JAL-2571 Corrected alignment width/height checks to visible only

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1685721..3de7c3c 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -31,8 +31,8 @@ import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -1446,13 +1446,21 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   {
     if (sequence != null)
     {
-      ColumnSelection cs = ap.av.getColumnSelection();
-      if (cs == null)
+      /* ColumnSelection cs = ap.av.getColumnSelection();
+       if (cs == null)
+       {
+         cs = new ColumnSelection();
+       }
+       cs.hideInsertionsFor(sequence);
+       ap.av.setColumnSelection(cs);*/
+
+      HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+      if (hidden == null)
       {
-        cs = new ColumnSelection();
+        hidden = new HiddenColumns();
       }
-      cs.hideInsertionsFor(sequence);
-      ap.av.setColumnSelection(cs);
+      hidden.hideInsertionsFor(sequence);
+      ap.av.getAlignment().setHiddenColumns(hidden);
     }
     refresh();
   }
@@ -1896,13 +1904,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       if (start <= end)
       {
         seqs.add(sg.getSequenceAt(i).getDatasetSequence());
-        features.add(new SequenceFeature(null, null, null, start, end,
-                "Jalview"));
+        features.add(new SequenceFeature(null, null, null, start, end, null));
       }
     }
 
     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap, null))
+            features, true, ap))
     {
       ap.alignFrame.setShowSeqFeatures(true);
       ap.highlightSearchResults(null);