2.5.1 release branding

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 2183f2d..470cc37 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,20 +1,19 @@
 /*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\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
 /*\r
  * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
@@ -69,7 +68,7 @@ public class StockholmFile extends AlignFile
    * be passed at construction time\r
    * \r
    * @throws IOException\r
-   *                 If there is an error with the input file\r
+   *           If there is an error with the input file\r
    */\r
   public void parse() throws IOException\r
   {\r
@@ -207,14 +206,14 @@ public class StockholmFile extends AlignFile
                 {\r
                   char c = byChar[k];\r
                   if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
-                                                                        // uses\r
-                                                                        // '.'\r
-                                                                        // for\r
-                                                                        // feature\r
-                                                                        // background\r
+                  // uses\r
+                  // '.'\r
+                  // for\r
+                  // feature\r
+                  // background\r
                   {\r
                     int new_pos = posmap[k]; // look up nearest seqeunce\r
-                                              // position to this column\r
+                    // position to this column\r
                     SequenceFeature feat = new SequenceFeature(type, desc,\r
                             new_pos, new_pos, 0f, null);\r
 \r
@@ -493,7 +492,7 @@ public class StockholmFile extends AlignFile
       String pos = annots.substring(i, i + 1);\r
       Annotation ann;\r
       ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
-                                              // be written out\r
+      // be written out\r
       if (ss)\r
       {\r
         ann.secondaryStructure = jalview.schemes.ResidueProperties\r