X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarCigar.java;h=96f3f6f2b669d2bc35fb1edddd6827ce47080b33;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=57848eb0f911d225322d2ee36994922540fa30a6;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 57848eb..96f3f6f 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,50 +1,64 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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
+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;
-    }
+
+  /**
+   * 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
+   * @param GapChar
+   *          char
    * @todo Implement this jalview.datamodel.Cigar method
    */
   public String getSequenceString(char GapChar)
   {
-    if (length==0)
+    if (length == 0)
+    {
       return "";
+    }
     String refString = refCigar.getSequenceString(GapChar);
-    if (refString!=null) {
-      return (length==0) ? "" : (String) getSequenceAndDeletions(refString, GapChar)[0];
-    } else
+    if (refString != null)
+    {
+      return (length == 0) ? "" : (String) getSequenceAndDeletions(
+              refString, GapChar)[0];
+    }
+    else
+    {
       return null;
+    }
   }
 
 }