Merge branch 'master' into portforward/JAL-2675_2102b1to2103

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3e2eba9..846ba64 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -455,8 +455,8 @@ 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())
       {
@@ -523,7 +523,7 @@ 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)
     {
@@ -609,8 +609,8 @@ 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);
 
@@ -716,7 +716,7 @@ 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++)
     {
 
@@ -1377,8 +1377,8 @@ 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);
@@ -1561,7 +1561,9 @@ 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());
   }
@@ -1929,8 +1931,8 @@ 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,
@@ -1944,8 +1946,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       if (start <= end)
       {
         seqs.add(sg.getSequenceAt(i).getDatasetSequence());
-        features.add(
-                new SequenceFeature(null, null, null, start, end, null));
+        features.add(new SequenceFeature(null, null, start, end, null));
       }
     }
 
@@ -1958,7 +1959,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               .amendFeatures(seqs, features, true, ap))
       {
         ap.alignFrame.setShowSeqFeatures(true);
-        ap.highlightSearchResults(null);
+        ap.av.setSearchResults(null); // clear highlighting
+        ap.repaint(); // draw new/amended features
       }
     }
   }