JAL-1705 additional tests, validation regexp tweaks, javadoc

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index b2804f2..e77051d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -48,25 +48,28 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
   protected static final String NAME = "Name";
 
+  /*
+   * enum for 'type' parameter to the /sequence REST service
+   */
   public enum EnsemblSeqType
   {
     /**
-     * type=genomic for the full dna including introns
+     * type=genomic to fetch full dna including introns
      */
     GENOMIC("genomic"),
 
     /**
-     * type=cdna for transcribed dna including UTRs
+     * type=cdna to fetch dna including UTRs
      */
     CDNA("cdna"),
 
     /**
-     * type=cds for coding dna excluding UTRs
+     * type=cds to fetch coding dna excluding UTRs
      */
     CDS("cds"),
 
     /**
-     * type=protein for the peptide product sequence
+     * type=protein to fetch peptide product sequence
      */
     PROTEIN("protein");
 
@@ -201,7 +204,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * get 'dummy' genomic sequence with exon, cds and variation features
        */
       SequenceI genomicSequence = null;
-      EnsemblOverlap gffFetcher = new EnsemblOverlap();
+      EnsemblFeatures gffFetcher = new EnsemblFeatures();
       EnsemblFeatureType[] features = getFeaturesToFetch();
       AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
               features);
@@ -268,7 +271,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       MapList mapList = mapCdsToProtein(querySeq, proteinSeq);
       if (mapList != null)
       {
-        Mapping map = new Mapping(proteinSeq.getDatasetSequence(), mapList);
+        // clunky: ensure Uniprot xref if we have one is on mapped sequence
+        SequenceI ds = proteinSeq.getDatasetSequence();
+        ds.setSourceDBRef(proteinSeq.getSourceDBRef());
+        Mapping map = new Mapping(ds, mapList);
         DBRefEntry dbr = new DBRefEntry(getDbSource(), getDbVersion(),
                 accId, map);
         querySeq.getDatasetSequence().addDBRef(dbr);
@@ -919,6 +925,22 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         count++;
       }
     }
+
+    /*
+     * ugly sort to get sequence features in start position order
+     * - would be better to store in Sequence as a TreeSet instead?
+     */
+    Arrays.sort(peptide.getSequenceFeatures(),
+            new Comparator<SequenceFeature>()
+            {
+              @Override
+              public int compare(SequenceFeature o1, SequenceFeature o2)
+              {
+                int c = Integer.compare(o1.getBegin(), o2.getBegin());
+                return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
+                        : c;
+              }
+            });
     return count;
   }