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 f830fe6..3d961b1 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -62,7 +62,7 @@ import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -296,6 +296,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       RNAHelixColour.setEnabled(false);
       purinePyrimidineColour.setEnabled(false);
+      nucleotideColour.setEnabled(false);
     }
     // Some JVMS send keyevents to Top frame or lowest panel,
     // Havent worked out why yet. So add to both this frame and seqCanvas for
@@ -1255,7 +1256,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // }
     else if (source == RNAHelixColour)
     {
-      new RNAHelicesColourChooser(viewport, alignPanel);
+      changeColour(new RNAHelicesColour(viewport.getAlignment()));
+      // new RNAHelicesColourChooser(viewport, alignPanel);
     }
     else if (source == modifyPID)
     {
@@ -1480,10 +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)
@@ -2623,27 +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);
   }
@@ -2654,7 +2662,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
+              viewport.getViewportColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
@@ -2665,7 +2673,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
+              viewport.getViewportColourScheme(), "Background");
       SliderPanel.showConservationSlider();
     }
   }
@@ -3436,7 +3444,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("label.colour_text"));
     colourTextMenuItem.addItemListener(this);
     displayNonconservedMenuItem.setLabel(MessageManager
-            .getString("label.show_non_conversed"));
+            .getString("label.show_non_conserved"));
     displayNonconservedMenuItem.addItemListener(this);
     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
     wrapMenuItem.addItemListener(this);
@@ -3459,45 +3467,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.setState(true);
     applyToAllGroups.addItemListener(this);
-    clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+    clustalColour.setLabel(MessageManager
+            .getString("label.colourScheme_clustal"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel(MessageManager.getString("label.zappo"));
+    zappoColour.setLabel(MessageManager
+            .getString("label.colourScheme_zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel(MessageManager.getString("label.taylor"));
+    taylorColour.setLabel(MessageManager
+            .getString("label.colourScheme_taylor"));
     taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel(MessageManager
-            .getString("label.hydrophobicity"));
+            .getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
-    helixColour
-            .setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour.setLabel(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.strand_propensity"));
+            .getString("label.colourScheme_strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+    turnColour.setLabel(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+    buriedColour.setLabel(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager
-            .getString("label.purine_pyrimidine"));
+            .getString("label.colourScheme_purine/pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
     // RNAInteractionColour.setLabel(MessageManager
     // .getString("label.rna_interaction"));
     // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager
-            .getString("action.by_rna_helixes"));
+            .getString("label.colourScheme_rna_helices"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel(MessageManager
             .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
-            .getString("label.percentage_identity"));
+            .getString("label.colourScheme_%_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel(MessageManager
-            .getString("label.blosum62_score"));
+            .getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
-    tcoffeeColour
-            .setLabel(MessageManager.getString("label.tcoffee_scores"));
+    tcoffeeColour.setLabel(MessageManager
+            .getString("label.colourScheme_t-coffee_scores"));
     // it will be enabled only if a score file is provided
     tcoffeeColour.setEnabled(false);
     tcoffeeColour.addActionListener(this);
@@ -3509,7 +3522,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     abovePIDThreshold.setLabel(MessageManager
             .getString("label.above_identity_threshold"));
     abovePIDThreshold.addItemListener(this);
-    nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.setLabel(MessageManager
+            .getString("label.colourScheme_nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
             .getString("label.modify_identity_threshold"));
@@ -3549,7 +3563,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem.addActionListener(this);
     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
-            .getString("label.average_distance_bloslum62"));
+            .getString("label.average_distance_blosum62"));
     avDistanceTreeBlosumMenuItem.addActionListener(this);
     njTreeBlosumMenuItem.setLabel(MessageManager
             .getString("label.neighbour_blosum62"));