X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=c3ec9514f77a99b68700071947b5d6be16d236ca;hb=07394c1c2d9d4ae05c85cd6d9644e4d17f2818a2;hp=7e5f0c317d4a47774261377dba15b8eff0e87022;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 7e5f0c3..c3ec951 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -89,10 +89,12 @@ import java.util.regex.Pattern;
  * @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, DataSourceType fileSourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, fileSourceType);
 
   }
 
@@ -212,6 +214,7 @@ public class TCoffeeScoreFile extends AlignFile {
     return result;
   }
 
+  @Override
   public void parse() throws IOException
   {
     /*
@@ -396,8 +399,9 @@ public class TCoffeeScoreFile extends AlignFile {
     }
   }
 
-  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-  
+  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+          .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
   /**
    * Read a scores block ihe provided stream.
    * 
@@ -458,10 +462,11 @@ public class TCoffeeScoreFile extends AlignFile {
       String val = line.substring(p + 1).trim();
 
       Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
-      if( m.matches() ) {
-    	  val = m.group(1);
+      if (m.matches())
+      {
+        val = m.group(1);
       }
-      
+
       result.items.put(id, val);
 
     } while ((line = reader.nextLine()) != null);
@@ -522,8 +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
@@ -550,8 +554,11 @@ public class TCoffeeScoreFile extends AlignFile {
   {
     if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
     {
-      String info = String.format("align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), al.getHeight(), getWidth(), getHeight() );
-      warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info;
+      String info = String.format(
+              "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+              al.getHeight(), getWidth(), getHeight());
+      warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+              + info;
       return false;
     }
     boolean added = false;
@@ -638,7 +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.";