JAL-3490 match count independent of contiguous matches count

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 14c3818..78b0dd1 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -895,11 +895,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {
@@ -910,12 +911,12 @@ public class SeqPanel extends JPanel
                 .findComplementFeaturesAtResidue(ds, pos);
         if (mf != null)
         {
-          List<String> pv = mf.findProteinVariants();
-          for (String s : pv)
+          for (SequenceFeature sf : mf.features)
           {
-            if (!infos.contains(s))
+            String pv = mf.findProteinVariants(sf);
+            if (pv.length() > 0 && !infos.contains(pv))
             {
-              infos.addAll(pv);
+              infos.add(pv);
             }
           }
         }
@@ -1065,7 +1066,7 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            seqARep.appendFeatures(tooltipText, pos, mf.features, fr2);
+            seqARep.appendFeatures(tooltipText, pos, mf, fr2);
           }
         }
       }