/*
 *                    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.bio.dp;

import java.io.Serializable;

import org.biojava.bio.dist.Distribution;
import org.biojava.bio.dist.DistributionFactory;
import org.biojava.bio.symbol.Alphabet;
import org.biojava.bio.symbol.IllegalAlphabetException;

/**
 * @author Matthew Pocock
 */
public class SimpleWeightMatrix implements WeightMatrix, Serializable {
  private static final long serialVersionUID = 73394340224964858L;
    
  private final Distribution [] columns;
  private final Alphabet alpha;

  public Alphabet getAlphabet() {
    return alpha;
  }

  public int columns() {
    return this.columns.length;
  }
  
  public Distribution getColumn(int column) {
    return columns[column];
  }

  public SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)
  throws IllegalAlphabetException {
    this.alpha = alpha;
    this.columns = new Distribution[columns];
    for(int i = 0; i < columns; i++) {
      this.columns[i] = dFact.createDistribution(alpha);
    }
  }
  
  public SimpleWeightMatrix(Distribution[] columns)
  throws IllegalAlphabetException {
    this.alpha = columns[0].getAlphabet();
    for(int c = 0; c < columns.length; c++) {
      if(columns[c].getAlphabet() != alpha) {
        throw new IllegalAlphabetException(
          "All columns must emit the same alphabet. Expecting " +
          alpha.getName() + ", but found " + columns[c].getAlphabet().getName()
        );
      }
    }
    this.columns = columns;
  }
  
  public int hashCode() {
      int hc = 0;
      for (int c = 0; c < columns.length; ++c) {
          hc = (23 * hc) + columns[c].hashCode();
      }
      return hc;
  }
  
  public boolean equals(Object o) {
      if (o instanceof WeightMatrix) {
          WeightMatrix wm = (WeightMatrix) o;
          if (wm.columns() != this.columns()) {
              return false;
          }
          if (wm.getAlphabet() != this.getAlphabet()) {
              return false;
          }
          
          for (int c = 0; c < columns(); ++c) {
              if (! this.getColumn(c).equals(wm.getColumn(c))) {
                  return false;
              }
          }
          return true;
      }
      return false;
  }
}