X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=dc622f5c592c7794537842297753132a7c9f9839;hb=571d15a897c11bdc2dda76ce03686604596f220d;hp=31d049aecfa630214b43006f0d481bb3a33b0db3;hpb=e94dbf72fe43a100b938e9ca60b9b1b1508a521f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 31d049a..dc622f5 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -284,6 +284,16 @@ 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())
       {
@@ -561,8 +571,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+        alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
       }
       break;
 
@@ -588,8 +598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                2 * viewport.getStartSeq() - viewport.getEndSeq());
       }
       break;
 
@@ -600,8 +610,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                + viewport.endSeq - viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                viewport.getEndSeq());
       }
       break;
 
@@ -2378,7 +2388,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
@@ -2410,7 +2420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
@@ -2631,30 +2641,7 @@ 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 +2652,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showPIDSlider();
     }
   }
@@ -2676,33 +2663,50 @@ 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()
@@ -3530,9 +3534,11 @@ 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"));