JAL-2594 avoid stack trace creating feature on gapped region

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3de7c3c..756b77b 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -57,6 +57,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Hashtable;
@@ -1444,24 +1445,59 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-    if (sequence != null)
+
+    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);
+    }
+
+    boolean markedPopup = false;
+    // mark inserts in current selection
+    if (ap.av.getSelectionGroup() != null)
     {
-      /* ColumnSelection cs = ap.av.getColumnSelection();
-       if (cs == null)
-       {
-         cs = new ColumnSelection();
-       }
-       cs.hideInsertionsFor(sequence);
-       ap.av.setColumnSelection(cs);*/
+      // mark just the columns in the selection group to be hidden
+      inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av
+              .getSelectionGroup().getEndRes() + 1);
 
-      HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
-      if (hidden == null)
+      // and clear that part of the mask
+      mask.andNot(inserts);
+
+      // now clear columns without gaps
+      for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
       {
-        hidden = new HiddenColumns();
+        if (sq == sequence)
+        {
+          markedPopup = true;
+        }
+        inserts.and(sq.getInsertionsAsBits());
       }
-      hidden.hideInsertionsFor(sequence);
-      ap.av.getAlignment().setHiddenColumns(hidden);
     }
+    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)
+    {
+      inserts.and(sequence.getInsertionsAsBits());
+    }
+
+    // finally, preserve hidden regions outside selection
+    inserts.or(mask);
+
+    // and set hidden columns accordingly
+    hidden.hideMarkedBits(inserts);
+
+    ap.av.getAlignment().setHiddenColumns(hidden);
     refresh();
   }
 
@@ -1908,11 +1944,17 @@ 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);
+      }
     }
   }