Merge branch 'develop' into menard

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 1455c63..178caad 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -24,18 +24,22 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
+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;
+
 /**
  * A file parse for T-Coffee score ascii format. This file contains the
  * alignment consensus for each resude in any sequence.
@@ -89,16 +93,15 @@ import java.util.Map;
  * @author Paolo Di Tommaso
  * 
  */
-public class TCoffeeScoreFile extends AlignFile
-{
-
-  public TCoffeeScoreFile(String inFile, String type) throws IOException
+public class TCoffeeScoreFile extends AlignFile {
+       
+  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
 
   }
 
-  public TCoffeeScoreFile(FileParse source) throws IOException
+  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }