code: /*
   * #%L
   * Simmetrics Core
   * %%
   * Copyright (C) 2014 - 2016 Simmetrics Authors
   * %%
   * Licensed under the Apache License, Version 2.0 (the "License");
   * you may not use this file except in compliance with the License.
   * You may obtain a copy of the License at
   * 
   *      http://www.apache.org/licenses/LICENSE-2.0
   * 
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   * #L%
   */
  
  
  package org.simmetrics.metrics.functions;
  
  /**
   * A substitution function assigns value to the substitution of one character
   * for another matching against another string.
   * <p>
   * A positive value indicates the characters are similar, a negative value
   * indicates they are dissimilar.
   * 
   * <p>
   * This class is immutable and thread-safe.
   * 
   * @see Gap
   * @see <a
   *      href="https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm">Wikipedia
   *      - Smith–Waterman algorithm</a>
   *
   */
  public interface Substitution {
  	/**
  	 * Rates the substitution of character <code>a.getChar(aIndex)</code>
  	 * against <code>b.getChar(bIndex)</code>.
  	 * 
  	 * @param a
  	 *            a string to check in
  	 * @param aIndex
  	 *            index of character at string <code>a</code> to compare
  	 * @param b
  	 *            another string to check in
  	 * @param bIndex
  	 *            index of character at string <code>b</code> to compare
  	 * @return a score indicating the characters (dis) similarity
  	 */
  	public float compare(String a, int aIndex, String b, int bIndex);
  
  	/**
  	 * Returns the maximum value a gap can have
  	 * 
  	 * @return the maximum value a gap can have
  	 */
  	public float max();
  
  	/**
  	 * Returns the minimum value a gap can have
  	 * 
  	 * @return the minimum value a gap can have
  	 */
  	public float min();
  }
  