JAL-3193 removal of rest.ensemblgenomes.org

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index e6bae9b..82c809b 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)
@@ -107,16 +107,15 @@ public class CrossRef
         findXrefSourcesForSequence(seq, dna, sources);
       }
     }
-    sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
-                                      // redundant datasets
+
+    // hack to prevent EMBL xrefs resulting in redundant datasets
+    sources.remove(DBRefSource.EMBL);
+
     if (dna)
     {
-      sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
-                                           // EnsemblGenomes xref option shown
-                                           // from cdna panel
-      sources.remove(DBRefSource.ENSEMBLGENOMES);
+      // hack to prevent Ensembl xref option shown from cdna panel
+      sources.remove(DBRefSource.ENSEMBL);
     }
-    // redundant datasets
     return sources;
   }
 
@@ -151,7 +150,7 @@ 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 +217,7 @@ 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 +429,8 @@ 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)
       {