JAL-2527 Updates following code review

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index e4c2056..ed1497a 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,7 +21,9 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.bin.Cache;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -31,7 +33,6 @@ import java.awt.image.BufferedImage;
 
 import javax.swing.JComponent;
 
-
 public class OverviewCanvas extends JComponent
 {
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
@@ -52,9 +53,13 @@ public class OverviewCanvas extends JComponent
 
   private jalview.renderer.seqfeatures.FeatureRenderer fr;
 
-  OverviewDimensions od;
+  private OverviewDimensions od;
+
+  private OverviewRenderer or = null;
+
+  private AlignViewportI av;
 
-  AlignViewportI av;
+  private OverviewResColourFinder cf;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
           AlignViewportI alignvp)
@@ -64,18 +69,30 @@ 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);
   }
 
+  /**
+   * Update the overview dimensions object used by the canvas (e.g. if we change
+   * from showing hidden columns to hiding them or vice versa)
+   * 
+   * @param overviewDims
+   */
   public void resetOviewDims(OverviewDimensions overviewDims)
   {
     od = overviewDims;
   }
 
-  /*
-   * Signals to drawing code that the associated alignment viewport
-   * has changed and a redraw will be required
+  /**
+   * Signals to drawing code that the associated alignment viewport has changed
+   * and a redraw will be required
    */
   public boolean restartDraw()
   {
@@ -84,6 +101,10 @@ public class OverviewCanvas extends JComponent
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -93,6 +114,16 @@ public class OverviewCanvas extends JComponent
     }
   }
 
+  /**
+   * Draw the overview sequences
+   * 
+   * @param showSequenceFeatures
+   *          true if sequence features are to be shown
+   * @param showAnnotation
+   *          true if the annotation is to be shown
+   * @param transferRenderer
+   *          the renderer to transfer feature colouring from
+   */
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
           FeatureRenderer transferRenderer)
   {
@@ -102,15 +133,13 @@ public class OverviewCanvas extends JComponent
     {
       fr.transferSettings(transferRenderer);
     }
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
-    // why do we need to set preferred size again? was set in
-    // updateOverviewImage
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    OverviewRenderer or = new OverviewRenderer(sr, finder, od);
-    miniMe = or.draw(od.getRows(av.getRanges(), av.getAlignment()),
-            od.getColumns(av.getRanges(), av.getColumnSelection()));
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+    miniMe = or.draw(od.getRows(av.getAlignment()),
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();
 
@@ -119,7 +148,7 @@ public class OverviewCanvas extends JComponent
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
               av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getRanges(), av.getColumnSelection()));
+              od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();