JAL-2015 JAL-1956 rollout of FeatureColourI in place of

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0d1fd35..40fbd6d 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
@@ -234,8 +235,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
-    showAlignmentAnnotations.setState(viewport.isShowAnnotation());
-    showSequenceAnnotations.setState(viewport.isShowAnnotation());
+    showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAlignmentAnnotations.setState(true);
+    showSequenceAnnotations.setState(false);
 
     seqLimits.setState(viewport.getShowJVSuffix());
 
@@ -757,6 +760,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.showAllHiddenColumns();
       }
+      viewport.sendSelection();
     }
   }
 
@@ -816,8 +820,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == annotationPanelMenuItem)
     {
-      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+      boolean showAnnotations = annotationPanelMenuItem.getState();
+      showAlignmentAnnotations.setEnabled(showAnnotations);
+      showSequenceAnnotations.setEnabled(showAnnotations);
+      viewport.setShowAnnotation(showAnnotations);
+      alignPanel.setAnnotationVisible(showAnnotations);
     }
     else if (source == sequenceFeatures)
     {
@@ -925,12 +932,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     boolean showForAlignment = showAlignmentAnnotations.getState();
     boolean showForSequences = showSequenceAnnotations.getState();
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
+    if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+    {
+      for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
       boolean visible = (aa.sequenceRef == null ? showForAlignment
               : showForSequences);
       aa.visible = visible;
+      }
     }
     alignPanel.validateAnnotationDimensions(true);
     validate();
@@ -1072,11 +1082,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == invertSequenceMenuItem)
     {
       invertSequenceMenuItem_actionPerformed();
+      // uncomment to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == invertColSel)
     {
       viewport.invertColumnSelection();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == remove2LeftMenuItem)
     {
@@ -1110,27 +1123,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.showAllHiddenColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideColumns)
     {
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideSequences
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideAllButSelection)
     {
       toggleHiddenRegions(false, false);
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideAllSelection)
     {
@@ -1139,12 +1159,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.hideAllSelectedSeqs();
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showAllHidden)
     {
       viewport.showAllHiddenColumns();
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showGroupConsensus)
     {
@@ -1385,7 +1407,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Map<String, Object> getDisplayedFeatureCols()
+  private Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
             && viewport.getFeaturesDisplayed() != null)
@@ -1747,9 +1769,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport, complement);
       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
               up ? null : complement.getHiddenRepSequences(), up);
-      // TODO need to trigger a repaint of the complementary panel - how?
-      // would prefer to handle in SplitFrame but it is not overriding key
-      // listener chiz
+      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
     }
   }
 
@@ -2072,15 +2092,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               .getAlignment().getWidth()) ? true : false;
       if (isEntireAlignWidth)
       {
-
         String title = MessageManager.getString("label.delete_all");
-        Panel mp = new Panel();
-        mp.setLayout(new FlowLayout());
-        mp.add(new Label(MessageManager.getString("warn.delete_all")));
-
-        final JVDialog dialog = new JVDialog(this, title, true, 400,
-                200);
-        dialog.setMainPanel(mp);
+        Panel infoPanel = new Panel();
+        infoPanel.setLayout(new FlowLayout());
+        infoPanel
+                .add(new Label(MessageManager.getString("warn.delete_all")));
+
+        final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+        dialog.setMainPanel(infoPanel);
+        dialog.ok.setLabel(MessageManager.getString("action.ok"));
+        dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
         dialog.setVisible(true);
 
         if (!dialog.accept)
@@ -2265,7 +2286,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {
@@ -2290,18 +2311,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
-        trimRegion = new TrimRegionCommand("Remove Left",
-                TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+                column, viewport.getAlignment());
         viewport.setStartRes(0);
       }
       else
       {
-        trimRegion = new TrimRegionCommand("Remove Right",
-                TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+                column, viewport.getAlignment());
       }
 
       statusBar.setText(MessageManager.formatMessage(
@@ -2605,6 +2622,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
 
@@ -3755,6 +3773,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.add(statusBar, BorderLayout.SOUTH);
   }
 
+  @Override
   public void setStatus(String string)
   {
     statusBar.setText(string);