fileFormat enum wip changes

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index fce7fc5..c3ec951 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -91,9 +91,10 @@ import java.util.regex.Pattern;
  */
 public class TCoffeeScoreFile extends AlignFile
 {
-  public TCoffeeScoreFile(String inFile, String type) throws IOException
+  public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, fileSourceType);
 
   }
 
@@ -213,6 +214,7 @@ public class TCoffeeScoreFile extends AlignFile
     return result;
   }
 
+  @Override
   public void parse() throws IOException
   {
     /*
@@ -525,8 +527,7 @@ public class TCoffeeScoreFile extends AlignFile
   /**
    * TCOFFEE score colourscheme
    */
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
@@ -644,7 +645,7 @@ public class TCoffeeScoreFile extends AlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     // TODO Auto-generated method stub
     return "Not valid.";