JAL-3127 pass reference to AlignViewportI when creating an instance of ColourSchemeI

diff --git a/examples/groovy/colourConserved.groovy b/examples/groovy/colourConserved.groovy
index 4a15922..35c54d5 100644 (file)
--- a/examples/groovy/colourConserved.groovy
+++ b/examples/groovy/colourConserved.groovy
@@ -24,6 +24,7 @@ import jalview.schemes.ColourSchemes
 import jalview.datamodel.AnnotatedCollectionI
 import jalview.datamodel.SequenceI
 import jalview.datamodel.SequenceCollectionI
+import jalview.api.AlignViewportI
 import jalview.util.Comparison
 
 /*
@@ -42,7 +43,7 @@ conserved = { ->
     /*
      * to make a new instance for each alignment view
      */
-    getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> conserved() },
+    getInstance: { AlignViewportI view, AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> conserved() },
     
     /*
      * method only needed if colour scheme has to recalculate

diff --git a/examples/groovy/colourSchemes.groovy b/examples/groovy/colourSchemes.groovy
index d5ca973..3f1f953 100644 (file)
--- a/examples/groovy/colourSchemes.groovy
+++ b/examples/groovy/colourSchemes.groovy
@@ -4,6 +4,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceCollectionI;
+import jalview.api.AlignViewportI
 
 /*
  * Example script that registers two new alignment colour schemes
@@ -25,7 +26,7 @@ candy = { ->
     /*
      * to make a new instance for each alignment view
      */
-    getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> candy() },
+    getInstance: { AlignViewportI view, AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> candy() },
     
     /*
      * method only needed if colour scheme has to recalculate

diff --git a/examples/groovy/colourUnconserved.groovy b/examples/groovy/colourUnconserved.groovy
index 68730f3..e186766 100644 (file)
--- a/examples/groovy/colourUnconserved.groovy
+++ b/examples/groovy/colourUnconserved.groovy
@@ -24,6 +24,7 @@ import jalview.schemes.ColourSchemes
 import jalview.datamodel.AnnotatedCollectionI
 import jalview.datamodel.SequenceI
 import jalview.datamodel.SequenceCollectionI
+import jalview.api.AlignViewportI
 import jalview.util.Comparison
 
 /*

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 262948d..055584a 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -25,14 +25,11 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -200,7 +197,8 @@ public class AlignViewport extends AlignmentViewport
       if (colour != null)
       {
         residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+                ColourSchemeProperty.getColourScheme(this, alignment,
+                        colour));
         if (residueShading != null)
         {
           residueShading.setConsensus(hconsensus);

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 6ee75bd..cb26fb5 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -631,7 +631,7 @@ public class TreeCanvas extends Panel
 
       Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
 
-      Vector<SequenceI> sequences = new Vector<SequenceI>();
+      Vector<SequenceI> sequences = new Vector<>();
       for (int j = 0; j < l.size(); j++)
       {
         SequenceI s1 = (SequenceI) l.elementAt(j).element();
@@ -657,7 +657,8 @@ public class TreeCanvas extends Panel
         }
         else
         {
-          cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+          cs = ColourSchemeProperty.getColourScheme(av, sg,
+                  ColourSchemeProperty
                   .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3270144..88b359f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -541,7 +541,8 @@ public class Jalview
           data.replaceAll("%20", " ");
 
           ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport().getAlignment(), data);
+                  .getColourScheme(af.getViewport(),
+                          af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 94b38ed..4d1f800 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3328,6 +3328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport,
             viewport.getAlignment(), viewport.getHiddenRepSequences());
     changeColour(cs);
   }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7e77bec..ef24011 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -290,7 +290,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 384635b..9626309 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(sg, ap.av.getHiddenRepSequences()));
+                acg.getInstance(av, sg, ap.av.getHiddenRepSequences()));
       }
     }
   }

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 9285754..0c31a2a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4553,7 +4553,8 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.viewport, al,
+                view.getBgColour());
       }
     }
 
@@ -4893,7 +4894,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.viewport, al,
                       viewAnnColour.getColourScheme()),
               viewAnnColour.getAboveThreshold());
     }

