JAL-3127 drop redundant hidden representative sequences hash as parameter in ColourSc...

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index a5a3591..a82b98d 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -107,8 +107,7 @@ public class AlignViewController implements AlignViewControllerI
         viewport.getAlignment().addGroup(gps[g]);
         if (colours != null)
         {
-          gps[g].setColourScheme(colours.getInstance(viewport, gps[g],
-                  viewport.getHiddenRepSequences()));
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 9626309..13390da 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -454,7 +454,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
           continue;
         }
         sg.setColourScheme(
-                acg.getInstance(av, sg, ap.av.getHiddenRepSequences()));
+                acg.getInstance(av, sg));
       }
     }
   }

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f1bdd31..f353d28 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1006,8 +1006,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         // Propagate group colours in each view
         if (viewport.getGlobalColourScheme() != null)
         {
-          cs = viewport.getGlobalColourScheme().getInstance(viewport, sg,
-                  null);
+          cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
           sg.setColourScheme(cs);
           sg.getGroupColourScheme().setThreshold(
                   viewport.getResidueShading().getThreshold(),

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 334998f..2790626 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -78,8 +78,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+          AnnotatedCollectionI sg)
   {
     AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
             getColourScheme(), aboveAnnotationThreshold);

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 202fc25..8188f4d 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -24,12 +24,10 @@ import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewportI;
 import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.Map;
 
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
@@ -48,8 +46,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new Blosum62ColourScheme();
   }

diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 290ace8..e6672fc 100755 (executable)
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -22,11 +22,8 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -77,8 +74,7 @@ public class BuriedColourScheme extends ScoreColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new BuriedColourScheme();
   }

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 3a9f8f7..b1cfe82 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -337,11 +337,10 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+          AnnotatedCollectionI sg)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
-            hiddenRepSequences);
+            view.getHiddenRepSequences());
     css.includeGaps = includeGaps;
     return css;
   }

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 02ea887..7b79d88 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -67,12 +67,10 @@ public interface ColourSchemeI
    *          - the parent viewport
    * @param sg
    *          - the collection of sequences to be coloured
-   * @param hiddenRepSequences
    * @return copy of current scheme with any inherited settings transferred
    */
   ColourSchemeI getInstance(AlignViewportI viewport,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+          AnnotatedCollectionI sg);
 
   /**
    * Answers true if the colour scheme is suitable for the given data, else

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index c3d0ea0..42465f2 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -146,7 +146,7 @@ public class ColourSchemes
     }
     ColourSchemeI cs = schemes.get(name.toLowerCase());
     return cs == null ? null
-            : cs.getInstance(viewport, forData, hiddenRepSequences);
+            : cs.getInstance(viewport, forData);
   }
 
   /**

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 41acef3..dc7971b 100644 (file)
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -23,8 +23,6 @@ package jalview.schemes;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 
 import java.awt.Color;
@@ -53,8 +51,7 @@ public class CovariationColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
   }

diff --git a/src/jalview/schemes/FollowerColourScheme.java b/src/jalview/schemes/FollowerColourScheme.java
index 2cfb072..24b7713 100644 (file)
--- a/src/jalview/schemes/FollowerColourScheme.java
+++ b/src/jalview/schemes/FollowerColourScheme.java
@@ -22,10 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
 
 /**
  * Colourscheme that takes its colours from some other colourscheme
@@ -55,8 +51,7 @@ public class FollowerColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new FollowerColourScheme();
   }

diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index d260ce6..2724f77 100755 (executable)
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -22,11 +22,8 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 public class HelixColourScheme extends ScoreColourScheme
 {
@@ -60,8 +57,7 @@ public class HelixColourScheme extends ScoreColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new HelixColourScheme();
   }

diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index fcdc10f..d886bdf 100755 (executable)
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -22,11 +22,8 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -77,8 +74,7 @@ public class HydrophobicColourScheme extends ScoreColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new HydrophobicColourScheme();
   }

diff --git a/src/jalview/schemes/IdColourScheme.java b/src/jalview/schemes/IdColourScheme.java
index cd26666..65dbcc9 100644 (file)
--- a/src/jalview/schemes/IdColourScheme.java
+++ b/src/jalview/schemes/IdColourScheme.java
@@ -57,8 +57,7 @@ public class IdColourScheme implements ColourSchemeI
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new IdColourScheme(view, coll);
   }

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index be672e3..4977107 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -22,10 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -61,8 +57,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new NucleotideColourScheme();
   }

