X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewCanvas.java;h=586ac2c883f19a3b40d733ee1a6bdc5878121a49;hb=7ef5bcab5bca73d8a5ba1dd8db67fcf7888a6d46;hp=ec2c49fa3548a6924c090b711fe1bf29ba1c4b4d;hpb=348fe2d15827689d155df9345e4f10753cab6ac9;p=jalview.git

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index ec2c49f..586ac2c 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -20,12 +20,6 @@
  */
 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.Color;
 import java.awt.Dimension;
 import java.awt.Graphics;
@@ -33,8 +27,26 @@ import java.awt.image.BufferedImage;
 
 import javax.swing.JPanel;
 
+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;
+
 public class OverviewCanvas extends JPanel
 {
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+          .darker();
+
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
   // This is set true if the alignment view changes whilst
@@ -78,10 +90,12 @@ public class OverviewCanvas extends JPanel
 
     boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
     Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+            OVERVIEW_DEFAULT_GAP);
     Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
-    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+            OVERVIEW_DEFAULT_HIDDEN);
+    Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE;
+    
+    cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
 
     setSize(od.getWidth(), od.getHeight());
   }
@@ -132,7 +146,7 @@ public class OverviewCanvas extends JPanel
    *          the renderer to transfer feature colouring from
    */
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
-          FeatureRenderer transferRenderer)
+          FeatureRendererModel transferRenderer)
   {
     miniMe = null;
 
@@ -181,7 +195,7 @@ public class OverviewCanvas extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);
+    // super.paintComponent(g);
 
     if (restart)
     {
@@ -206,7 +220,8 @@ public class OverviewCanvas extends JPanel
       {
         // if there is annotation, scale the alignment and annotation
         // separately
-        if (od.getGraphHeight() > 0)
+        if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019
+        )
         {
           BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
                   od.getWidth(), od.getSequencesHeight());
@@ -247,16 +262,16 @@ public class OverviewCanvas extends JPanel
     {
       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;
@@ -266,4 +281,31 @@ public class OverviewCanvas extends JPanel
       }
     }
   }
+
+  public Color getGapColour()
+  {
+    return cf.getGapColour();
+  }
+
+  public Color getHiddenColour()
+  {
+    return cf.getHiddenColour();
+  }
+
+  public Color getResidueColour()
+  {
+    return cf.getResidueColour();
+  }
+
+  /**
+   * Sets the colours to use for gaps, residues and hidden regions
+   * 
+   * @param gaps
+   * @param residues
+   * @param hidden
+   */
+  public void setColours(Color gaps, Color residues, Color hidden)
+  {
+    cf = new OverviewResColourFinder(gaps, residues, hidden);
+  }
 }