@@ -0,0 +1,1115 @@
+/**%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.algorithm;%0A%0A/**%0A * A terminal GAP is a GAP in the beginning or in the end of a sequence. Usually, the penalties for a%0A * terminal GAP is different from the others.%0A * %0A * @author Alessandro Daniele, Fabio Cesarato, Andrea Giraldin%0A *%0A */%0Apublic enum TerminalGAPsStrategy %7B%0A%09/**%0A%09 * as other GAPs, a terminal GAP has both GOP and GEP%0A%09 */%0A%09BOTH_PENALTIES,%0A%09/**%0A%09 * there is no penalty for opening a terminal GAP, only for extending it%0A%09 */%0A%09ONLY_GEP%0A%7D%0A

Add enum TerminalGAPsStrategy