X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewResColourFinder.java;h=a497d92d00d722af17995ec4eea7eb2853818b75;hb=9109818e704dd0945567b234af8f3d34ba4b2b67;hp=793d349dbc1771dbf7910cc0a185161a68e3f776;hpb=fb548a8458941602b0b8b45da5aaf60206e10ec2;p=jalview.git

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 793d349..a497d92 100644
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -20,6 +20,7 @@
  */
 package jalview.renderer;
 
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
@@ -27,18 +28,71 @@ import java.awt.Color;
 
 public class OverviewResColourFinder extends ResidueColourFinder
 {
+  final Color GAP_COLOUR; // default colour to use at gaps
+
+  final Color RESIDUE_COLOUR; // default colour to use at residues
+
+  final Color HIDDEN_COLOUR; // colour for hidden regions
+
+  boolean useLegacy = false;
+
+  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_HIDDEN = Color.darkGray
+          .darker();
+
+  /**
+   * Constructor without colour settings (used by applet)
+   */
+  public OverviewResColourFinder()
+  {
+    this(false, OVERVIEW_DEFAULT_GAP, 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)
+  {
+    if (useLegacyColouring)
+    {
+      GAP_COLOUR = Color.white;
+      RESIDUE_COLOUR = Color.lightGray;
+      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
+    // specifies a gap colour, in which case gaps honour the colour scheme
+    // settings
     if (shader.getColourScheme() != null)
     {
       if (Comparison.isGap(currentChar)
-              && !shader.getColourScheme().hasGapColour())
+              && (!shader.getColourScheme().hasGapColour()))
       {
-        resBoxColour = Color.lightGray;
+        resBoxColour = GAP_COLOUR;
       }
       else
       {
@@ -47,9 +101,43 @@ public class OverviewResColourFinder extends ResidueColourFinder
     }
     else if (Comparison.isGap(currentChar))
     {
-      resBoxColour = Color.lightGray;
+      resBoxColour = GAP_COLOUR;
     }
 
     return resBoxColour;
   }
+
+  /**
+   * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
+   * overview displays the colours regardless.
+   */
+  @Override
+  protected Color getResidueBoxColour(boolean showBoxes,
+          ResidueShaderI shader,
+          SequenceGroup[] allGroups, SequenceI seq, int i)
+  {
+    ResidueShaderI currentShader;
+    SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+            i);
+    if (currentSequenceGroup != null)
+    {
+      currentShader = currentSequenceGroup.getGroupColourScheme();
+    }
+    else
+    {
+      currentShader = shader;
+    }
+
+    return getBoxColour(currentShader, seq, i);
+  }
+
+  /**
+   * Supply hidden colour
+   * 
+   * @return colour of hidden regions
+   */
+  protected Color getHiddenColour()
+  {
+    return HIDDEN_COLOUR;
+  }
 }