From 58962a97c9819d186ce347072e8750dbcae16f0f Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 25 Aug 2017 14:13:48 +0100
Subject: [PATCH 1/1] JAL-2587 Removed annoying double repaint on hide
 insertions

---
 src/jalview/gui/PopupMenu.java |   22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 756b77b..2c4eb7a 100644
--- 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);
@@ -1556,7 +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());
   }
@@ -1925,8 +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,
-- 
1.7.10.2