(JAL-893) update to VARNAv3.9-dev version

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index f2eae2a..ad704c3 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -80,7 +80,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
     {
@@ -91,7 +91,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -125,25 +125,35 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   }
 
   /**
-   * draw coloured sequence to the current graphics cursor
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *          DOCUMENT ME!
    * @param seq
+   *          DOCUMENT ME!
    * @param sg
+   *          DOCUMENT ME!
    * @param start
+   *          DOCUMENT ME!
    * @param end
+   *          DOCUMENT ME!
+   * @param x1
+   *          DOCUMENT ME!
    * @param y1
-   * @param drawBox - draw background
-   * @param drawText - draw text (if shading style permits)
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
    */
   public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
-          int end, int y1, boolean drawBox, boolean drawText)
+          int end, int y1)
   {
     allGroups = sg;
 
-    if (drawBox) {
-      drawBoxes(seq, start, end, y1);
-    }
+    drawBoxes(seq, start, end, y1);
 
-    if (av.validCharWidth && drawText)
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }
@@ -195,7 +205,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.globalColourScheme, seq, i);
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
 
       }
@@ -318,7 +328,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
 
           }
 
@@ -333,7 +343,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.globalColourScheme, seq, i);
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -349,7 +359,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.globalColourScheme, seq, i);
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -358,9 +368,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
               graphics.setColor(av.textColour2);
             }
           }
-          if (av.showUnconserved)
+          if (av.getShowUnconserved())
           {
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
 
           }