Merge branch 'develop' into Jalview-JS/develop

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index daa602d..8e67992 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,16 +21,20 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.image.BufferedImage;
 
-import javax.swing.JComponent;
+import javax.swing.JPanel;
 
-public class OverviewCanvas extends JComponent
+public class OverviewCanvas extends JPanel
 {
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
@@ -58,6 +62,8 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
   private ProgressPanel progressPanel;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
@@ -69,9 +75,15 @@ 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,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
     setSize(od.getWidth(), od.getHeight());
   }
 
@@ -121,7 +133,7 @@ public class OverviewCanvas extends JComponent
    *          the renderer to transfer feature colouring from
    */
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
-          FeatureRenderer transferRenderer)
+          FeatureRendererModel transferRenderer)
   {
     miniMe = null;
 
@@ -130,8 +142,13 @@ 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()));
 
@@ -141,11 +158,9 @@ public class OverviewCanvas extends JComponent
     {
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-              av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment()));
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
     or.removePropertyChangeListener(progressPanel);
     or = null;
@@ -167,6 +182,8 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
+    //super.paintComponent(g);
+
     if (restart)
     {
       if (lastMiniMe == null)
@@ -188,8 +205,11 @@ public class OverviewCanvas extends JComponent
               && ((getWidth() != od.getWidth())
                       || (getHeight() != od.getHeight())))
       {
-        // if there is annotation, scale the alignment and annotation separately
-        if (od.getGraphHeight() > 0)
+        // if there is annotation, scale the alignment and annotation
+        // separately
+        if (od.getGraphHeight() > 0 
+                       && od.getSequencesHeight() > 0  // BH 2019
+                       )
         {
           BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
                   od.getWidth(), od.getSequencesHeight());
@@ -219,28 +239,28 @@ public class OverviewCanvas extends JComponent
           od.setHeight(getHeight());
         }
 
-        // scale lastMiniMe to the new size
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-
         // make sure the box is in the right place
         od.setBoxPosition(av.getAlignment().getHiddenSequences(),
                 av.getAlignment().getHiddenColumns());
       }
-      else // not a resize
-      {
-        // fall back to normal behaviour
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-      }
+      // fall back to normal behaviour
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
     }
-
+    else
+    {
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+    }
+    
     // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
 
+
   public void dispose()
   {
     dispose = true;
+    od = null;
     synchronized (this)
     {
       restart = true;