JAL-2527 Updates following code review

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 5f6a1f6..ed1497a 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -71,10 +71,11 @@ public class OverviewCanvas extends JComponent
     sr.renderGaps = false;
     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());
+    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);
   }
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d66bbf0..3c94f26 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -80,7 +80,8 @@ public class OverviewPanel extends JPanel
     this.av = alPanel.av;
     this.ap = alPanel;
 
-    showHidden = Cache.getDefault("SHOW_OV_HIDDEN_AT_START", true);
+    showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+            true);
     if (showHidden)
     {
       od = new OverviewDimensionsShowHidden(av.getRanges(),

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 3c0faab..7ceb04e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -113,15 +113,19 @@ public class Preferences extends GPreferences
 
   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 
+  public static final String GAP_COLOUR = "GAP_COLOUR";
+
+  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
   private static final int MIN_FONT_SIZE = 1;
 
   private static final int MAX_FONT_SIZE = 30;
 
-  private static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
 
-  private static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
 
-  private static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
           .darker();
 
   /**
@@ -323,15 +327,15 @@ public class Preferences extends GPreferences
      * Set overview panel defaults
      */
     gapColour.setBackground(
-            Cache.getDefaultColour("GAP_COLOUR", OVERVIEW_DEFAULT_GAP));
+            Cache.getDefaultColour(GAP_COLOUR, OVERVIEW_DEFAULT_GAP));
     hiddenColour.setBackground(
-            Cache.getDefaultColour("HIDDEN_COLOUR",
+            Cache.getDefaultColour(HIDDEN_COLOUR,
                     OVERVIEW_DEFAULT_HIDDEN));
-    useLegacyGap.setSelected(Cache.getDefault("USE_LEGACY_GAP", false));
+    useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
     showHiddenAtStart
-            .setSelected(Cache.getDefault("SHOW_OV_HIDDEN_AT_START", true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 
     /*
      * Set Structure tab defaults.
@@ -658,8 +662,8 @@ public class Preferences extends GPreferences
     /*
      * Save Overview settings
      */
-    Cache.setColourProperty("GAP_COLOUR", gapColour.getBackground());
-    Cache.setColourProperty("HIDDEN_COLOUR", hiddenColour.getBackground());
+    Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+    Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
             Boolean.toString(useLegacyGap.isSelected()));
     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index fa45769..dfd2c2d 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -183,8 +183,6 @@ public class GPreferences extends JPanel
   /*
    * Overview tab components
    */
-  protected JPanel overviewTab;
-
   protected JPanel gapColour = new JPanel();
 
   protected JPanel hiddenColour = new JPanel();
@@ -195,8 +193,6 @@ public class GPreferences extends JPanel
 
   protected JLabel gapLabel;
 
-  protected JButton resetButton;
-
   /*
    * Connections tab components
    */
@@ -1093,7 +1089,7 @@ public class GPreferences extends JPanel
     c6.insets = new Insets(0, 0, 0, 15);
     overviewPanel.add(hiddenColour, c6);
 
-    resetButton = new JButton(
+    JButton resetButton = new JButton(
             MessageManager.getString("label.reset_to_defaults"));
 
     resetButton.addActionListener(new ActionListener()

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 07fc6e3..b606ba3 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
 import java.awt.Color;
@@ -41,9 +42,8 @@ public class OverviewResColourFinder extends ResidueColourFinder
    */
   public OverviewResColourFinder()
   {
-    GAP_COLOUR = Color.lightGray;
-    RESIDUE_COLOUR = Color.white;
-    HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+    this(false, Preferences.OVERVIEW_DEFAULT_GAP,
+            Preferences.OVERVIEW_DEFAULT_HIDDEN);
   }
 
   /**
@@ -84,8 +84,8 @@ public class OverviewResColourFinder extends ResidueColourFinder
     // settings
     if (shader.getColourScheme() != null)
     {
-      if (!shader.getColourScheme().hasGapColour()
-              && Comparison.isGap(currentChar))
+      if (Comparison.isGap(currentChar)
+              && (!shader.getColourScheme().hasGapColour()))
       {
         resBoxColour = GAP_COLOUR;
       }