JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1352cf2..544835d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -44,9 +44,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
-import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.PIDColourScheme;
 import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
@@ -607,35 +605,33 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // TODO: logic refactored from AlignFrame changeColour -
     // TODO: autorecalc stuff should be changed to rely on the worker system
     // check to see if we should implement a changeColour(cs) method rather than
-    // put th logic in here
+    // put the logic in here
     // - means that caller decides if they want to just modify state and defer
     // calculation till later or to do all calculations in thread.
     // via changecolour
 
     /*
-     * only instantiate collection colour scheme once, thereafter update it
+     * only instantiate alignment colouring once, thereafter update it;
      * this means that any conservation or PID threshold settings
      * persist when the alignment colour scheme is changed
      */
     if (globalColourScheme == null)
     {
-      globalColourScheme = new ResidueShader();
+      globalColourScheme = new ResidueShader(viewStyle);
     }
     globalColourScheme.setColourScheme(cs);
 
-    // boolean recalc = false;
-    // TODO: do threshold and increment belong in ViewStyle or colour scheme?
-    // problem: groups need this but do not currently have a ViewStyle
+    // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
+    // ...problem: groups need these, but do not currently have a ViewStyle
 
     if (cs != null)
     {
-      if (getConservationSelected() || getAbovePIDThreshold()
-              || cs instanceof PIDColourScheme
-              || cs instanceof Blosum62ColourScheme)
+      // if (getConservationSelected() || getAbovePIDThreshold()
+      // || cs instanceof PIDColourScheme
+      // || cs instanceof Blosum62ColourScheme)
+      if (getConservationSelected())
       {
         globalColourScheme.setConservation(hconservation);
-        globalColourScheme
-                .setConservationApplied(getConservationSelected());
       }
       globalColourScheme.alignmentChanged(alignment, hiddenRepSequences);
     }
@@ -1840,7 +1836,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       selectionGroup.setEndRes(alWidth - 1);
     }
 
-    resetAllColourSchemes();
+    updateAllColourSchemes();
     calculator.restartWorkers();
     // alignment.adjustSequenceAnnotations();
   }
@@ -1848,17 +1844,17 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * reset scope and do calculations for all applied colourschemes on alignment
    */
-  void resetAllColourSchemes()
+  void updateAllColourSchemes()
   {
-    ResidueShaderI cs = globalColourScheme;
-    if (cs != null)
+    ResidueShaderI rs = globalColourScheme;
+    if (rs != null)
     {
-      cs.alignmentChanged(alignment, hiddenRepSequences);
+      rs.alignmentChanged(alignment, hiddenRepSequences);
 
-      cs.setConsensus(hconsensus);
-      if (cs.conservationApplied())
+      rs.setConsensus(hconsensus);
+      if (rs.conservationApplied())
       {
-        cs.setConservation(Conservation.calculateConservation("All",
+        rs.setConservation(Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alignment.getWidth(), false,
                 getConsPercGaps(), false));
       }