X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewResColourFinder.java;h=8206b32e30ee94962236b51e8b2fdc43a41bf2b3;hb=f300e30df117ff4be7d1df5c781161efd0285e5f;hp=ec638a7a0ac11ac2dc6bcc7df8aad13078f3616c;hpb=d735b6b655d0689760abf7e5063c36200310a544;p=jalview.git

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index ec638a7..8206b32 100644
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -28,58 +28,99 @@ import java.awt.Color;
 
 public class OverviewResColourFinder extends ResidueColourFinder
 {
-  final Color GAP_COLOUR = new Color(240, 240, 240);
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
 
-  @Override
-  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+          .darker();
+
+  final Color gapColour; // colour to use for gaps
+
+  final int gapColourInt; // RGB value of gapColour
+
+  final Color residueColour; // colour to use for uncoloured residues
+
+  final Color hiddenColour; // colour for hidden regions
+
+  boolean useLegacy = false;
+
+  /**
+   * Constructor without colour settings (used by applet)
+   */
+  public OverviewResColourFinder()
   {
-    Color resBoxColour = Color.white;
-    char currentChar = seq.getCharAt(i);
+    this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+  }
 
-    // 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)
+  /**
+   * 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)
     {
-      if (Comparison.isGap(currentChar)
-              && !shader.getColourScheme().hasGapColour())
-      {
-        resBoxColour = GAP_COLOUR;
-      }
-      else
-      {
-        resBoxColour = shader.findColour(currentChar, i, seq);
-      }
+      gapColour = Color.white;
+      residueColour = Color.lightGray;
     }
-    else if (Comparison.isGap(currentChar))
+    else
     {
-      resBoxColour = GAP_COLOUR;
+      gapColour = gapCol;
+      residueColour = Color.WHITE;
     }
+    gapColourInt = gapColour.getRGB();
+    hiddenColour = hiddenCol;
+  }
 
-    return resBoxColour;
+  /**
+   * Overrides the method to return the currently configured Overview colours
+   * for gaps, or residues with no colour scheme set. A custom colour scheme
+   * which specifies a colour for gaps overrides the normal gap colour.
+   */
+  @Override
+  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  {
+    char currentChar = seq.getCharAt(i);
+    boolean isGap = Comparison.isGap(currentChar);
+    if (shader.getColourScheme() == null)
+    {
+      return (isGap ? gapColour : residueColour);
+    }
+    return (isGap && !shader.getColourScheme().hasGapColour() ? gapColour
+            : shader.findColour(currentChar, i, seq));
   }
 
   /**
-   * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
-   * overview displays the colours regardless.
+   * 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 shader, SequenceGroup[] allGroups, SequenceI seq,
+          int i)
   {
-    ResidueShaderI currentShader;
     SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
             i);
-    if (currentSequenceGroup != null)
-    {
-      currentShader = currentSequenceGroup.getGroupColourScheme();
-    }
-    else
-    {
-      currentShader = shader;
-    }
-
+    ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
+            : currentSequenceGroup.getGroupColourScheme());
     return getBoxColour(currentShader, seq, i);
   }
+
+  /**
+   * Returns the coloured configured for hidden regions in the Overview
+   * 
+   * @return
+   */
+  protected Color getHiddenColour()
+  {
+    return hiddenColour;
+  }
 }