From c5e7525fa1ce59385fd3e249c2fe4056f4b5371e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Jun 2017 10:43:01 +0100
Subject: [PATCH] =?utf8?q?JAL-2291=20=E2=80=98Hide=20Insertions=E2=80=99=20n?=
 =?utf8?q?ow=20operates=20on=20selection=20or=20if=20none=20available,=20the?=
 =?utf8?q?=20sequence=20that=20was=20right-clicked=20on.?=
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---
 src/jalview/gui/PopupMenu.java |   43 +++++++++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3de7c3c..8f01162 100644
--- 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;
@@ -1444,21 +1445,39 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-    if (sequence != null)
+    HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+    if (hidden == 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)
+      hidden = new HiddenColumns();
+    }
+    if (ap.av.getSelectionGroup() != null)
+    {
+      BitSet inserts = new BitSet();
+      inserts.set(0, ap.av.getAlignment().getWidth());
+      ;
+      for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
       {
-        hidden = new HiddenColumns();
+        inserts.and(sq.getInsertionsAsBits());
       }
+      int firstSet = 0, lastSet = 0;
+      do
+      {
+        if (inserts.get(firstSet))
+        {
+          lastSet = inserts.nextClearBit(firstSet) - 1;
+          hidden.hideColumns(firstSet, lastSet);
+          firstSet = lastSet + 1;
+        }
+        else
+        {
+          firstSet = inserts.nextSetBit(firstSet);
+        }
+      } while (firstSet > -1);
+
+    }
+    else
+    if (sequence != null)
+    {
       hidden.hideInsertionsFor(sequence);
       ap.av.getAlignment().setHiddenColumns(hidden);
     }
-- 
1.7.10.2