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 331e738..eb494e3 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -400,7 +400,8 @@ public class Jalview2XML_V1
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.viewport, al,
+                view.getBgColour());
       }
 
       // if (cs != null)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ed3d29a..d114a8a 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2126,7 +2126,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * switch to the chosen colour scheme (or null for None)
      */
     ColourSchemeI colourScheme = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, sg,
+            .getColourScheme(colourSchemeName, ap.av, sg,
                     ap.av.getHiddenRepSequences());
     sg.setColourScheme(colourScheme);
     if (colourScheme instanceof Blosum62ColourScheme

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 72b0bcc..35a5475 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -564,7 +564,8 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     AlignmentI al = getAlignmentPanel().av.getAlignment();
     ColourSchemeI cs = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, al, null);
+            .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+                    null);
     getBinding().setJalviewColourScheme(cs);
   }
 

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index fa30e13..278e682 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1017,7 +1017,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+          cs = ColourSchemeProperty.getColourScheme(av, sg,
+                  ColourSchemeProperty
                   .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index c28ea5f..334998f 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -76,7 +77,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
@@ -185,7 +187,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       else
       {
-        seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+        seqannot = new IdentityHashMap<>();
       }
       // resolve the context containing all the annotation for the sequence
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 02f9b3e..202fc25 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
@@ -46,7 +47,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new Blosum62ColourScheme();

diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index a3b85b9..290ace8 100755 (executable)
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -75,7 +76,8 @@ public class BuriedColourScheme extends ScoreColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new BuriedColourScheme();

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ec13343..3a9f8f7 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -335,7 +336,8 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index d70b4e2..02ea887 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -62,11 +63,15 @@ public interface ColourSchemeI
    * new instance for each call to this method, as different instances may have
    * differing shading by consensus or percentage identity applied.
    * 
+   * @param viewport
+   *          - 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(AnnotatedCollectionI sg,
+  ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
   /**

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index fc92cd9..2d5b23d 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.util.ColorUtils;
 
@@ -75,7 +76,8 @@ public class ColourSchemeProperty
    * @param name
    * @return
    */
-  public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+  public static ColourSchemeI getColourScheme(AlignViewportI view,
+          AnnotatedCollectionI forData,
           String name)
   {
     if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
@@ -89,6 +91,7 @@ public class ColourSchemeProperty
      * create a new instance of it
      */
     ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+            view,
             forData, null);
     if (scheme != null)
     {

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 99e9759..c3d0ea0 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -65,7 +66,7 @@ public class ColourSchemes
      * store in an order-preserving map, so items can be added to menus 
      * in the order in which they are 'discovered'
      */
-    schemes = new LinkedHashMap<String, ColourSchemeI>();
+    schemes = new LinkedHashMap<>();
 
     for (JalviewColourScheme cs : JalviewColourScheme.values())
     {
@@ -76,6 +77,7 @@ public class ColourSchemes
       {
         System.err.println("Error instantiating colour scheme for "
                 + cs.toString() + " " + e.getMessage());
+        e.printStackTrace();
       }
     }
   }
@@ -126,6 +128,7 @@ public class ColourSchemes
    * 
    * @param name
    *          name of the colour scheme
+   * @param viewport
    * @param forData
    *          the data to be coloured
    * @param optional
@@ -134,7 +137,7 @@ public class ColourSchemes
    * @return
    */
   public ColourSchemeI getColourScheme(String name,
-          AnnotatedCollectionI forData,
+          AlignViewportI viewport, AnnotatedCollectionI forData,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     if (name == null)
@@ -142,7 +145,8 @@ public class ColourSchemes
       return null;
     }
     ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+    return cs == null ? null
+            : cs.getInstance(viewport, forData, hiddenRepSequences);
   }
 
   /**
@@ -158,7 +162,7 @@ public class ColourSchemes
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    return getColourScheme(name, forData, null);
+    return getColourScheme(name, null, forData, null);
   }
 
   /**

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 923bd85..41acef3 100644 (file)
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
@@ -38,9 +39,9 @@ import java.util.Map;
  */
 public class CovariationColourScheme extends ResidueColourScheme
 {
-  public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
+  public Map<String, Color> helixcolorhash = new Hashtable<>();
 
