-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-public class CigarCigar extends CigarSimple\r
-{\r
- SeqCigar refCigar;\r
-\r
- /**\r
- * Apply CIGAR operations to the result of another cigar\r
- * \r
- * @param cigar\r
- * Cigar\r
- */\r
- CigarCigar(SeqCigar cigar)\r
- {\r
- super();\r
- refCigar = cigar;\r
- }\r
-\r
- /**\r
- * \r
- * @return String formed by applying CIGAR operations to the reference object\r
- * @param GapChar\r
- * char\r
- * @todo Implement this jalview.datamodel.Cigar method\r
- */\r
- public String getSequenceString(char GapChar)\r
- {\r
- if (length == 0)\r
- {\r
- return "";\r
- }\r
- String refString = refCigar.getSequenceString(GapChar);\r
- if (refString != null)\r
- {\r
- return (length == 0) ? "" : (String) getSequenceAndDeletions(\r
- refString, GapChar)[0];\r
- }\r
- else\r
- {\r
- return null;\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+public class CigarCigar extends CigarSimple
+{
+ SeqCigar refCigar;
+
+ /**
+ * Apply CIGAR operations to the result of another cigar
+ *
+ * @param cigar
+ * Cigar
+ */
+ CigarCigar(SeqCigar cigar)
+ {
+ super();
+ refCigar = cigar;
+ }
+
+ /**
+ *
+ * @return String formed by applying CIGAR operations to the reference object
+ * @param GapChar
+ * char
+ * @todo Implement this jalview.datamodel.Cigar method
+ */
+ public String getSequenceString(char GapChar)
+ {
+ if (length == 0)
+ {
+ return "";
+ }
+ String refString = refCigar.getSequenceString(GapChar);
+ if (refString != null)
+ {
+ return (length == 0) ? ""
+ : (String) getSequenceAndDeletions(refString, GapChar)[0];
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+}