Merge branch 'develop' of https://source.jalview.org/git/jalview.git into menard

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 1531301..45bfd43 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -82,13 +82,13 @@ import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  */
 public class TCoffeeScoreFile extends AlignFile {
        
-  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     super(inFile, type);
     
   }
 
-  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     super(source);
   }
@@ -490,7 +490,7 @@ public class TCoffeeScoreFile extends AlignFile {
              }
            }
            // this will overwrite any existing t-coffee scores for the alignment
-           AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,false,s,null);
+           AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,TCOFFEE_SCORE,false,s, null);
            if (s!=null)
            {
              aa.label="T-COFFEE";