Merge branch 'features/JAL-1605_html-svg-export' into develop

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index b6eeba3..92d5beb 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,26 +1,35 @@
 /*
- * 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.
- * 
+ * 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/>.
+ * 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.appletgui;
 
-import java.awt.*;
+import jalview.api.FeatureRenderer;
+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
 {
@@ -61,7 +70,7 @@ 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))
     {
@@ -72,17 +81,42 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return resBoxColour;
   }
 
+  /**
+   * Get the residue colour at the given sequence position - as determined by
+   * the sequence group colour (if any), else the colour scheme, possibly
+   * overridden by a feature colour.
+   * 
+   * @param seq
+   * @param position
+   * @param fr
+   * @return
+   */
+  @Override
+  public Color getResidueColour(final SequenceI seq, int position,
+          FeatureRenderer fr)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    Color col = getResidueBoxColour(seq, position);
+
+    if (fr != null)
+    {
+      col = fr.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
     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)))
@@ -98,24 +132,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   public Color findSequenceColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
     drawBoxes(seq, i, i, 0);
     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 +146,10 @@ 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);
     }
@@ -235,7 +257,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         {
           // cheat - use this if we have a consensus for each group: s =
           // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.consensus, i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
         }
       }
       else
@@ -257,9 +280,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             graphics.setColor(resBoxColour);
           }
         }
-        if (av.getShowunconserved())
+        if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.consensus, i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
 
         }
       }