Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / datamodel / CigarCigar.java

diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index fbba60f..9643d9d 100644 (file)
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,61 +1,64 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\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
+/*
+ * 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;
+    }
+  }
+
+}