X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=a3a24220119426f554e883955744c0810089b9a4;hb=f0efe3029537bbbbe788e16eb85cb0af9c0fb81e;hp=8710031224b66d4d562ae880ef61c95bf0799b2d;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8710031..a3a2422 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -360,23 +360,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       });
       add(menuItem);
 
-      if (sequence.isHMMConsensusSequence())
-      {
-        JMenuItem selectHMM = new JCheckBoxMenuItem();
-        selectHMM.setText(MessageManager.getString("label.select_hmm"));
-        selectHMM.addActionListener(new ActionListener()
-        {
-
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            selectHMM_actionPerformed(e);
-          }
-        });
-        add(selectHMM);
-      }
-
-
       if (alignPanel.av.getSelectionGroup() != null
               && alignPanel.av.getSelectionGroup().getSize() > 1)
       {
@@ -1370,13 +1353,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(displayNonconserved);
   }
 
-
-  protected void selectHMM_actionPerformed(ActionEvent e)
-  {
-    SequenceI hmm = ap.av.getSequenceSelection()[0];
-    ap.alignFrame.setSelectedHMMSequence(hmm);
-  }
-
   /**
    * Constructs the entries for the colour menu
    */
@@ -1587,15 +1563,8 @@ 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
@@ -1603,10 +1572,7 @@ 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())
@@ -1617,29 +1583,18 @@ 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();
   }