JAL-1620 version bump and release notes

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 121204c..abd44c0 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * 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.
+ * 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.
  */
 /**
@@ -27,6 +29,7 @@ import java.io.*;
 import java.util.*;
 
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
@@ -291,9 +294,7 @@ public class JPredFile extends AlignFile
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
-        throw new IOException("JPredConcise: Entry ("
-                + ids.elementAt(i).toString()
-                + ") has an unexpected number of columns");
+        throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()}));
       }
 
       if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
@@ -317,9 +318,7 @@ public class JPredFile extends AlignFile
       } catch (Exception e)
       {
         tal = null;
-        IOException ex = new IOException(
-                "Couldn't parse concise annotation for prediction profile.\n"
-                        + e);
+        IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()}));
         e.printStackTrace(); // java 1.1 does not have :
                              // ex.setStackTrace(e.getStackTrace());
         throw ex;
@@ -349,7 +348,7 @@ public class JPredFile extends AlignFile
    * @param args
    *          DOCUMENT ME!
    */
-  public static void main(String[] args) 
+  public static void main(String[] args)
   {
     try
     {