X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=759c63b688af6d96f2e3f63802ec95ae1ab2b6cb;hb=147ed3621f0e15c5fb5ad44f59d4821fb01e8b1c;hp=2ef71cce5d6fff162391756b1425434754dcce56;hpb=6d06be2714c9cba8c69148d5e2d26b50b7051840;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ef71cc..759c63b 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1453,15 +1453,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-
-    HiddenColumns hidden = new HiddenColumns();
-    BitSet inserts = new BitSet(), mask = new BitSet();
-
-    // set mask to preserve existing hidden columns outside selected group
-    if (ap.av.hasHiddenColumns())
-    {
-      ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
-    }
+    HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+    BitSet inserts = new BitSet();
 
     boolean markedPopup = false;
     // mark inserts in current selection
@@ -1469,10 +1462,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     {
       // mark just the columns in the selection group to be hidden
       inserts.set(ap.av.getSelectionGroup().getStartRes(),
-              ap.av.getSelectionGroup().getEndRes() + 1);
-
-      // and clear that part of the mask
-      mask.andNot(inserts);
+              ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
 
       // now clear columns without gaps
       for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
@@ -1483,29 +1473,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
         inserts.and(sq.getInsertionsAsBits());
       }
-    }
-    else
-    {
-      // initially, mark all columns to be hidden
-      inserts.set(0, ap.av.getAlignment().getWidth());
-
-      // and clear out old hidden regions completely
-      mask.clear();
+      hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+              ap.av.getSelectionGroup().getEndRes());
     }
 
     // now mark for sequence under popup if we haven't already done it
-    if (!markedPopup && sequence != null)
+    else if (!markedPopup && sequence != null)
     {
-      inserts.and(sequence.getInsertionsAsBits());
-    }
+      inserts.or(sequence.getInsertionsAsBits());
 
-    // finally, preserve hidden regions outside selection
-    inserts.or(mask);
-
-    // and set hidden columns accordingly
-    hidden.hideMarkedBits(inserts);
-
-    ap.av.getAlignment().setHiddenColumns(hidden);
+      // and set hidden columns accordingly
+      hidden.hideColumns(inserts);
+    }
     refresh();
   }
 
@@ -1743,7 +1722,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
 
     sequence.setDescription(dialog.getDescription());
@@ -1946,8 +1925,7 @@ 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, null));
+        features.add(new SequenceFeature(null, null, start, end, null));
       }
     }
 
@@ -1960,7 +1938,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               .amendFeatures(seqs, features, true, ap))
       {
         ap.alignFrame.setShowSeqFeatures(true);
-        ap.highlightSearchResults(null);
+        ap.av.setSearchResults(null); // clear highlighting
+        ap.repaint(); // draw new/amended features
       }
     }
   }