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;
  
  import static com.google.common.base.Preconditions.checkArgument;
  
  /**
   * A gap function that calculates the gap penalty as <code>A+(B * GapLegth)</code>.
   * 
   * <p>
   * This class is immutable and thread-safe.
   * 
   * @see Substitution
   * @see <a href="https://en.wikipedia.org/wiki/Gap_penalty">Wikipedia - Gap
   *      Penalty</a>
   *
   */
  public final class AffineGap implements Gap {
  
  	private final float startValue;
  	private final float gapValue;
  
  	/**
  	 * Constructs a constant gap function that assigns a penalty of
  	 * <code>startValue + gapValue * gapLenght </code> to a gap. .
  	 * 
  	 * @param startValue
  	 *            a non-positive initial penalty for creating a gap
  	 * @param gapValue
  	 *            a non-positive constant gap value
  	 */
  	public AffineGap(float startValue, float gapValue) {
  		checkArgument(startValue <= 0.0f);
  		checkArgument(gapValue <= 0.0f);
  
  		this.startValue = startValue;
  		this.gapValue = gapValue;
  	}
  
  	@Override
  	public final float value(int fromIndex, int toIndex) {
  		checkArgument(fromIndex < toIndex, "fromIndex must be before toIndex");
  		return startValue + gapValue * (toIndex - fromIndex - 1);
  	}
  
  	@Override
  	public final float max() {
  		return startValue;
  	}
  
  	@Override
  	public final float min() {
  		return Float.NEGATIVE_INFINITY;
  	}
  
  	@Override
  	public String toString() {
  		return "AffineGap [startValue=" + startValue + ", gapValue=" + gapValue
  				+ "]";
  	}
  
  }
  