Merge branch 'features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview' into...

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9d44479..46bd4fd 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -383,7 +383,7 @@ public class APopupMenu extends java.awt.PopupMenu
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     Menu linkMenu = new Menu(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)
     {
@@ -485,8 +485,8 @@ public class APopupMenu extends java.awt.PopupMenu
      * 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);
@@ -825,8 +825,8 @@ public class APopupMenu extends java.awt.PopupMenu
       }
 
       int gSize = sg.getSize();
-      List<SequenceI> seqs = new ArrayList<SequenceI>();
-      List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+      List<SequenceI> seqs = new ArrayList<>();
+      List<SequenceFeature> features = new ArrayList<>();
 
       for (int i = 0; i < gSize; i++)
       {
@@ -930,7 +930,7 @@ public class APopupMenu extends java.awt.PopupMenu
     {
       seq.setName(dialog.getName());
       seq.setDescription(dialog.getDescription());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -1163,7 +1163,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
   void refresh()
   {
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   protected void clustalColour_actionPerformed()
@@ -1339,7 +1339,7 @@ public class APopupMenu extends java.awt.PopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     ap.av.getAlignment().deleteGroup(sg);
     ap.av.setSelectionGroup(null);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   void createGroupMenuItem_actionPerformed()
@@ -1440,8 +1440,8 @@ public class APopupMenu extends java.awt.PopupMenu
      * 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);