/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis.scoremodels;

import jalview.api.analysis.ScoreModelI;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.StringTokenizer;

public class ScoreMatrix extends PairwiseSeqScoreModel implements
        ScoreModelI
{
  public static final short UNMAPPED = (short) -1;

  private static final String DELIMITERS = " ,\t";

  private static final String COMMENT_CHAR = "#";

  private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";

  private static final int MAX_ASCII = 127;

  /*
   * the name of the model as shown in menus
   */
  private String name;

  /*
   * the characters that the model provides scores for
   */
  private char[] symbols;

  /*
   * the score matrix; both dimensions must equal the number of symbols
   * matrix[i][j] is the substitution score for replacing symbols[i] with symbols[j]
   */
  private float[][] matrix;

  /*
   * quick lookup to convert from an ascii character value to the index
   * of the corresponding symbol in the score matrix 
   */
  private short[] symbolIndex;

  /*
   * true for Protein Score matrix, false for dna score matrix
   */
  private boolean peptide;

  /**
   * Constructor
   * 
   * @param name
   *          Unique, human readable name for the matrix
   * @param alphabet
   *          the symbols to which scores apply
   * @param matrix
   *          Pairwise scores indexed according to the symbol alphabet
   */
  public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
  {
    this.matrix = matrix;
    this.name = name;
    this.symbols = alphabet;

    symbolIndex = buildSymbolIndex(alphabet);

    /*
     * crude heuristic for now...
     */
    peptide = alphabet.length >= 20;
  }

  /**
   * Returns an array A where A[i] is the position in the alphabet array of the
   * character whose value is i. For example if the alphabet is { 'A', 'D', 'X'
   * } then A['D'] = A[68] = 1.
   * <p>
   * Unmapped characters (not in the alphabet) get an index of -1.
   * <p>
   * Mappings are added automatically for lower case symbols (for non case
   * sensitive scoring), unless they are explicitly present in the alphabet (are
   * scored separately in the score matrix).
   * 
   * @param alphabet
   * @return
   */
  static short[] buildSymbolIndex(char[] alphabet)
  {
    short[] index = new short[MAX_ASCII + 1];
    Arrays.fill(index, UNMAPPED);
    short pos = 0;
    for (char c : alphabet)
    {
      if (c <= MAX_ASCII)
      {
        index[c] = pos;
      }

      /*
       * also map lower-case character (unless separately mapped)
       */
      if (c >= 'A' && c <= 'Z')
      {
        short lowerCase = (short) (c + ('a' - 'A'));
        if (index[lowerCase] == UNMAPPED)
        {
          index[lowerCase] = pos;
        }
      }
      pos++;
    }
    return index;
  }

  @Override
  public String getName()
  {
    return name;
  }

  @Override
  public boolean isDNA()
  {
    return !peptide;
  }

  @Override
  public boolean isProtein()
  {
    return peptide;
  }

  @Override
  public float[][] getMatrix()
  {
    return matrix;
  }

  /**
   * Returns the pairwise score for substituting c with d, or zero if c or d is
   * an unscored or unexpected character
   */
  @Override
  public float getPairwiseScore(char c, char d)
  {
    if (c > MAX_ASCII)
    {
      System.err.println(String.format(BAD_ASCII_ERROR, c));
      return 0;
    }
    if (d > MAX_ASCII)
    {
      System.err.println(String.format(BAD_ASCII_ERROR, d));
      return 0;
    }

    int cIndex = symbolIndex[c];
    int dIndex = symbolIndex[d];
    if (cIndex != UNMAPPED && dIndex != UNMAPPED)
    {
      return matrix[cIndex][dIndex];
    }
    return 0;
  }

  /**
   * pretty print the matrix
   */
  @Override
  public String toString()
  {
    return outputMatrix(false);
  }

  /**
   * Print the score matrix, optionally formatted as html, with the alphabet symbols as column headings and at the start of each row
   * @param html
   * @return
   */
  public String outputMatrix(boolean html)
  {
    StringBuilder sb = new StringBuilder(512);

