Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 7ff1c65..49260a4 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -77,6 +77,14 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
   private boolean includeGaps = true;
 
+  /**
+   * Default constructor (required for Class.newInstance())
+   */
+  public ClustalxColourScheme()
+  {
+
+  }
+
   public ClustalxColourScheme(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
@@ -268,12 +276,13 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char c, int j, SequenceI seq)
+  protected Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 
+    // TODO why the test for includeGaps here?
     if (cons2.length <= j
-            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
     }
@@ -298,17 +307,15 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     if (i == 4)
     {
+      /*
+       * override to colour C pink if 100% conserved
+       */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
         currentColour = ClustalColour.PINK.colour;
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
     return currentColour;
   }
 
@@ -330,7 +337,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
@@ -350,4 +357,10 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     return JalviewColourScheme.Clustal.toString();
   }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
 }