/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */
package org.broad.igv.synteny;

//~--- JDK imports ------------------------------------------------------------

import org.broad.igv.exceptions.ParserException;
import org.broad.igv.feature.Strand;

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

/**
 * @author jrobinso
 */
public class BlastParser {

    /**
     * Method description
     * <p/>
     * queryID,subjectID,percentIden,alignmentLength,
     * mismatches,gapOpenings,queryStart,queryStop,subjectStart,subjectStop,eval,bitScore
     * <p/>
     * 1	9	87.73	864	106	0	100842	101705	222166	221303	0	872
     *
     * @param file
     * @return
     */
    public List<BlastMapping> parse(String file) {

        List<BlastMapping> mappings = new ArrayList();

        BufferedReader reader = null;

        boolean tabblastn = file.contains(".tabblastn");

        int queryChrIdx = 0;
        int queryStartIdx = tabblastn ? 6 : 1;
        int queryEndIdx = tabblastn ? 7 : 2;
        int queryStrandIdx = tabblastn ? -1 : 3;

        int subjectChrIdx = tabblastn ? 1 : 4;
        int subjectStartIdx = tabblastn ? 8 : 5;
        int subjectEndIdx = tabblastn ? 9 : 6;
        int subjectStrandIdx = tabblastn ? -1 : 7;

        int nTokens = tabblastn ? 10 : 8;

        long lineCount = 0;
        String nextLine = null;
        boolean dataParsed = false;

        try {
            reader = new BufferedReader(new FileReader(file));

            while ((nextLine = reader.readLine()) != null) {
                lineCount++;
                String[] tokens = nextLine.split("\t");
                if (tokens.length >= nTokens) {
                    dataParsed = true;
                    String queryCht = tokens[queryChrIdx];

                    int queryStart;
                    int queryEnd;
                    try {
                        queryStart = Integer.parseInt(tokens[queryStartIdx]);
                        queryEnd = Integer.parseInt(tokens[queryEndIdx]);
                    }
                    catch (NumberFormatException ne) {
                        throw new RuntimeException("Non-numeric value found in either start or end column");
                    }
                    Strand queryStrand = Strand.NONE;
                    if (!tabblastn) {
                        int str = Integer.parseInt(tokens[queryStrandIdx]);
                        queryStrand = str == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
                    }

                    String subjectChr = tokens[subjectChrIdx];

                    int subjectStart;
                    int subjectEnd;
                    try {
                        subjectStart = Integer.parseInt(tokens[subjectStartIdx]);
                        subjectEnd = Integer.parseInt(tokens[subjectEndIdx]);
                    }
                    catch (NumberFormatException ne) {
                        throw new RuntimeException("Non-numeric value found in " +
                                " either subject start or end column");
                    }
                    Strand subjectStrand = Strand.NONE;
                    if (!tabblastn) {
                        try {
                            int str = Integer.parseInt(tokens[subjectStrandIdx]);
                            subjectStrand = str == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
                        }
                        catch (NumberFormatException ne) {
                            throw new RuntimeException("Non-numeric value found in " +
                                    " either subject strand column");
                        }
                    }

                    float percentIden = tabblastn ? Float.parseFloat(tokens[2]) : 100.0f;

                    BlastMapping.Block queryBlock = new BlastMapping.Block(queryCht, queryStart, queryEnd, queryStrand);
                    BlastMapping.Block subjectBlock = new BlastMapping.Block(subjectChr, subjectStart, subjectEnd, subjectStrand);

                    mappings.add(new BlastMapping(queryBlock, subjectBlock, percentIden));
                }
            }

            if (!dataParsed) {
                throw new RuntimeException("Data not loaded. Number of columns is less than " + nTokens + ".");
            }

        } catch (Exception ex) {
            if (lineCount != 0) {
                throw new ParserException(ex.getMessage(), lineCount, nextLine);
            } else {
                throw new RuntimeException(ex);
            }
        } finally {
            if (reader != null) {
                try {
                    reader.close();

                } catch (IOException iOException) {
                }
            }
        }

        return mappings;
    }
}
