JAL-2384 JAL-2371 update ResidueShader on change of colour by

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9876bb3..2646ede 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -75,6 +75,7 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Canvas;
@@ -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())
       {
@@ -410,6 +421,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void keyPressed(KeyEvent evt)
   {
+    ViewportRanges ranges = viewport.getRanges();
+
     if (viewport.cursorMode
             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
@@ -561,8 +574,8 @@ 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 = ranges.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
       }
       break;
 
@@ -588,8 +601,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
+        alignPanel.setScrollValues(ranges.getStartRes(),
+                2 * ranges.getStartSeq() - ranges.getEndSeq());
       }
       break;
 
@@ -600,8 +613,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                + viewport.endSeq - viewport.startSeq);
+        alignPanel
+                .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
       }
       break;
 
@@ -1058,6 +1071,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       delete_actionPerformed();
     }
+    else if (source == createGroup)
+    {
+      createGroup_actionPerformed();
+    }
+    else if (source == unGroup)
+    {
+      unGroup_actionPerformed();
+    }
     else if (source == grpsFromSelection)
     {
       makeGrpsFromSelection_actionPerformed();
@@ -2053,7 +2074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -2289,6 +2310,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   void trimAlignment(boolean trimLeft)
   {
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
@@ -2311,20 +2334,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        seqs = viewport.getAlignment().getSequencesArray();
+        seqs = al.getSequencesArray();
       }
 
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
-                column, viewport.getAlignment());
-        viewport.setStartRes(0);
+                column, al);
+        ranges.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
-                column, viewport.getAlignment());
+                column, al);
       }
 
       statusBar.setText(MessageManager.formatMessage(
@@ -2333,23 +2356,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                       .toString() }));
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg : viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
-          viewport.getAlignment().deleteGroup(sg);
+          al.deleteGroup(sg);
         }
       }
 
-      viewport.firePropertyChange("alignment", null, viewport
-              .getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, al.getSequences());
     }
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2377,22 +2402,24 @@ 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);
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2409,16 +2436,15 @@ 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);
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.getAlignment()));
+            al));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
@@ -2631,30 +2657,7 @@ 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 +2668,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showPIDSlider();
     }
   }
@@ -2676,7 +2679,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getViewportColourScheme(), "Background");
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showConservationSlider();
     }
   }
@@ -2686,9 +2689,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = conservationMenuItem.getState();
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
-
-    // viewport.setAbovePIDThreshold(false);
-    // abovePIDThreshold.setState(false);
+    viewport.getResidueShading().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -2707,8 +2708,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = abovePIDThreshold.getState();
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
-    // conservationMenuItem.setState(false);
-    // viewport.setConservationSelected(false);
+    if (!selected)
+    {
+      viewport.getResidueShading().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -3342,7 +3346,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
+    createGroup.addActionListener(this);
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
+    unGroup.addActionListener(this);
+
     annotationColumnSelection.setLabel(MessageManager
             .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);