JAL-2527 Wired up cached values to overview

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index 718c15b..9597b44 100644 (file)
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -112,7 +113,7 @@ public class OverviewCanvas extends Component
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
     or = new OverviewRenderer(fr, od, av.getAlignment(),
-            av.getResidueShading());
+            av.getResidueShading(), new OverviewResColourFinder());
     miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
     offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
 

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 987d6c1..3ea5e9b 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.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -65,7 +67,6 @@ public class OverviewCanvas extends JComponent
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    // sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
   }
 
@@ -126,8 +127,13 @@ public class OverviewCanvas extends JComponent
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
+    boolean useLegacy = Cache.getDefault("USE_LEGACY_GAP", false);
+    Color gapCol = Cache.getDefaultColour("GAP_COLOUR", new Color(240, 240, 240));
+    Color hiddenCol = Cache.getDefaultColour("HIDDEN_COLOUR", Color.DARK_GRAY.darker());
+    OverviewResColourFinder cf = new OverviewResColourFinder(useLegacy,
+            gapCol, hiddenCol);
     or = new OverviewRenderer(fr, od, av.getAlignment(),
-            av.getResidueShading());
+            av.getResidueShading(), cf);
     miniMe = or.draw(od.getRows(av.getAlignment()),
             od.getColumns(av.getAlignment()));
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 28de801..d66bbf0 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.OverviewDimensions;
@@ -79,9 +80,19 @@ public class OverviewPanel extends JPanel
     this.av = alPanel.av;
     this.ap = alPanel;
 
-    od = new OverviewDimensionsShowHidden(av.getRanges(),
+    showHidden = Cache.getDefault("SHOW_OV_HIDDEN_AT_START", true);
+    if (showHidden)
+    {
+      od = new OverviewDimensionsShowHidden(av.getRanges(),
             (av.isShowAnnotation()
                     && av.getAlignmentConservationAnnotation() != null));
+    }
+    else
+    {
+      od = new OverviewDimensionsHideHidden(av.getRanges(),
+              (av.isShowAnnotation()
+                      && av.getAlignmentConservationAnnotation() != null));
+    }
 
     setSize(od.getWidth(), od.getHeight());
 
@@ -158,7 +169,6 @@ public class OverviewPanel extends JPanel
           }
         }
         else
-        // if (!av.getWrapAlignment())
         {
           if (!od.isPositionInBox(evt.getX(), evt.getY()))
           {

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 56dba82..992a1b2 100644 (file)
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -42,6 +42,8 @@ public class OverviewRenderer
   // transparency of hidden cols/seqs overlay
   private final float TRANSPARENCY = 0.5f;
 
+  private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+
   private FeatureColourFinder finder;
 
   // image to render on
@@ -61,14 +63,14 @@ public class OverviewRenderer
 
   private ResidueShaderI shader;
 
-  private ResidueColourFinder resColFinder;
+  private OverviewResColourFinder resColFinder;
 
   public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
           AlignmentI alignment,
-          ResidueShaderI resshader)
+          ResidueShaderI resshader, OverviewResColourFinder colFinder)
   {
     finder = new FeatureColourFinder(fr);
-    resColFinder = new OverviewResColourFinder();
+    resColFinder = colFinder;
 
     al = alignment;
     shader = resshader;
@@ -228,7 +230,7 @@ public class OverviewRenderer
     int colIndex = 0;
     int pixelCol = 0;
 
-    Color hidden = Color.DARK_GRAY.darker();
+    Color hidden = resColFinder.getHiddenColour();
 
     Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
 

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index c591f54..b28aa27 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -28,12 +28,42 @@ import java.awt.Color;
 
 public class OverviewResColourFinder extends ResidueColourFinder
 {
-  final Color GAP_COLOUR = new Color(240, 240, 240);
+  final Color GAP_COLOUR;
+
+  final Color RESIDUE_COLOUR;
+
+  final Color HIDDEN_COLOUR;
+
+  boolean useLegacy = false;
+
+  public OverviewResColourFinder()
+  {
+    GAP_COLOUR = new Color(240, 240, 240);
+    RESIDUE_COLOUR = Color.white;
+    HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+  }
+
+  public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
+          Color hiddenCol)
+  {
+    if (useLegacyColouring)
+    {
+      GAP_COLOUR = Color.white;
+      RESIDUE_COLOUR = new Color(240, 240, 240);
+      HIDDEN_COLOUR = hiddenCol;
+    }
+    else
+    {
+      GAP_COLOUR = gapCol;
+      RESIDUE_COLOUR = Color.white;
+      HIDDEN_COLOUR = hiddenCol;
+    }
+  }
 
   @Override
   public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    Color resBoxColour = Color.white;
+    Color resBoxColour = RESIDUE_COLOUR;
     char currentChar = seq.getCharAt(i);
 
     // In the overview window, gaps are coloured grey, unless the colour scheme
@@ -82,4 +112,9 @@ public class OverviewResColourFinder extends ResidueColourFinder
 
     return getBoxColour(currentShader, seq, i);
   }
+
+  protected Color getHiddenColour()
+  {
+    return HIDDEN_COLOUR;
+  }
 }