JAL-3383 removing colour caching (to a separate branch)

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

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index ff52f1d..7207dea 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -22,20 +22,13 @@ package jalview.renderer;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.util.Comparison;
 
 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;
@@ -43,6 +36,18 @@ public class OverviewResColourFinder extends ResidueColourFinder
   public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
           .darker();
 
+  final Color gapColour; // colour to use for gaps
+
+  final int gapColourInt;
+
+  final Color residueColour; // colour to use for uncoloured residues
+
+  final int residueColourInt;
+
+  final Color hiddenColour; // colour for hidden regions
+
+  boolean useLegacy = false;
+
   /**
    * Constructor without colour settings (used by applet)
    */
@@ -66,27 +71,27 @@ public class OverviewResColourFinder extends ResidueColourFinder
   {
     if (useLegacyColouring)
     {
-      GAP_COLOUR = Color.white;
-      RESIDUE_COLOUR = Color.lightGray;
-      HIDDEN_COLOUR = hiddenCol;
+      gapColour = Color.white;
+      residueColour = Color.lightGray;
     }
     else
     {
-      GAP_COLOUR = gapCol;
-      RESIDUE_COLOUR = Color.white;
-      HIDDEN_COLOUR = hiddenCol;
+      gapColour = gapCol;
+      residueColour = Color.WHITE;
     }
+    gapColourInt = gapColour.getRGB();
+    residueColourInt = residueColour.getRGB();
+    hiddenColour = hiddenCol;
   }
 
   @Override
   public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    seq.resetColors();
-    Color c = seq.getColor(i);
-    if (c != null)
-    {
-      return c;
-    }
+    return new Color(getBoxColourInt(shader, seq, i));
+  }
+
+  public int getBoxColourInt(ResidueShaderI shader, SequenceI seq, int i)
+  {
     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
@@ -94,27 +99,62 @@ public class OverviewResColourFinder extends ResidueColourFinder
     boolean isGap = Comparison.isGap(currentChar);
     if (shader.getColourScheme() == null)
     {
-      return seq.setColor(i, isGap ? GAP_COLOUR : RESIDUE_COLOUR);
+      return (isGap ? gapColourInt : residueColourInt);
     }
-    return seq.setColor(i,
-            isGap && !shader.getColourScheme().hasGapColour() ? GAP_COLOUR
-                    : shader.findColour(currentChar, i, seq));
+    return (isGap && !shader.getColourScheme().hasGapColour() ? gapColourInt
+            : shader.findColourInt(currentChar, i, seq));
+  }
+
+  @Override
+  public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
+          SequenceGroup[] allGroups, final SequenceI seq, int i,
+          FeatureColourFinder finder)
+  {
+    Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq, i);
+
+    // if there's a FeatureColourFinder we might override the residue colour
+    // here with feature colouring
+    col = finder == null || finder.noFeaturesDisplayed() ? col
+            : finder.findFeatureColour(col, seq, i);
+    return col;
+  }
+
+
+  public int getResidueColourInt(boolean showBoxes, ResidueShaderI shader,
+          SequenceGroup[] allGroups, final SequenceI seq, int i,
+          FeatureColourFinder finder)
+  {
+    int col = getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i);
+
+    // if there's a FeatureColourFinder we might override the residue colour
+    // here with feature colouring
+    col = finder == null || finder.noFeaturesDisplayed() ? col
+            : finder.findFeatureColourInt(col, seq, i);
+    return col;
   }
 
-  /**
-   * {@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)
   {
+    return new Color(
+            getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i));
+  }
+
+  /**
+   * In the overview, the showBoxes setting is ignored, as the overview displays
+   * the colours regardless.
+   */
+  protected int getResidueBoxColourInt(boolean showBoxes,
+          ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+          int i)
+  {
     SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
             i);
     ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
             : currentSequenceGroup.getGroupColourScheme());
-    return getBoxColour(currentShader, seq, i);
+    return getBoxColourInt(currentShader, seq, i);
   }
 
   /**
@@ -124,6 +164,6 @@ public class OverviewResColourFinder extends ResidueColourFinder
    */
   protected Color getHiddenColour()
   {
-    return HIDDEN_COLOUR;
+    return hiddenColour;
   }
 }