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 509758b..abd44c0 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.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 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.
  */
 /**
  * PredFile.java
@@ -25,16 +28,8 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
@@ -75,20 +70,13 @@ public class JPredFile extends AlignFile
    * 
    * @throws IOException
    *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public JPredFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public JPredFile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -306,9 +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()
@@ -332,9 +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;
@@ -363,15 +347,8 @@ public class JPredFile extends AlignFile
    * 
    * @param args
    *          DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public static void main(String[] args)
   {
     try
     {