    /*
     * heading row with alphabet
     */
    if (html)
    {
      sb.append("<table border=\"1\">");
      sb.append(html ? "<tr><th></th>" : "");
    }
    for (char sym : symbols)
    {
      if (html)
      {
        sb.append("<th>&nbsp;").append(sym).append("&nbsp;</th>");
      }
      else
      {
        sb.append("\t").append(sym);
      }
    }
    sb.append(html ? "</tr>\n" : "\n");

    /*
     * table of scores
     */
    for (char c1 : symbols)
    {
      if (html)
      {
        sb.append("<tr><td>");
      }
      sb.append(c1).append(html ? "</td>" : "");
      for (char c2 : symbols)
      {
        sb.append(html ? "<td>" : "\t")
                .append(matrix[symbolIndex[c1]][symbolIndex[c2]])
                .append(html ? "</td>" : "");
      }
      sb.append(html ? "</tr>\n" : "\n");
    }
    if (html)
    {
      sb.append("</table>");
    }
    return sb.toString();
  }

  /**
   * Parse a score matrix from the given input stream and returns a ScoreMatrix
   * object. If parsing fails, error messages are written to syserr and null is
   * returned. It is the caller's responsibility to close the input stream.
   * 
   * @param is
   * @return
   */
  public static ScoreMatrix parse(InputStream is)
  {
    ScoreMatrix sm = null;
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    int lineNo = 0;
    String name = null;
    String alphabet = null;
    float[][] scores = null;
    int size = 0;
    int row = 0;

    try
    {
      String data;

      while ((data = br.readLine()) != null)
      {
        lineNo++;
        data = data.trim();
        if (data.startsWith(COMMENT_CHAR))
        {
          continue;
        }
        if (data.toLowerCase().startsWith("scorematrix"))
        {
          /*
           * Parse name from ScoreMatrix <name>
           */
          if (name != null)
          {
            System.err
                    .println("Warning: 'ScoreMatrix' repeated in file at line "
                            + lineNo);
          }
          StringTokenizer nameLine = new StringTokenizer(data, DELIMITERS);
          if (nameLine.countTokens() != 2)
          {
            System.err
                    .println("Format error: expected 'ScoreMatrix <name>', found '"
                            + data + "' at line " + lineNo);
            return null;
          }
          nameLine.nextToken();
          name = nameLine.nextToken();
          continue;
        }
        else if (name == null)
        {
          System.err
                  .println("Format error: 'ScoreMatrix <name>' should be the first non-comment line");
          return null;
        }

        /*
         * next line after ScoreMatrix should be the alphabet of scored symbols
         */
        if (alphabet == null)
        {
          alphabet = data;
          size = alphabet.length();
          scores = new float[size][];
          continue;
        }

        /*
         * too much information?
         */
        if (row >= size && data.length() > 0) {
          System.err
                  .println("Unexpected extra input line in score model file "
                          + data);
          return null;
        }
        
        /*
         * subsequent lines should be the symbol scores
         */
        StringTokenizer scoreLine = new StringTokenizer(data, DELIMITERS);
        if (scoreLine.countTokens() != size)
        {
          System.err.println(String.format(
                  "Expected %d tokens at line %d but found %d", size,
                  lineNo, scoreLine.countTokens()));
          return null;
        }
        scores[row] = new float[size];
        int col = 0;
        String value = null;
        while (scoreLine.hasMoreTokens()) {
          try {
            value = scoreLine.nextToken();
            scores[row][col] = Float.valueOf(value);
            col++;
          } catch (NumberFormatException e)
          {
            System.err.println(String.format(
                    "Invalid score value %s at line %d column %d", value,
                    lineNo, col));
            return null;
          }
        }
        row++;
      }
    } catch (IOException e)
    {
      System.err.println("Error reading score matrix file: "
              + e.getMessage() + " at line " + lineNo);
    }

    /*
     * out of data - check we found enough
     */
    if (row < size)
    {
      System.err
              .println(String
                      .format("Expected %d rows of score data in score matrix but only found %d",
                              size, row));
      return null;
    }

    /*
     * If we get here, then name, alphabet and scores have been parsed successfully
     */
    sm = new ScoreMatrix(name, alphabet.toCharArray(), scores);
    return sm;
  }
}