Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 59ba8a3..4ba7e41 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -106,6 +107,16 @@ public class CrossRef
         findXrefSourcesForSequence(seq, dna, sources);
       }
     }
+    sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
+                                      // redundant datasets
+    if (dna)
+    {
+      sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
+                                           // EnsemblGenomes xref option shown
+                                           // from cdna panel
+      sources.remove(DBRefSource.ENSEMBLGENOMES);
+    }
+    // redundant datasets
     return sources;
   }
 
@@ -209,8 +220,7 @@ public class CrossRef
 
     rseqs = new ArrayList<SequenceI>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
-    matcher = new SequenceIdMatcher(
-            dataset.getSequences());
+    matcher = new SequenceIdMatcher(dataset.getSequences());
 
     for (SequenceI seq : fromSeqs)
     {
@@ -619,8 +629,7 @@ public class CrossRef
                      * attribute in equality test; this avoids creating many
                      * otherwise duplicate exon features on genomic sequence
                      */
-                    SequenceFeature newFeature = new SequenceFeature(
-                            feat)
+                    SequenceFeature newFeature = new SequenceFeature(feat)
                     {
                       @Override
                       public boolean equals(Object o)
@@ -656,6 +665,7 @@ public class CrossRef
     }
     return imported;
   }
+
   /**
    * Sets the inverse sequence mapping in the corresponding dbref of the mapped
    * to sequence (if any). This is used after fetching a cross-referenced
@@ -855,8 +865,8 @@ public class CrossRef
     MapList mapping = null;
     SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
             : mapFrom.getDatasetSequence();
-    SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo
-            : mapTo.getDatasetSequence();
+    SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo : mapTo
+            .getDatasetSequence();
     /*
      * look for a reverse mapping, if found make its inverse. 
      * Note - we do this on dataset sequences only.