Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 57070f2..04e34cd 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,11 +21,14 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.event.ActionEvent;
@@ -69,6 +72,9 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+
+  private OverviewResColourFinder cf;
+
   private float alpha = 0f;
 
   private long startTime = -1;
@@ -86,9 +92,15 @@ public class OverviewCanvas extends JComponent
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
 
+    boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+    Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+            Preferences.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            Preferences.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
     setSize(od.getWidth(), od.getHeight());
 
     timer = new Timer(SPEED, new ActionListener()
@@ -120,6 +132,7 @@ public class OverviewCanvas extends JComponent
         }
       }
     });
+
   }
 
   /**
@@ -178,8 +191,13 @@ public class OverviewCanvas extends JComponent
       fr.transferSettings(transferRenderer);
     }
 
-    or = new OverviewRenderer(sr, fr, od);
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+
     or.addPropertyChangeListener(progressPanel);
+
     miniMe = or.draw(od.getRows(av.getAlignment()),
             od.getColumns(av.getAlignment()));