JAL-1065 - Visualize T-Coffee quality scores for an alignment

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index b6eeba3..32ff59a 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,10 +17,15 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
 
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
@@ -82,7 +87,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -103,19 +108,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return resBoxColour;
   }
 
-  /**
-   * draw coloured sequence to the current graphics cursor
-   * @param seq
-   * @param sg
-   * @param start
-   * @param end
-   * @param y1
-   * @param drawBox - draw background
-   * @param drawText - draw text (if shading style permits)
-   */
-
   public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
-          int end, int y1, boolean drawBox, boolean drawText)
+          int end, int y1)
   {
     if (seq == null)
     {
@@ -123,11 +117,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
 
     allGroups = sg;
-    if (drawBox) {
-      drawBoxes(seq, start, end, y1);
-    }
 
-    if (av.validCharWidth && drawText)
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }