Merge branch 'JAL-1199-Stk_writing' into rnaml_test

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 444d0e0..abdfed0 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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
  * 
  * 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 
@@ -25,15 +25,6 @@ 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.*;
 
 /**
@@ -75,20 +66,13 @@ 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);
   }
@@ -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
     {