JAL-3187 removal of variant feature (non-virtual) transfer to protein

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index e6bae9b..40401fb 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -99,7 +99,7 @@ public class CrossRef
    */
   public List<String> findXrefSourcesForSequences(boolean dna)
   {
-    List<String> sources = new ArrayList<String>();
+    List<String> sources = new ArrayList<>();
     for (SequenceI seq : fromSeqs)
     {
       if (seq != null)
@@ -151,7 +151,7 @@ public class CrossRef
        * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
        */
       DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
-      List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
+      List<SequenceI> foundSeqs = new ArrayList<>();
 
       /*
        * find sequences in the alignment which xref one of these DBRefs
@@ -218,7 +218,7 @@ public class CrossRef
   public Alignment findXrefSequences(String source, boolean fromDna)
   {
 
-    rseqs = new ArrayList<SequenceI>();
+    rseqs = new ArrayList<>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
     matcher = new SequenceIdMatcher(dataset.getSequences());
 
@@ -430,8 +430,8 @@ public class CrossRef
     if (retrieved != null)
     {
       boolean addedXref = false;
-      List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(),
-              doNotAdd = new ArrayList<SequenceI>();
+      List<SequenceI> newDsSeqs = new ArrayList<>(),
+              doNotAdd = new ArrayList<>();
 
       for (SequenceI retrievedSequence : retrieved)
       {
@@ -921,7 +921,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else