X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarCigar.java;h=f5619cf7dc68f97d6558a82008ad460bfd3aae07;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=83cce199f85870bf36cde1db5eed9bcc2c1d3295;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 83cce19..f5619cf 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,59 +1,62 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
+    }
+  }
+
+}