proxy commit for Anne Menard <menard.annec@gmail.com> throw generic exceptions (just...

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index b3aae51..e79c017 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -21,14 +21,6 @@ import java.io.*;
 
 import java.awt.event.*;
 import javax.swing.*;
-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.gui.*;
@@ -57,7 +49,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   String tmpPDBFile;
 
   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+          AlignmentPanel ap, String protocol) throws Exception
 
   {
     this.pdbentry = pdbentry;

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1b3aa8b..fb14a46 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,14 +22,6 @@ import java.util.*;
 
 import java.awt.*;
 
-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.analysis.AlignSeq;
 import jalview.datamodel.*;
@@ -47,12 +39,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(String inFile, String inType) throws Exception
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(FileParse source) throws Exception
   {
     super(source);
   }
@@ -62,7 +54,7 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public void parse() throws Exception
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6826266..e5bd3d6 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3732,10 +3732,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @throws InterruptedException\r
    * @throws ExceptionUnmatchedClosingParentheses\r
    */\r
-  public boolean loadScoreFile(String source) throws IOException,\r
-          ExceptionFileFormatOrSyntax, ParserConfigurationException,\r
-          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,\r
-          InterruptedException, ExceptionUnmatchedClosingParentheses\r
+  public boolean loadScoreFile(String source) throws Exception\r
   {\r
 \r
     TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 22c891d..ef7dad0 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -43,15 +43,9 @@ public class AssociatePdbFileWithSeq
  * assocate the given PDB file with 
  * @param choice
  * @param sequence
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws IOException 
  */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws Exception
   {
     PDBEntry entry = new PDBEntry();
     try

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3b43e6b..ef19521 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1984,7 +1984,7 @@ public class PopupMenu extends JPopupMenu
     oal = null;
   }
 
-  public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public void pdbFromFile_actionPerformed() throws IOException
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index cfd37b0..c0f8531 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -85,15 +85,9 @@ public abstract class AlignFile extends FileParse
    *          Filename to read from.
    * @param type
    *          What type of file to read from (File, URL)
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public AlignFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
     initData();
@@ -110,16 +104,9 @@ public abstract class AlignFile extends FileParse
    * off.
    * 
    * @param source
-   * @throws IOException
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public AlignFile(FileParse source) throws Exception
   {
     super(source);
     initData();
@@ -264,15 +251,9 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
- * @throws ExceptionFileFormatOrSyntax 
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+
    */
-  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
+  public abstract void parse() throws Exception;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index b5617c6..71c95b5 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -55,23 +55,14 @@ public class BLCFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public BLCFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public BLCFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public BLCFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public BLCFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d1225c4..c789139 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -39,12 +39,12 @@ public class ClustalFile extends AlignFile
   {
   }
 
-  public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public ClustalFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public ClustalFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index f413540..f809443 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -59,23 +59,14 @@ public class FastaFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public FastaFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FastaFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public FastaFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FastaFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index afbd223..c65bded 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -65,29 +65,14 @@ public class FeaturesFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
-   * @throws SAXException
-   * @throws ParserConfigurationException
-   * @throws ExceptionFileFormatOrSyntax
-   * @throws ExceptionLoadingFailed
-   * @throws ExceptionPermissionDenied
-   * @throws InterruptedException
-   * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception 
    */
-  public FeaturesFile(String inFile, String type) throws IOException,
-          ExceptionFileFormatOrSyntax, ParserConfigurationException,
-          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
-          InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FeaturesFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public FeaturesFile(FileParse source) throws IOException,
-          ExceptionFileFormatOrSyntax, ParserConfigurationException,
-          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
-          InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FeaturesFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 509758b..fc77ad6 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -72,23 +72,14 @@ public class JPredFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public JPredFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public JPredFile(FileParse source) throws Exception
   {
     super(source);
   }
@@ -363,15 +354,9 @@ public class JPredFile extends AlignFile
    * 
    * @param args
    *          DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public static void main(String[] args) throws Exception
   {
     try
     {

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index c3ee382..dcbe37d 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -55,23 +55,14 @@ public class MSFfile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public MSFfile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public MSFfile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index cdd0b98..d910b0f 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -41,12 +41,12 @@ public class PIRFile extends AlignFile
   {
   }
 
-  public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PIRFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PIRFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index af91390..30b5076 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -39,12 +39,12 @@ public class PfamFile extends AlignFile
   {
   }
 
-  public PfamFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PfamFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public PfamFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PfamFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 3fffab3..95fb203 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -63,23 +63,14 @@ public class PileUpfile extends MSFfile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
+ * @throws Exception 
    */
-  public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PileUpfile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PileUpfile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index 9256283..53d2790 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -54,12 +54,12 @@ public class SimpleBlastFile extends AlignFile
   {
   }
 
-  public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public SimpleBlastFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public SimpleBlastFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 07a5c80..86cb4ae 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -62,12 +62,12 @@ public class StockholmFile extends AlignFile
   {\r
   }\r
 \r
-  public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+  public StockholmFile(String inFile, String type) throws Exception \r
   {\r
     super(inFile, type);\r
   }\r
 \r
-  public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+  public StockholmFile(FileParse source) throws Exception \r
   {\r
     super(source);\r
   }\r
@@ -85,7 +85,7 @@ public class StockholmFile extends AlignFile
    *           If there is an error with the input file\r
  * @throws ExceptionUnmatchedClosingParentheses \r
    */\r
-  public void parse() throws IOException, ExceptionUnmatchedClosingParentheses\r
+  public void parse()\r
   {\r
          FileReader fr = null;\r
          fr = new FileReader(inFile); \r

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 56994ae..9776b56 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -97,13 +97,13 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  */
 public class TCoffeeScoreFile extends AlignFile {
        
-  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public TCoffeeScoreFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
 
   }
 
-  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public TCoffeeScoreFile(FileParse source) throws Exception
   {
     super(source);
   }

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index ce23728..78de7bf 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -42,7 +42,7 @@ public class TCoffeeScoreFileTest {
     final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
        
        @Test
-       public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testReadHeader() throws Exception {
 
            TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
            assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
@@ -64,7 +64,7 @@ public class TCoffeeScoreFileTest {
        
        
        @Test
-       public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testWrongFile() throws Exception {
            try {
                        TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
                        assertFalse(result.isValid());
@@ -76,7 +76,7 @@ public class TCoffeeScoreFileTest {
        } 
 
        @Test
-       public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testHeightAndWidth() throws Exception {
                TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
                assertTrue(result.isValid());
                assertEquals( 8, result.getHeight() );
@@ -116,7 +116,7 @@ public class TCoffeeScoreFileTest {
        }
 
        @Test
-       public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testParse() throws Exception {
 
                TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 
@@ -133,7 +133,7 @@ public class TCoffeeScoreFileTest {
 
        
        @Test
-       public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testGetAsList() throws Exception {
                
           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
           assertTrue(parser.getWarningMessage(),parser.isValid());
@@ -152,7 +152,7 @@ public class TCoffeeScoreFileTest {
        
        
        @Test
-       public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+       public void testGetAsArray() throws Exception {
                
           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
           assertTrue(parser.getWarningMessage(),parser.isValid());