Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 665b3f4..3d961b1 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -63,7 +63,6 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColour;
-import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -1483,10 +1482,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
     }
 
-    if (viewport.applet.getParameter("jnetfile") != null)
+    if (viewport.applet.getParameter("jnetfile") != null
+            || viewport.applet.getParameter("jpredfile") != null)
     {
       url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+      url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+              .getParameter("jnetfile") : viewport.applet
+              .getParameter("jpredfile")));
     }
 
     if (viewport.applet.getParameter("defaultColour") != null)
@@ -2626,27 +2628,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void changeColour(ColourSchemeI cs)
   {
-
+    // FIXME threshold, conservation, increment belong inside
+    // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
     if (cs != null)
     {
       if (viewport.getAbovePIDThreshold())
       {
         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
-                cs, "Background"));
+                viewport.getViewportColourScheme(), "Background"));
       }
 
       if (viewport.getConservationSelected())
       {
-        cs.setConservationApplied(true);
+        // cs.setConservationApplied(true);
         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
-                cs, "Background"));
-      }
-      else
-      {
-        cs.setConservationApplied(false);
+                viewport.getViewportColourScheme(), "Background"));
       }
+      // else
+      // {
+      // cs.setConservationApplied(false);
+      // }
     }
     viewport.setGlobalColourScheme(cs);
+    viewport.getViewportColourScheme().setConservationApplied(
+            viewport.getConservationSelected());
 
     alignPanel.paintAlignment(true);
   }
@@ -2657,7 +2662,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
+              viewport.getViewportColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
@@ -2668,7 +2673,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
+              viewport.getViewportColourScheme(), "Background");
       SliderPanel.showConservationSlider();
     }
   }