-  public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+  public Map<Integer, String> positionsToHelix = new Hashtable<>();
 
   int numHelix = 0;
 
@@ -51,7 +52,8 @@ public class CovariationColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);

diff --git a/src/jalview/schemes/FollowerColourScheme.java b/src/jalview/schemes/FollowerColourScheme.java
index 57c19e5..2cfb072 100644 (file)
--- a/src/jalview/schemes/FollowerColourScheme.java
+++ b/src/jalview/schemes/FollowerColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -53,7 +54,8 @@ public class FollowerColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new FollowerColourScheme();

diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 7123d93..d260ce6 100755 (executable)
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -58,7 +59,8 @@ public class HelixColourScheme extends ScoreColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new HelixColourScheme();

diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 69af3c9..fcdc10f 100755 (executable)
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -75,7 +76,8 @@ public class HydrophobicColourScheme extends ScoreColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new HydrophobicColourScheme();

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index abae733..be672e3 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -59,7 +60,8 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new NucleotideColourScheme();

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index fc922b9..6275b74 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
@@ -92,7 +93,8 @@ public class PIDColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new PIDColourScheme();

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 1b36f30..5c0cc1a 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -59,7 +60,8 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new PurinePyrimidineColourScheme();

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index dbc9c03..0011d5c 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -45,7 +46,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * Maps sequence positions to the RNA helix they belong to. Key: position,
    * Value: helix TODO: Revise or drop in favour of annotation position numbers
    */
-  public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+  public Hashtable<Integer, String> positionsToHelix = new Hashtable<>();
 
   /**
    * Number of helices in the RNA secondary structure
@@ -132,7 +133,7 @@ public class RNAHelicesColour extends ResidueColourScheme
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
       numHelix = 0;
-      positionsToHelix = new Hashtable<Integer, String>();
+      positionsToHelix = new Hashtable<>();
 
       // Figure out number of helices
       // Length of rnasecstr is the number of pairs of positions that base pair
@@ -206,7 +207,8 @@ public class RNAHelicesColour extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     return new RNAHelicesColour(sg);

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index d236803..c2bdd96 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -73,7 +74,8 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new RNAInteractionColourScheme();

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e1b60ca..e0011be 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -119,7 +120,8 @@ public class ScoreColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new ScoreColourScheme(symbolIndex, scores, min, max);

diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index 5f11c29..f318b42 100755 (executable)
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -75,7 +76,8 @@ public class StrandColourScheme extends ScoreColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new StrandColourScheme();

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 812dca7..f901892 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -83,10 +84,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
 
     // assume only one set of TCOFFEE scores - but could have more than one
     // potentially.
-    List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> annots = new ArrayList<>();
     // Search alignment to get all tcoffee annotation and pick one set of
     // annotation to use to colour seqs.
-    seqMap = new IdentityHashMap<SequenceI, Color[]>();
+    seqMap = new IdentityHashMap<>();
     AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
             ? alignment
             : alignment.getContext();
@@ -143,7 +144,8 @@ public class TCoffeeColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     return new TCoffeeColourScheme(sg);

diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index ac8abbc..74448e3 100755 (executable)
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -50,7 +51,8 @@ public class TaylorColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new TaylorColourScheme();

diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 67116b8..0af913b 100755 (executable)
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -75,7 +76,8 @@ public class TurnColourScheme extends ScoreColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new TurnColourScheme();

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bf62e45..16c9f78 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -56,7 +57,8 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     return new UserColourScheme(this);

diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index c32a39c..ee3bae6 100755 (executable)
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -59,7 +60,8 @@ public class ZappoColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll,
           Map<SequenceI, SequenceCollectionI> hrs)
   {
     return new ZappoColourScheme();

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 53bb0e7..8b65c3d 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -139,7 +139,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
-    assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
+    assertNotNull(
+            ColourSchemeProperty.getColourScheme(af.getViewport(),
+                    af.getViewport()
             .getAlignment(), af.getViewport().getGlobalColourScheme()
             .getSchemeName()), "Recognise T-Coffee score from string");
 

diff --git a/test/jalview/schemes/AnnotationColourGradientTest.java b/test/jalview/schemes/AnnotationColourGradientTest.java
index b7a5164..4a5e057 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(al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
 
