Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges...

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 6fdb49c..76f2705 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++)
       {
@@ -835,7 +835,7 @@ public class APopupMenu extends java.awt.PopupMenu
         if (start <= end)
         {
           seqs.add(sg.getSequenceAt(i));
-          features.add(new SequenceFeature(null, null, null, start, end,
+          features.add(new SequenceFeature(null, null, start, end,
                   "Jalview"));
         }
       }
@@ -847,7 +847,8 @@ public class APopupMenu extends java.awt.PopupMenu
         {
           ap.alignFrame.sequenceFeatures.setState(true);
           ap.av.setShowSequenceFeatures(true);
-          ap.highlightSearchResults(null);
+          ap.av.setSearchResults(null); // clear highlighting
+          ap.repaint(); // draw new/amended features
         }
       }
     }
@@ -900,10 +901,7 @@ public class APopupMenu extends java.awt.PopupMenu
               .formatMessage("label.annotation_for_displayid", new Object[]
               { seq.getDisplayId(true) }));
       new SequenceAnnotationReport(null).createSequenceAnnotationReport(
-              contents, seq, true, true,
-              (ap.seqPanel.seqCanvas.fr != null)
-                      ? ap.seqPanel.seqCanvas.fr.getMinMax()
-                      : null);
+              contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
       contents.append("</p>");
     }
     Frame frame = new Frame();
@@ -929,7 +927,7 @@ public class APopupMenu extends java.awt.PopupMenu
     {
       seq.setName(dialog.getName());
       seq.setDescription(dialog.getDescription());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -1162,7 +1160,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
   void refresh()
   {
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   protected void clustalColour_actionPerformed()
@@ -1338,7 +1336,7 @@ 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()
@@ -1439,8 +1437,8 @@ 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);