Merge branch 'develop' into menard

diff --cc src/jalview/io/TCoffeeScoreFile.java
index 178caad,ad5f52a..56994ae
--- 1/src/jalview/io/TCoffeeScoreFile.java
--- 2/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@@ -30,16 -30,9 +30,18 @@@ import java.util.HashMap
  import java.util.LinkedHashMap;
  import java.util.List;
  import java.util.Map;
+ import java.util.regex.Matcher;
+ import java.util.regex.Pattern;
  
 +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.

diff --cc test/jalview/io/TCoffeeScoreFileTest.java
index 2c09148,3147054..1ee4936
--- 1/test/jalview/io/TCoffeeScoreFileTest.java
--- 2/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@@ -21,35 -21,25 +21,33 @@@ import static org.junit.Assert.*
  import jalview.io.TCoffeeScoreFile.Block;
  import jalview.io.TCoffeeScoreFile.Header;
  
- import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileNotFoundException;
- import java.io.FileReader;
  import java.io.IOException;
- import java.io.StringReader;
  import java.util.List;
  
 +import javax.xml.parsers.ParserConfigurationException;
 +
  import org.junit.Test;
 +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;
  
  public class TCoffeeScoreFileTest {
  
        final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
-         final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
+     final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
        
        @Test
 -      public void testReadHeader() throws IOException, FileNotFoundException {
 +      public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
  
-               TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
-               assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
-               Header header = scoreFile.header;
+           TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
+           assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
+               
+           Header header = scoreFile.header;
                assertNotNull(header);
                assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
                assertEquals( 90, header.score );
@@@ -66,11 -56,12 +64,12 @@@
        
        
        @Test
 -      public void testWrongFile() {
 +      public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
            try {
-               TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
-               assertFalse(result.isValid());
-           } catch (IOException x)
+                       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
+                       assertFalse(result.isValid());
+           } 
+           catch (IOException x)
            {
              assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
            }