report.
         * IMPROVED consistency tries to import data much tight to the data model
         * (I hope you got the idea, if not, have a look to the code.
         * I suggest to use improved unless you have reasons to do not)
         */
        private enum PARSING_CONSISTENCY {
                IMPROVED,
                LITERAL
        }
        private static final Logger log = Logger.getLogger(BlastTabularParser.class.getName());


        private File targetFile;
        private int fileLinesCount;
        private PARSING_CONSISTENCY parsingConsistency = PARSING_CONSISTENCY.IMPROVED;


        // data imported private:
        int queryIdNumber = 0;
        HashMap<String,String> queryIdMapping = new HashMap<String,String>();
        String programName=null, queryName = null, databaseFile = null;
        private String queryId      ;
        private String subjectId    ;
        private String percIdentity ;
        private String alnLength    ;
        private String mismatchCount;
        private String gapOpenCount ;
        private String queryStart   ;
        private String queryEnd     ;
        private String subjectStart ;
        private String subjectEnd   ;
        private String evalue       ;
        private String bitScore     ;


        @Override
        public List<String> getFileExtensions() {
                List<String> l = new ArrayList<String>();
                l.add("blasttabular");
                l.add("blasttxt");
                return l;
        }

        @Override
        public void setFile(File f) {
                targetFile = f;
        }

        @Override
        public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
                List<Result> results = new ArrayList<Result>();

                log.info("Query for hits");
                LineNumberReader  lnr = new LineNumberReader(new FileReader(targetFile));
                lnr.skip(Long.MAX_VALUE);
                fileLinesCount = lnr.getLineNumber();
                log.info(fileLinesCount + " hits approximately in all results");
                lnr.close();

                FileInputStream fileInputStream = new FileInputStream(targetFile);
                Scanner scanner = new Scanner(fileInputStream);

                String line = fetchData(scanner);
                int lineNumber=0;
                while (lineNumber < fileLinesCount){
                        try {
                                BlastResultBuilder resultBuilder = new BlastResultBuilder();
                                resultBuilder
                                                .setQueryID(queryId)
                                                .setDbFile(databaseFile)
                                                .setProgram(programName)
                                                .setQueryDef(queryName)
                                                .setReference(blastReference);

                                List<Hit> hits = new ArrayList<Hit>();

                                String currentQueryId = queryId;
                                while (currentQueryId.equals(queryId) && lineNumber < fileLinesCount){
                                        BlastHitBuilder hitBuilder = new BlastHitBuilder();

                                        List<Hsp> hsps = new ArrayList<Hsp>();

                                        String currentSubjectId=subjectId;
                                        while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount){
                                                if (new Double(evalue) > maxEScore) {
                                                        line = fetchData(scanner);
                                                        lineNumber++;
                                                        continue;
                                                }
                                                BlastHspBuilder hspBuilder = new BlastHspBuilder();
                                                hspBuilder
                                                        .setHspAlignLen(new Integer(alnLength))
                                                        .setHspGaps(new Integer(gapOpenCount))
                                                        .setHspQueryFrom(new Integer(queryStart))
                                                        .setHspQueryTo(new Integer(queryEnd))
                                                        .setHspHitFrom(new Integer(subjectStart))
                                                        .setHspHitTo(new Integer(subjectEnd))
                                                        .setHspEvalue(new Double(evalue))
                                                        .setHspBitScore(new Double(bitScore))
                                                        .setPercentageIdentity(new Double(percIdentity)/100)
                                                        .setMismatchCount(new Integer(mismatchCount));
                                                hsps.add(hspBuilder.createBlastHsp());
                                                if (scanner.hasNext()) line = fetchData(scanner);
                                                lineNumber++;
                                        }
                                        hits.add(hitBuilder.setHsps(hsps).createBlastHit());
                                }
                                results.add(resultBuilder.setHits(hits).createBlastResult());
                        } catch (NumberFormatException e) {
                                throw new ParseException("Invalid numeric value met at line "+ lineNumber+" in:\n"+line,0);
                        }
                }
                return results;
        }

        private String fetchData(Scanner scanner){
                String line;
                String[] split;

                line = scanner.nextLine();
                while (line.startsWith("#")){
                        // blast tabular with header options contains some more informations
                        if (line.matches("#\\s.?BLAST.+")) programName = line.replace("#\\s","");
                        if (line.startsWith("# Query:")) queryName = line.replace("# Query: ","");
                        if (line.startsWith("# Database:")) databaseFile = line.replace("# Database: ","");

                        // needed because blast report can end with a comment...
                        if (!scanner.hasNext()) return null;
                        line = scanner.nextLine();
                }

                // Here, programName != null checks if there was a header in the file
                boolean headerFound = programName != null;

                split = line.split("\\t");
                queryId      =split[0];
                subjectId    =split[1];
                percIdentity =split[2];
                alnLength    =split[3];
                mismatchCount=split[4];
                gapOpenCount =split[5];
                queryStart   =split[6];
                queryEnd     =split[7];
                subjectStart =split[8];
                subjectEnd   =split[9];
                evalue       =split[10];
                bitScore     =split[11];

                // blast tabular reports only the first word of the query name.
                // If it was specified in the header it is better to use that definition
                if (parsingConsistency == PARSING_CONSISTENCY.IMPROVED && headerFound) {
                        if (queryIdMapping.get(queryId)==null) {
                                queryIdNumber ++;
                                queryIdMapping.put(queryId,"Query_" + queryIdNumber);
                        }
                        // If a complete definition of the query name was readed, than we can use
                        // a queryID schema that is consistent with blast xml report
                        queryId = queryIdMapping.get(queryId);
                }
                if (!headerFound) queryName = queryId;

                return line;
        }

        @Override
        public void storeObjects(List<Result> results) throws IOException, ParseException {
                throw new UnsupportedOperationException("Not supported yet.");
        }

        /**
         * Intended for use with run module.
         * Although possible, does not make a lot of sense to have it with limited
         * information such those in tabular report
         * @param sequences
         */
        @Override
        public void setQueryReferences(List<Sequence> sequences) {
                throw new UnsupportedOperationException("Not supported for this parser.");
        }
        /**
         * Intended for use with run module.
         * Although possible, does not make a lot of sense to have it with limited
         * information such those in tabular report
         * @param sequences
         */
        @Override
        public void setDatabaseReferences(List<Sequence> sequences) {
                throw new UnsupportedOperationException("Not supported for this parser.");
        }
         /**
         * Tries to define a different level of consistency during parsing.
         * LITERAL is intended a strict parsing much tight to the report.
         * IMPROVED consistency tries to import data much tight to the data model
         * (I hope you got the idea, if not, have a look to the code.
         * I suggest to use improved unless you have reasons to do not)
         */
        public void setParsingConsistency(PARSING_CONSISTENCY parsingConsistency) {
                this.parsingConsistency = parsingConsistency;
        }

}