JAL-2371 CollectionColourScheme renamed ResidueShader and moved to

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 018b227..4ae0ed2 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -39,11 +39,11 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.JalviewColourScheme;
@@ -330,7 +330,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
    * 
    * @param cs
    */
-  protected void setSelectedColour(CollectionColourSchemeI cs)
+  protected void setSelectedColour(ResidueShaderI cs)
   {
     if (cs == null || cs.getColourScheme() == null)
     {
@@ -1147,62 +1147,62 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+    sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
             ap.av.getHiddenRepSequences()));
     refresh();
   }
 
   protected void zappoColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
+    getGroup().cs = new ResidueShader(new ZappoColourScheme());
     refresh();
   }
 
   protected void taylorColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
+    getGroup().cs = new ResidueShader(new TaylorColourScheme());
     refresh();
   }
 
   protected void hydrophobicityColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
+    getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
     refresh();
   }
 
   protected void helixColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
+    getGroup().cs = new ResidueShader(new HelixColourScheme());
     refresh();
   }
 
   protected void strandColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
+    getGroup().cs = new ResidueShader(new StrandColourScheme());
     refresh();
   }
 
   protected void turnColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
+    getGroup().cs = new ResidueShader(new TurnColourScheme());
     refresh();
   }
 
   protected void buriedColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
+    getGroup().cs = new ResidueShader(new BuriedColourScheme());
     refresh();
   }
 
   public void nucleotideMenuItem_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
+    getGroup().cs = new ResidueShader(new NucleotideColourScheme());
     refresh();
   }
 
   public void purinePyrimidineColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(
+    getGroup().cs = new ResidueShader(
             new PurinePyrimidineColourScheme());
     refresh();
   }
@@ -1245,7 +1245,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new CollectionColourScheme(new PIDColourScheme());
+    sg.cs = new ResidueShader(new PIDColourScheme());
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
     refresh();
@@ -1255,7 +1255,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
 
-    sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
+    sg.cs = new ResidueShader(new Blosum62ColourScheme());
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));