-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-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;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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