JAL-1447 patch to correctly recognise FASTA files containing '*'

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 28f777f..155e236 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 /**
  * PredFile.java
@@ -207,8 +208,8 @@ public class JPredFile extends AlignFile
 
           for (int j = 0; j < i; j++)
           {
-            scores.setElementAt((Object) ((Float) scores.elementAt(j))
-                    .toString(), j);
+            scores.setElementAt(
+                    (Object) ((Float) scores.elementAt(j)).toString(), j);
           }
 
           scores.addElement((Object) ascore);
@@ -296,8 +297,7 @@ public class JPredFile extends AlignFile
       }
 
       if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
-              .startsWith("align;"))
-              && (QuerySeqPosition == -1))
+              .startsWith("align;")) && (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
       }