@@ -0,0 +1,1681 @@
+/**%0A * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin%0A * %0A * Licensed under the Apache License, Version 2.0 (the %22License%22);%0A * you may not use this file except in compliance with the License.%0A * You may obtain a copy of the License at%0A * %0A *     http://www.apache.org/licenses/LICENSE-2.0%0A * %0A * Unless required by applicable law or agreed to in writing, software%0A * distributed under the License is distributed on an %22AS IS%22 BASIS,%0A * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.%0A * See the License for the specific language governing permissions and%0A * limitations under the License.%0A */%0Apackage com.salsaw.salsa.cli;%0A%0Apublic class ClustalFileMapper %7B%0A%09// FIELDS%0A%09private final String inputFilePath;%0A%09private String guideTreeFilePath;%0A%09private String guidePhylogeneticTreeFile;%0A%09%0A%09// CONSTRUCTOR%0A%09public ClustalFileMapper(String inputFilePath)%7B%0A%09%09this.inputFilePath = inputFilePath;%0A%09%7D%0A%09%0A%09// GET/ SET%0A%09public String getInputFilePath()%7B%0A%09%09return this.inputFilePath;%0A%09%7D%0A%09%0A%09public String getGuideTreeFilePath()%7B%0A%09%09return this.guideTreeFilePath;%0A%09%7D%0A%09%0A%09public String getGuidePhylogeneticTreeFile()%7B%0A%09%09return this.guidePhylogeneticTreeFile;%0A%09%7D%0A%09%0A%09public void setGuideTreeFilePath(String guideTreeFilePath)%7B%0A%09%09this.guideTreeFilePath = guideTreeFilePath;%0A%09%7D%0A%0A%09public void setGuidePhylogeneticTreeFile(String guidePhylogeneticTreeFile)%7B%0A%09%09this.guidePhylogeneticTreeFile = guidePhylogeneticTreeFile;%0A%09%7D%0A%09%0A%09// METHODS%0A%09public String getTreeFilePath()%7B%0A%09%09// Return guide tree if phylogenetic tree isn't set%0A%09%09if (this.guidePhylogeneticTreeFile == null)%0A%09%09%7B%0A%09%09%09return this.guideTreeFilePath;%0A%09%09%7D%0A%09%09return this.guidePhylogeneticTreeFile;%0A%09%7D%09%0A%7D%0A

Add class to easy manage clustal parameters