Add support RNAML format

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 59a010d..a26ec61 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -25,6 +25,14 @@ 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 jalview.datamodel.*;
 
 /**
@@ -66,13 +74,18 @@ public class JPredFile extends AlignFile
    * 
    * @throws IOException
    *           DOCUMENT ME!
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
    */
-  public JPredFile(String inFile, String type) throws IOException
+  public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(inFile, type);
   }
 
-  public JPredFile(FileParse source) throws IOException
+  public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(source);
   }
@@ -347,8 +360,13 @@ public class JPredFile extends AlignFile
    * 
    * @param args
    *          DOCUMENT ME!
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
    */
-  public static void main(String[] args)
+  public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     try
     {