JAL-3148 SequenceRenderer, ResidueColourFinder overloads and

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3d1442d..22c467d 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -28,6 +28,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
@@ -37,6 +38,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel.ColourBy;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -185,7 +187,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
             new PDBEntry[]
             { pdbentry }, new SequenceI[][] { seq }, protocol);
-    jmb.setColourBySequence(true);
+    jmb.setColourBy(ColourBy.Sequence);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
       if (protocol == DataSourceType.PASTE)
@@ -455,41 +457,41 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == zappo)
     {
       setEnabled(zappo);
-      jmb.setJalviewColourScheme(new ZappoColourScheme());
+      setColourScheme(new ZappoColourScheme());
     }
     else if (evt.getSource() == taylor)
     {
       setEnabled(taylor);
-      jmb.setJalviewColourScheme(new TaylorColourScheme());
+      setColourScheme(new TaylorColourScheme());
     }
     else if (evt.getSource() == hydro)
     {
       setEnabled(hydro);
-      jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+      setColourScheme(new HydrophobicColourScheme());
     }
     else if (evt.getSource() == helix)
     {
       setEnabled(helix);
-      jmb.setJalviewColourScheme(new HelixColourScheme());
+      setColourScheme(new HelixColourScheme());
     }
     else if (evt.getSource() == strand)
     {
       setEnabled(strand);
-      jmb.setJalviewColourScheme(new StrandColourScheme());
+      setColourScheme(new StrandColourScheme());
     }
     else if (evt.getSource() == turn)
     {
       setEnabled(turn);
-      jmb.setJalviewColourScheme(new TurnColourScheme());
+      setColourScheme(new TurnColourScheme());
     }
     else if (evt.getSource() == buried)
     {
       setEnabled(buried);
-      jmb.setJalviewColourScheme(new BuriedColourScheme());
+      setColourScheme(new BuriedColourScheme());
     }
     else if (evt.getSource() == purinepyrimidine)
     {
-      jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+      setColourScheme(new PurinePyrimidineColourScheme());
     }
     else if (evt.getSource() == user)
     {
@@ -524,7 +526,12 @@ public class AppletJmol extends EmbmenuFrame implements
     }
   }
 
-  /**
+  private void setColourScheme(ColourSchemeI cs) 
+  {
+    jmb.setJalviewColourScheme(cs, ap);
+  }
+
+/**
    * tick or untick the seqColour menu entry or jmoColour entry depending upon
    * if it was selected or not.
    * 
@@ -534,7 +541,7 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     jmolColour.setState(itm == jmolColour);
     seqColour.setState(itm == seqColour);
-    jmb.setColourBySequence(itm == seqColour);
+    jmb.setColourBy(itm == seqColour ? ColourBy.Sequence : ColourBy.Viewer);
   }
 
   @Override
@@ -543,7 +550,7 @@ public class AppletJmol extends EmbmenuFrame implements
     if (evt.getSource() == jmolColour)
     {
       setEnabled(jmolColour);
-      jmb.setColourBySequence(false);
+      jmb.setColourBy(ColourBy.Viewer);
     }
     else if (evt.getSource() == seqColour)
     {
@@ -695,7 +702,7 @@ public class AppletJmol extends EmbmenuFrame implements
    */
   public void setJalviewColourScheme(UserColourScheme ucs)
   {
-    jmb.setJalviewColourScheme(ucs);
+    setColourScheme(ucs);
   }
 
   public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)