/**
 * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 * 
 * 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.
 */
package com.salsaw.salsa.algorithm;

/**
 * Manage and perform the local search
 * 
 * @author Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 *
 */
public final class LocalSearch {

}

@@ -669,16 +669,45 @@
 rithm;%0A%0A
+import java.util.ArrayList;%0A%0A
 /**%0A * M
@@ -848,11 +848,1595 @@
 earch %7B%0A
+%09// FILEDS%0A%09private Alignment align;%0A%09private ArrayList%3CGAP%3E GAPS;%0A%09private int numberOfGAPS;%0A%09private int gamma;%0A%09private int minIterations;%0A%09private float probabiltyOfSplit;%0A%0A%09private TerminalGAPsStrategy terminal;%0A%09%0A%09// CONSTRUCTOR%0A%09%0A%09// METHODS%0A%09%0A%09/**%0A%09 * GAPPosition is the index of the GAP to be moved (inside GAPS vector). The method returns TRUE if there were an improvement.%0A%09 * Variable left tells the method the direction of the movement. split tells if there were a split and this information%0A%09 * is used only to choose properly the new position of the GAP. splitAndMove will manage all the rest.%0A%09 * %0A%09 * @param GAPPosition%0A%09 * @param left%0A%09 * @return%0A%09 */%0A%09private final boolean move(int GAPPosition, boolean left)%7B%0A%09%09return move(GAPPosition, left, false);%0A%09%7D%0A%09%0A%09/**%0A%09 * GAPPosition is the index of the GAP to be moved (inside GAPS vector). The method returns TRUE if there were an improvement.%0A%09 * Variable left tells the method the direction of the movement. split tells if there were a split and this information%0A%09 * is used only to choose properly the new position of the GAP. splitAndMove will manage all the rest.%0A%09 * %0A%09 * @param GAPPosition%0A%09 * @param left%0A%09 * @param split%0A%09 * @return%0A%09 */%0A%09private final boolean move(int GAPPosition, boolean left, boolean split)%7B%0A%09%09// TODO - report from c code%0A%09%09return false;%0A%09%7D%0A%09%0A%09/**%0A%09 * Like move() method, but it split the GAP before moving it%0A%09 * %0A%09 * @param GAPPosition%0A%09 * @param left%0A%09 * @return%0A%09 */%0A%09private final boolean splitAndMove(int GAPPosition, boolean left)%7B%0A%09%09// TODO - report from c code%0A%09%09return false;%0A%09%7D
 %0A%7D%0A

Write backbone for LocalSearch