JAL-98 ProfilesI container for profiles for columns

[jalview.git] / src / jalview / schemes / ResidueColourScheme.java

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 56c573c..f6b7c5e 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -21,10 +21,12 @@
 package jalview.schemes;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
@@ -53,7 +55,7 @@ public class ResidueColourScheme implements ColourSchemeI
   /*
    * Consensus data indexed by column
    */
-  Profile[] consensus;
+  ProfilesI consensus;
 
   /*
    * Conservation string as a char array 
@@ -181,19 +183,20 @@ public class ResidueColourScheme implements ColourSchemeI
       residue -= ('a' - 'A');
     }
 
-    if (consensus == null || consensus.length < column
-            || consensus[column] == null)
+    if (consensus == null)
     {
       return false;
     }
 
+    ProfileI profile = consensus.get(column);
+
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
-    if (consensus[column].getModalResidue().contains(
-            String.valueOf(residue)))
+    if (profile != null
+            && profile.getModalResidue().contains(String.valueOf(residue)))
     {
-      if (consensus[column].getPercentageIdentity(ignoreGaps) >= threshold)
+      if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
       {
         return true;
       }
@@ -233,7 +236,7 @@ public class ResidueColourScheme implements ColourSchemeI
    *          DOCUMENT ME!
    */
   @Override
-  public void setConsensus(Profile[] consensus)
+  public void setConsensus(ProfilesI consensus)
   {
     if (consensus == null)
     {
@@ -311,33 +314,13 @@ public class ResidueColourScheme implements ColourSchemeI
     float bleachFactor = (11 - (conservationScore - '0')) / 10f;
 
     /*
-     * scale this by the percentage slider / 20
-     */
-    bleachFactor *= (inc / 20f);
-
-    int red = currentColour.getRed();
-    int green = currentColour.getGreen();
-    int blue = currentColour.getBlue();
-
-    /*
-     * bleach colours towards white (255, 255, 255),
-     * depending on the consensus score and the conservation slider value
-     * scores of:                      0  1  2  3  4  5  6  7  8  9
+     * scale this up by 0-5 (percentage slider / 20)
+     * as a result, scores of:         0  1  2  3  4  5  6  7  8  9
      * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
      */
-    red += (255 - red) * bleachFactor;
-    green += (255 - green) * bleachFactor;
-    blue += (255 - blue) * bleachFactor;
+    bleachFactor *= (inc / 20f);
 
-    if (red > 255 || green > 255 || blue > 255)
-    {
-      currentColour = Color.white;
-    }
-    else
-    {
-      currentColour = new Color(red, green, blue);
-    }
-    return currentColour;
+    return ColorUtils.bleachColour(currentColour, bleachFactor);
   }
 
   @Override