refactored to propery separate addToDocument,addFromDocument, updateToDocument, updat...

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

diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 5f8f78b..f5619cf 100644 (file)
--- 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;
-  }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program 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 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\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