last version stay many bugs ..

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 86696d7..837fee0 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -34,6 +34,7 @@ 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;
 
 /**
  * DOCUMENT ME!
@@ -90,8 +91,9 @@ public abstract class AlignFile extends FileParse
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
  * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
     initData();
@@ -114,8 +116,9 @@ public abstract class AlignFile extends FileParse
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
  * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
     initData();
@@ -265,8 +268,9 @@ public abstract class AlignFile extends FileParse
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
  * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException;
+  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.