X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=9023c4e8d2498bc9e67d26ef5c7b8ff27dfa7861;hb=910e92c4ec8b94b41d5b4c1e9b82438a4203207c;hp=f2eae2a110e45f590f1f68702e32248082cb8eea;hpb=8f050c10c0bd044493b7537b6c6d119c7c29c986;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index f2eae2a..9023c4e 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,26 +1,31 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-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.FontMetrics;
+import java.awt.Graphics;
 
 /**
  * DOCUMENT ME!
@@ -80,7 +85,7 @@ 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 +96,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -111,7 +116,7 @@ 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);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -125,25 +130,35 @@ 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 +210,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.globalColourScheme, seq, i);
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
 
       }
@@ -318,7 +333,8 @@ 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 +349,7 @@ 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 +365,7 @@ 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 +374,10 @@ 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,
+                    '.');
 
           }