X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=34ce3bf99db93a2bdc75743c6ef4c5da66361096;hb=caf13e6a9dc82023cd8648420201e5ad60ce0393;hp=2183f2d58f5cbfa18b647cf77b09cd3c4f0df3b9;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 2183f2d..34ce3bf 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
  * 
- * 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
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 /*
  * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
@@ -69,7 +68,7 @@ public class StockholmFile extends AlignFile
    * be passed at construction time
    * 
    * @throws IOException
-   *                 If there is an error with the input file
+   *           If there is an error with the input file
    */
   public void parse() throws IOException
   {
@@ -99,7 +98,7 @@ public class StockholmFile extends AlignFile
     }
 
     // We define some Regexes here that will be used regularily later
-    rend = new Regex("\\/\\/"); // Find the end of an alignment
+    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
     // id/from/to
     s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
@@ -207,14 +206,14 @@ public class StockholmFile extends AlignFile
                 {
                   char c = byChar[k];
                   if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
-                                                                        // uses
-                                                                        // '.'
-                                                                        // for
-                                                                        // feature
-                                                                        // background
+                  // uses
+                  // '.'
+                  // for
+                  // feature
+                  // background
                   {
                     int new_pos = posmap[k]; // look up nearest seqeunce
-                                              // position to this column
+                    // position to this column
                     SequenceFeature feat = new SequenceFeature(type, desc,
                             new_pos, new_pos, 0f, null);
 
@@ -364,8 +363,8 @@ public class StockholmFile extends AlignFile
           if (x.search(annContent))
           {
             // parse out and create alignment annotation directly.
-            parseAnnotationRow(annotations, x.stringMatched(1), x
-                    .stringMatched(2));
+            parseAnnotationRow(annotations, x.stringMatched(1),
+                    x.stringMatched(2));
           }
         }
         else if (annType.equals("GR"))
@@ -493,7 +492,7 @@ public class StockholmFile extends AlignFile
       String pos = annots.substring(i, i + 1);
       Annotation ann;
       ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
-                                              // be written out
+      // be written out
       if (ss)
       {
         ann.secondaryStructure = jalview.schemes.ResidueProperties