/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.util;

import jalview.datamodel.*;


public class Comparison {
    public static String GapChars = " .-";

    public static float compare(SequenceI ii, SequenceI jj) {
        return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
    }

    /**
     * this was supposed to be an ungapped pid calculation
     * @param ii SequenceI
     * @param jj SequenceI
     * @param start int
     * @param end int
     * @return float
     */
    public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
        String si = ii.getSequence();
        String sj = jj.getSequence();

        int ilen = si.length() - 1;
        int jlen = sj.length() - 1;

        while (jalview.util.Comparison.isGap(si.charAt(start + ilen))) {
            ilen--;
        }

        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {
            jlen--;
        }

        int count = 0;
        int match = 0;
        float pid = -1;

        if (ilen > jlen) {
            for (int j = 0; j < jlen; j++) {
                if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
                                j, start + j + 1))) {
                    match++;
                }

                count++;
            }

            pid = (float) match / (float) ilen * 100;
        } else {
            for (int j = 0; j < jlen; j++) {
                if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
                                j, start + j + 1))) {
                    match++;
                }

                count++;
            }

            pid = (float) match / (float) jlen * 100;
        }

        return pid;
    }

    /**
     * this is a gapped PID calculation
     *
     * @param s1 SequenceI
     * @param s2 SequenceI
     * @return float
     */
    public static float PID(SequenceI s1, SequenceI s2) {
        int len;

        if (s1.getSequence().length() > s2.getSequence().length()) {
            len = s1.getSequence().length();
        } else {
            len = s2.getSequence().length();
        }

        int bad = 0;

        for (int i = 0; i < len; i++) {
            char chr1;
            char chr2;

            if (i < s1.getSequence().length()) {
                chr1 = s1.getSequence().charAt(i);
            } else {
                chr1 = '.';
            }

            if (i < s2.getSequence().length()) {
                chr2 = s2.getSequence().charAt(i);
            } else {
                chr2 = '.';
            }

            if (!(jalview.util.Comparison.isGap(chr1)) &&
                    !(jalview.util.Comparison.isGap(chr2))) {
                if (chr1 != chr2) {
                    bad++;
                }
            }
        }

        return ((float) 100 * (len - bad)) / len;
    }

    // Another pid with region specification
    public static float PID(SequenceI s1, SequenceI s2, int start, int end) {
        int len;

        if (s1.getSequence().length() > s2.getSequence().length()) {
            len = s1.getSequence().length();
        } else {
            len = s2.getSequence().length();
        }

        if (end < len) {
            len = end;
        }

        if (len < start) {
            start = len - 1; // we just use a single residue for the difference
        }

        int bad = 0;

        for (int i = start; i < len; i++) {
            char chr1;
            char chr2;

            if (i < s1.getSequence().length()) {
                chr1 = s1.getSequence().charAt(i);
            } else {
                chr1 = '.';
            }

            if (i < s2.getSequence().length()) {
                chr2 = s2.getSequence().charAt(i);
            } else {
                chr2 = '.';
            }

            if (!(jalview.util.Comparison.isGap(chr1)) &&
                    !(jalview.util.Comparison.isGap(chr2))) {
                if (chr1 != chr2) {
                    bad++;
                }
            }
        }

        return ((float) 100 * (len - bad)) / len;
    }

    public static boolean isGap(char c) {
        return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;
    }
}