JAL-2403 constants for "NJ", "AV"

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 31d049a..221f793 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -22,6 +22,7 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -284,6 +285,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     if (viewport.getAlignment().isNucleotide())
     {
+      conservationMenuItem.setEnabled(false);
+      clustalColour.setEnabled(false);
+      BLOSUM62Colour.setEnabled(false);
+      zappoColour.setEnabled(false);
+      taylorColour.setEnabled(false);
+      hydrophobicityColour.setEnabled(false);
+      helixColour.setEnabled(false);
+      strandColour.setEnabled(false);
+      turnColour.setEnabled(false);
+      buriedColour.setEnabled(false);
       viewport.updateStrucConsensus(alignPanel);
       if (viewport.getAlignment().hasRNAStructure())
       {
@@ -2631,30 +2642,7 @@ 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,
-                viewport.getViewportColourScheme(), "Background"));
-      }
-
-      if (viewport.getConservationSelected())
-      {
-        // cs.setConservationApplied(true);
-        viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
-                viewport.getViewportColourScheme(), "Background"));
-      }
-      // else
-      // {
-      // cs.setConservationApplied(false);
-      // }
-    }
     viewport.setGlobalColourScheme(cs);
-    viewport.getViewportColourScheme().setConservationApplied(
-            viewport.getConservationSelected());
 
     alignPanel.paintAlignment(true);
   }
@@ -2665,7 +2653,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showPIDSlider();
     }
   }
@@ -2676,33 +2664,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showConservationSlider();
     }
   }
 
   protected void conservationMenuItem_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.getState());
+    boolean selected = conservationMenuItem.getState();
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
 
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setState(false);
+    // viewport.setAbovePIDThreshold(false);
+    // abovePIDThreshold.setState(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyConservation_actionPerformed();
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   public void abovePIDThreshold_actionPerformed()
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
-    conservationMenuItem.setState(false);
-    viewport.setConservationSelected(false);
+    boolean selected = abovePIDThreshold.getState();
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
+    // conservationMenuItem.setState(false);
+    // viewport.setConservationSelected(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyPID_actionPerformed();
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   public void sortPairwiseMenuItem_actionPerformed()
@@ -2801,22 +2806,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void averageDistanceTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
+    NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+            "Average distance tree using PID");
   }
 
   public void neighbourTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+            "Neighbour joining tree using PID");
   }
 
   protected void njTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+            "Neighbour joining tree using BLOSUM62");
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+            "Average distance tree using BLOSUM62");
   }
 
   void NewTreePanel(String type, String pwType, String title)
@@ -3530,9 +3539,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
             .getString("label.modify_identity_threshold"));
+    modifyPID.setEnabled(abovePIDThreshold.getState());
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
             .getString("label.modify_conservation_threshold"));
+    modifyConservation.setEnabled(conservationMenuItem.getState());
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));