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 50ec7e0..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;
@@ -759,6 +760,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.showAllHiddenColumns();
       }
+      viewport.sendSelection();
     }
   }
 
@@ -930,12 +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();
@@ -1077,11 +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)
     {
@@ -1115,27 +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)
     {
@@ -1144,12 +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)
     {
@@ -1390,7 +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)
@@ -2269,7 +2286,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {