JAL-2527 Code comments, tidy

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 8bea818..5f6a1f6 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,8 +21,9 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -54,8 +55,12 @@ public class OverviewCanvas extends JComponent
 
   private OverviewDimensions od;
 
+  private OverviewRenderer or = null;
+
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
   public OverviewCanvas(OverviewDimensions overviewDims,
           AlignViewportI alignvp)
   {
@@ -64,8 +69,13 @@ 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("USE_LEGACY_GAP", false);
+    Color gapCol = Cache.getDefaultColour("GAP_COLOUR", Color.lightGray);
+    Color hiddenCol = Cache.getDefaultColour("HIDDEN_COLOUR",
+            Color.DARK_GRAY.darker());
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
   }
 
   /**
@@ -90,6 +100,10 @@ public class OverviewCanvas extends JComponent
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -118,13 +132,13 @@ public class OverviewCanvas extends JComponent
     {
       fr.transferSettings(transferRenderer);
     }
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    OverviewRenderer or = new OverviewRenderer(sr, finder, od);
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
     miniMe = or.draw(od.getRows(av.getAlignment()),
-            od.getColumns(av.getAlignment().getHiddenColumns()));
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();
 
@@ -133,7 +147,7 @@ public class OverviewCanvas extends JComponent
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
               av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment().getHiddenColumns()));
+              od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();