JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 4f01cea..c54357e 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -483,9 +483,9 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
-    for (int ids = dsSeqs.size(); --ids >= 0;)
+    for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {
       SequenceI sq = dsSeqs.get(ids);
       boolean dupeFound = false;
@@ -494,11 +494,11 @@ public class CrossRef
       if (sq.isProtein() == fromDna)
       {
        List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
-        for (int idb = sqdbrefs.size(); --idb >= 0;)
+        for (int idb = 0, ndb = sqdbrefs.size(); idb < ndb; idb++)
         {
           DBRefEntry dbr = sqdbrefs.get(idb);  
           List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet, dbr, DBRefUtils.SEARCH_MODE_FULL);
-          for (int isr = searchrefs.size(); --isr >= 0;)
+          for (int isr = 0, nsr = searchrefs.size(); isr < nsr; isr++)
           {
             sourceRefs.remove(searchrefs.get(isr));
             dupeFound = true;
@@ -929,7 +929,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else