X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=ca8a22ab7e9c1867ffd7157319142d3910be892d;hb=755b86d6cc3096224224086dee99f5b577aaa7d2;hp=ad5f52a78b2a147a1b8e9b0a07220b81db3d8be7;hpb=74aab3b256df66c0dc8785c349565c191d3ef0f8;p=jalview.git

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ad5f52a..ca8a22a 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -88,7 +91,6 @@ import java.util.regex.Pattern;
  */
 public class TCoffeeScoreFile extends AlignFile
 {
-
   public TCoffeeScoreFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
@@ -395,8 +397,9 @@ public class TCoffeeScoreFile extends AlignFile
     }
   }
 
-  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-  
+  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+          .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
   /**
    * Read a scores block ihe provided stream.
    * 
@@ -457,10 +460,11 @@ public class TCoffeeScoreFile extends AlignFile
       String val = line.substring(p + 1).trim();
 
       Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
-      if( m.matches() ) {
-    	  val = m.group(1);
+      if (m.matches())
+      {
+        val = m.group(1);
       }
-      
+
       result.items.put(id, val);
 
     } while ((line = reader.nextLine()) != null);
@@ -549,8 +553,11 @@ public class TCoffeeScoreFile extends AlignFile
   {
     if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
     {
-      String info = String.format("align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), al.getHeight(), getWidth(), getHeight() );
-      warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info;
+      String info = String.format(
+              "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+              al.getHeight(), getWidth(), getHeight());
+      warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+              + info;
       return false;
     }
     boolean added = false;