X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarCigar.java;h=f453e2c7681dc82f2c5f70030a6db2e615bfe8cd;hb=1dabf099b7c77fb0a80039f72cef34669df9b2e1;hp=5f8f78bc6d1aff47670dcaeeb50c496217a0f246;hpb=60508bc218cee42c6fa3405db19f7790acafabab;p=jalview.git

diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 5f8f78b..f453e2c 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,32 +1,62 @@
-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;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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;
+    }
+  }
+
+}