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 6275b74..3a5c066 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -22,13 +22,11 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.Map;
 
 public class PIDColourScheme extends ResidueColourScheme
 {
@@ -94,8 +92,7 @@ public class PIDColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new PIDColourScheme();
   }

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 5c0cc1a..a8270cc 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -22,10 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
 
 /**
  * Class is based off of NucleotideColourScheme
@@ -61,8 +57,7 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new PurinePyrimidineColourScheme();
   }

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 0011d5c..33b275d 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -208,8 +208,7 @@ public class RNAHelicesColour extends ResidueColourScheme
 
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+          AnnotatedCollectionI sg)
   {
     return new RNAHelicesColour(sg);
   }

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index c2bdd96..8610417 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -22,11 +22,9 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 public class RNAInteractionColourScheme extends ResidueColourScheme
 {
@@ -75,8 +73,7 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new RNAInteractionColourScheme();
   }

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e0011be..eae76e1 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -22,12 +22,10 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -121,8 +119,7 @@ public class ScoreColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new ScoreColourScheme(symbolIndex, scores, min, max);
   }

diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index f318b42..ef55d69 100755 (executable)
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -22,11 +22,8 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -77,8 +74,7 @@ public class StrandColourScheme extends ScoreColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new StrandColourScheme();
   }

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index f901892..db85cc8 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -145,8 +145,7 @@ public class TCoffeeColourScheme extends ResidueColourScheme
 
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+          AnnotatedCollectionI sg)
   {
     return new TCoffeeColourScheme(sg);
   }

diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index 74448e3..e2a4516 100755 (executable)
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -22,10 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
 
 public class TaylorColourScheme extends ResidueColourScheme
 {
@@ -52,8 +48,7 @@ public class TaylorColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new TaylorColourScheme();
   }

diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 0af913b..7d8035a 100755 (executable)
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -22,11 +22,8 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -77,8 +74,7 @@ public class TurnColourScheme extends ScoreColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new TurnColourScheme();
   }

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 16c9f78..d77f2f5 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -22,8 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 import jalview.util.StringUtils;
 
@@ -58,8 +56,7 @@ public class UserColourScheme extends ResidueColourScheme
 
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+          AnnotatedCollectionI sg)
   {
     return new UserColourScheme(this);
   }

diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index ee3bae6..d69695f 100755 (executable)
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -22,10 +22,6 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -61,8 +57,7 @@ public class ZappoColourScheme extends ResidueColourScheme
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new ZappoColourScheme();
   }

diff --git a/test/jalview/schemes/AnnotationColourGradientTest.java b/test/jalview/schemes/AnnotationColourGradientTest.java
index 4a5e057..0b0eb24 100644 (file)
--- a/test/jalview/schemes/AnnotationColourGradientTest.java
+++ b/test/jalview/schemes/AnnotationColourGradientTest.java
@@ -184,7 +184,7 @@ public class AnnotationColourGradientTest
   {
     AnnotationColourGradient testee = new AnnotationColourGradient(ann,
             minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
-    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al);
 
     for (int col = 0; col < WIDTH; col++)
     {
@@ -226,7 +226,7 @@ public class AnnotationColourGradientTest
   {
     AnnotationColourGradient testee = new AnnotationColourGradient(ann,
             minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
-    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al);
   
     for (int col = 0; col < WIDTH; col++)
     {
@@ -259,7 +259,7 @@ public class AnnotationColourGradientTest
   {
     AnnotationColourGradient testee = new AnnotationColourGradient(ann,
             minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
-    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al);
 
     for (int col = 0; col < WIDTH; col++)
     {
@@ -278,7 +278,7 @@ public class AnnotationColourGradientTest
   {
     AnnotationColourGradient testee = new AnnotationColourGradient(ann,
             minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
-    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al);
 
     /*
      * flag corresponding to 'use original colours' checkbox

diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index f6f1953..5db3743 100644 (file)
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.java
@@ -56,8 +56,7 @@ public class ColourSchemesTest
 
     @Override
     public ColourSchemeI getInstance(AlignViewportI view,
-            AnnotatedCollectionI sg,
-            Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+            AnnotatedCollectionI sg)
     {
       final ColourSchemeI cs1 = ColourSchemes.getInstance()
               .getColourScheme(JalviewColourScheme.Taylor.toString(),
@@ -147,10 +146,9 @@ public class ColourSchemesTest
 
     @Override
     public ColourSchemeI getInstance(AlignViewportI view,
-            AnnotatedCollectionI sg,
-            Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+            AnnotatedCollectionI sg)
     {
-      return new MyClustal(sg,              hiddenRepSequences);
+      return new MyClustal(sg, view.getHiddenRepSequences());
     }
 
     @Override