/*
* 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.analysis;

import jalview.datamodel.*;
import jalview.util.*;
import java.util.*;

public class AlignmentUtil {

  private AlignmentUtil() {
  }

  public static int[][] percentIdentity2(AlignmentI align) {
    return percentIdentity2(align,0,align.getWidth()-1);
  }

  public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
    int [][] cons2 = new int[align.getWidth()][24];
    // Initialize the array
    for (int j=0;j<24;j++) {
      for (int i=0; i < align.getWidth();i++) {
        cons2[i][j] = 0;
      }
    }

    return cons2;
  }
  public static int getPixelHeight(int i, int j,int charHeight) {
    int h=0;
    while (i < j) {
      h += charHeight;
      i++;
    }
    return h;
  }


    public static Vector substitution_rates (AlignmentI align, int start, int end) {

	Vector rates = new Vector();

	int len = (end-start+1);

	// Turn seqs into char arrays

	int[][] seqint = new int[align.getHeight()][len];


	for (int j = 0; j < align.getHeight(); j++) {

	    SequenceI seq = align.getSequenceAt(j);

	    for (int i = 0 ; i < len; i++) {
		char c = seq.getCharAt(start + i - 1);

		if (c == 'A') {
		    seqint[j][i] = 0;
		} else if (c == 'C') {
		    seqint[j][i] = 1;
		} else if (c == 'T') {
		    seqint[j][i] = 2;
		} else if (c == 'G') {
		    seqint[j][i] = 3;
		} else {
		    seqint[j][i] = -1;
		}

	    }

	}


	//	print_matrix(seqint,2,len);	for (int j = 0; j < align.getHeight(); j++) {

	    for (int j = 0; j < align.getHeight(); j++) {

		for (int k = 0; k < align.getHeight(); k++) {

		int counts[][] = new int[4][4];
		int tot  = 0;
		int tots[] = new int[4];
		int fulltot = 0;
		int fulltots[] = new int[4];

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

		    if (k != j) {

			//			System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
			if (seqint[j][i] >= 0 &&
			    seqint[k][i] >= 0) {
			    counts[seqint[k][i]][seqint[j][i]]++;

			    //  print_matrix(counts,4,4);
			    tots[seqint[j][i]]++;
			    tot++;
			}
			if (seqint[j][i] != -1) {
			    fulltots[seqint[j][i]]++;
			    fulltot++;
			}
		    }
		}

		if (k != j) {

		    System.out.println();

		    System.out.println("Sequence " + align.getSequenceAt(j).getName() + " "  + align.getSequenceAt(k).getName());

		    System.out.println();
		    print_matrix(counts,4,4);
		    System.out.println();



		    double[][] out = new double[4][4];// = constant_multiply_matrix(counts,1.0/tot,4,4);

		    for (int i = 0; i < 4; i++) {
			for (int jj = 0; jj < 4; jj++) {
			    out[i][jj] = (double)counts[i][jj]/tots[jj];
			}
		    }

		    print_matrix(out,4,4);
		    System.out.println();


		    System.out.print("RATES\t");
		    System.out.print(align.getSequenceAt(j).getName() + "\t"  + align.getSequenceAt(k).getName() + "\t");

		    for (int i = 0; i < 4; i++) {
			for (int jj = 0; jj < 4; jj++) {
			    Format.print(System.out,"%4.3f\t",out[i][jj]);
			}
		    }
		    System.out.println();

 		    for (int i = 0; i < 4; i++) {
			Format.print(System.out,"%4.3f\t",(double)fulltots[i]*1.0/fulltot);
		    }

		    System.out.println();
		    System.out.print("\nGC ");

		    Format.print(System.out,"%4.3f\t",(double)(100*fulltots[1]+fulltots[3])/fulltot);

		    System.out.print((fulltots[1]+fulltots[3]) + "\t" + fulltot);


		    System.out.println();

		    rates.addElement(out);
		}

	    }
	}
	return rates;
    }

    public static double[][]  constant_multiply_matrix(int[][] matrix, double c,int n, int m) {
	double[][] out = new double[n][m];

	for (int i = 0; i < n; i++) {
	    for (int j = 0; j < m; j++) {

		out[i][j] = matrix[i][j]*c;
	    }
	}
	return out;
    }


    public static void print_matrix(int[][] matrix, int n, int m) {


	for (int i = 0; i < n; i++) {
	    for (int j = 0; j < m; j++) {

		System.out.print(matrix[i][j] + "\t");
	    }
	    System.out.println();
	}
    }
    public static void print_matrix(double[][] matrix, int n, int m) {


	for (int i = 0; i < n; i++) {
	    for (int j = 0; j < m; j++) {

		Format.print(System.out,"%4.3f\t",matrix[i][j]);

	    }
	    System.out.println();
	}
    }


}