JAL-2587 Removed annoying double repaint on hide insertions

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c7e3fd9..2c4eb7a 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -452,7 +452,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
@@ -519,7 +519,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    Map<String, List<String>> linkset = new LinkedHashMap<>();
 
     for (String link : links)
     {
@@ -603,8 +603,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * the insertion order, which is the order of the annotations on the
      * alignment.
      */
-    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
-    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
             AlignmentAnnotationUtils.asList(annotations), forSequences);
 
@@ -710,7 +710,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
-    Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+    Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
     for (int sq = 0; sq < seqs.length; sq++)
     {
 
@@ -1369,8 +1369,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * Temporary store to hold distinct calcId / type pairs for the tooltip.
      * Using TreeMap means calcIds are shown in alphabetical order.
      */
-    SortedMap<String, String> tipEntries = new TreeMap<String, String>();
-    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+    SortedMap<String, String> tipEntries = new TreeMap<>();
+    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
     AlignmentI al = this.ap.av.getAlignment();
     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
             tipEntries, candidates, al);
@@ -1445,14 +1445,28 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
+
     HiddenColumns hidden = new HiddenColumns();
-    BitSet inserts = new BitSet();
-    inserts.set(0, ap.av.getAlignment().getWidth());
+    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);
+    }
 
     boolean markedPopup = false;
     // mark inserts in current selection
     if (ap.av.getSelectionGroup() != null)
     {
+      // 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);
+
+      // now clear columns without gaps
       for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
       {
         if (sq == sequence)
@@ -1462,6 +1476,14 @@ 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();
+    }
 
     // now mark for sequence under popup if we haven't already done it
     if (!markedPopup && sequence != null)
@@ -1469,8 +1491,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       inserts.and(sequence.getInsertionsAsBits());
     }
 
-    // finally, hide and set hidden columns
+    // finally, preserve hidden regions outside selection
+    inserts.or(mask);
+
+    // and set hidden columns accordingly
     hidden.hideMarkedBits(inserts);
+
     ap.av.getAlignment().setHiddenColumns(hidden);
     refresh();
   }
@@ -1530,7 +1556,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void refresh()
   {
     ap.updateAnnotation();
-    ap.paintAlignment(true);
+    // removed paintAlignment(true) here:
+    // updateAnnotation calls paintAlignment already, so don't need to call
+    // again
 
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
   }
@@ -1899,8 +1927,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
-    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
 
     /*
      * assemble dataset sequences, and template new sequence features,
@@ -1918,11 +1946,17 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     }
 
-    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
+    /*
+     * an entirely gapped region will generate empty lists of sequence / features
+     */
+    if (!seqs.isEmpty())
     {
-      ap.alignFrame.setShowSeqFeatures(true);
-      ap.highlightSearchResults(null);
+      if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
+              seqs, features, true, ap))
+      {
+        ap.alignFrame.setShowSeqFeatures(true);
+        ap.highlightSearchResults(null);
+      }
     }
   }