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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index aeaa374..6fef9a4 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+ * This file is part of Jalview.\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
+ * 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
- * 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
+ * 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
@@ -52,7 +51,7 @@ public class CigarArray extends CigarBase
    * any of cigar are actually CigarArrays.\r
    * \r
    * @param cigar\r
-   *                Cigar[]\r
+   *          Cigar[]\r
    */\r
   public CigarArray(CigarSimple[] cigars)\r
   {\r
@@ -75,7 +74,7 @@ public class CigarArray extends CigarBase
   /**\r
    * @see Cigar.getSequenceAndDeletions\r
    * @param GapChar\r
-   *                char\r
+   *          char\r
    * @return Object[][]\r
    */\r
   protected Object[][] getArrayofSequenceAndDeletions(char GapChar)\r
@@ -106,7 +105,7 @@ public class CigarArray extends CigarBase
    * @return String formed by newline concatenated results of applying CIGAR\r
    *         operations to each reference object in turn.\r
    * @param GapChar\r
-   *                char\r
+   *          char\r
    * @return '\n' separated strings (empty results included as \n\n)\r
    */\r
   public String getSequenceString(char GapChar)\r
@@ -133,7 +132,7 @@ public class CigarArray extends CigarBase
    * return string results of applying cigar string to all reference cigars\r
    * \r
    * @param GapChar\r
-   *                char\r
+   *          char\r
    * @return String[]\r
    */\r
   public String[] getSequenceStrings(char GapChar)\r
@@ -158,9 +157,9 @@ public class CigarArray extends CigarBase
    * \r
    * @return Cigar[]\r
    * \r
-   * public CigarBase[] getEditedCigars() {\r
+   *         public CigarBase[] getEditedCigars() {\r
    * \r
-   * return new CigarBase[] {}; }\r
+   *         return new CigarBase[] {}; }\r
    */\r
   /**\r
    * applyDeletions edits underlying refCigars to propagate deleted regions, and\r
@@ -199,7 +198,7 @@ public class CigarArray extends CigarBase
         int delstart = cursor, delend = cursor + range[i] - 1; // inclusive\r
         delpos.addElement(new int[]\r
         { vcursor + offset, range[i] }); // index of right hand column after\r
-                                          // hidden region boundary\r
+        // hidden region boundary\r
         offset += range[i] - 1; // shift in visible column coordinates\r
         System.arraycopy(operation, i + 1, operation, i, length - i);\r
         System.arraycopy(range, i + 1, range, i, length - i);\r