Merge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1

[jalview.git] / src / jalview / renderer / OverviewResColourFinder.java

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 8fa0e23..b606ba3 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -22,27 +22,40 @@ package jalview.renderer;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
 import java.awt.Color;
 
 public class OverviewResColourFinder extends ResidueColourFinder
 {
-  final Color GAP_COLOUR;
+  final Color GAP_COLOUR; // default colour to use at gaps
 
-  final Color RESIDUE_COLOUR;
+  final Color RESIDUE_COLOUR; // default colour to use at residues
 
-  final Color HIDDEN_COLOUR;
+  final Color HIDDEN_COLOUR; // colour for hidden regions
 
   boolean useLegacy = false;
 
+  /**
+   * Constructor without colour settings (used by applet)
+   */
   public OverviewResColourFinder()
   {
-    GAP_COLOUR = Color.lightGray; // new Color(240, 240, 240);
-    RESIDUE_COLOUR = Color.white;
-    HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+    this(false, Preferences.OVERVIEW_DEFAULT_GAP,
+            Preferences.OVERVIEW_DEFAULT_HIDDEN);
   }
 
+  /**
+   * Constructor with colour settings
+   * 
+   * @param useLegacyColouring
+   *          whether to use legacy gap colouring (white gaps, grey residues)
+   * @param gapCol
+   *          gap colour if not legacy
+   * @param hiddenCol
+   *          hidden region colour (transparency applied by rendering code)
+   */
   public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
           Color hiddenCol)
   {
@@ -71,8 +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;
       }
@@ -113,6 +126,11 @@ public class OverviewResColourFinder extends ResidueColourFinder
     return getBoxColour(currentShader, seq, i);
   }
 
+  /**
+   * Supply hidden colour
+   * 
+   * @return colour of hidden regions
+   */
   protected Color getHiddenColour()
   {
     return HIDDEN_COLOUR;