X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=691aa7e94ead35414afc54b23583a443da24c8b2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=44e4dddb3abac00673844b0ccd154241452c324a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 44e4ddd..691aa7e 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 2.8.2)
+ * 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)))
@@ -205,7 +210,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.globalColourScheme, seq, i);
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
 
       }
@@ -328,7 +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,
+                    '.');
 
           }
 
@@ -343,7 +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())
             {
@@ -359,7 +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()
@@ -368,9 +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,
+                    '.');
 
           }
 
@@ -466,10 +473,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics
-                .drawString(String.valueOf(s), charOffset + x1
-                        + (av.charWidth * (i - start)),
-                        (y1 + av.charHeight) - pady);
+        graphics.drawString(String.valueOf(s), charOffset + x1
+                + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
       }
     }
   }