     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(al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
   
     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(al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
 
     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(al, null);
+    testee = (AnnotationColourGradient) testee.getInstance(null, al, null);
 
     /*
      * flag corresponding to 'use original colours' checkbox

diff --git a/test/jalview/schemes/ColourSchemePropertyTest.java b/test/jalview/schemes/ColourSchemePropertyTest.java
index 11562b8..f71d647 100644 (file)
--- a/test/jalview/schemes/ColourSchemePropertyTest.java
+++ b/test/jalview/schemes/ColourSchemePropertyTest.java
@@ -76,51 +76,54 @@ public class ColourSchemePropertyTest
     SequenceI seq = new Sequence("Seq1", "abcd");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
     // the strings here correspond to JalviewColourScheme.toString() values
-    ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al, "Clustal");
+    ColourSchemeI cs = ColourSchemeProperty.getColourScheme(null, al,
+            "Clustal");
     assertTrue(cs instanceof ClustalxColourScheme);
     // not case-sensitive
-    cs = ColourSchemeProperty.getColourScheme(al, "CLUSTAL");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "CLUSTAL");
     assertTrue(cs instanceof ClustalxColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "clustal");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
     assertTrue(cs instanceof ClustalxColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Blosum62");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
     assertTrue(cs instanceof Blosum62ColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "% Identity");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
     assertTrue(cs instanceof PIDColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Zappo");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
     assertTrue(cs instanceof ZappoColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Taylor");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
     assertTrue(cs instanceof TaylorColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Hydrophobic");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
     assertTrue(cs instanceof HydrophobicColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Helix Propensity");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
     assertTrue(cs instanceof HelixColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Strand Propensity");
+    cs = ColourSchemeProperty.getColourScheme(null, al,
+            "Strand Propensity");
     assertTrue(cs instanceof StrandColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Turn Propensity");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
     assertTrue(cs instanceof TurnColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Buried Index");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
     assertTrue(cs instanceof BuriedColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Nucleotide");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
     assertTrue(cs instanceof NucleotideColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "Purine/Pyrimidine");
+    cs = ColourSchemeProperty.getColourScheme(null, al,
+            "Purine/Pyrimidine");
     assertTrue(cs instanceof PurinePyrimidineColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
     assertTrue(cs instanceof TCoffeeColourScheme);
-    cs = ColourSchemeProperty.getColourScheme(al, "RNA Helices");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "RNA Helices");
     assertTrue(cs instanceof RNAHelicesColour);
     // 'None' is a special value
-    assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
-    assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+    assertNull(ColourSchemeProperty.getColourScheme(null, al, "None"));
+    assertNull(ColourSchemeProperty.getColourScheme(null, al, "none"));
     // default is to convert the name into a fixed colour
-    cs = ColourSchemeProperty.getColourScheme(al, "elephants");
+    cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
     assertTrue(cs instanceof UserColourScheme);
 
     /*
      * explicit aa colours
      */
     UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
-            .getColourScheme(al,
+            .getColourScheme(null, al,
             "R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
     assertEquals(ucs.findColour('H'), Color.white);
     assertEquals(ucs.findColour('R'), Color.red);

diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index 0aaa38c..f6f1953 100644 (file)
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.java
@@ -5,6 +5,7 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -54,7 +55,8 @@ public class ColourSchemesTest
     }
 
     @Override
-    public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+    public ColourSchemeI getInstance(AlignViewportI view,
+            AnnotatedCollectionI sg,
             Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
     {
       final ColourSchemeI cs1 = ColourSchemes.getInstance()
@@ -144,7 +146,8 @@ public class ColourSchemesTest
     }
 
     @Override
-    public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+    public ColourSchemeI getInstance(AlignViewportI view,
+            AnnotatedCollectionI sg,
             Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
     {
       return new MyClustal(sg,              hiddenRepSequences);