Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[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 19065f2..001e18e 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -62,8 +62,6 @@ import org.json.simple.parser.ParseException;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  protected static final String NAME = "Name";
-
   protected static final String DESCRIPTION = "description";
 
   /*
@@ -332,8 +330,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
          * copy exon features to protein, compute peptide variants from dna 
          * variants and add as features on the protein sequence ta-da
          */
-        AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
-                mapList);
+        // JAL-3187 render on the fly instead
+        // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
       }
     } catch (Exception e)
     {
@@ -442,10 +440,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * Parses a JSON response into a list of sequences
+   * Parses a JSON response for a single sequence ID query
    * 
    * @param br
-   * @return
+   * @return a single jalview.datamodel.Sequence
    * @see http://rest.ensembl.org/documentation/info/sequence_id
    */
   protected List<SequenceI> parseSequenceJson(BufferedReader br)
@@ -867,9 +865,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected boolean featureMayBelong(SequenceFeature sf, String identifier)
   {
     String parent = (String) sf.getValue(PARENT);
-    // using contains to allow for prefix "gene:", "transcript:" etc
     if (parent != null
-            && !parent.toUpperCase().contains(identifier.toUpperCase()))
+            && !parent.equalsIgnoreCase(identifier))
     {
       // this genomic feature belongs to a different transcript
       return false;
@@ -877,6 +874,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     return true;
   }
 
+  /**
+   * Answers a short description of the sequence fetcher
+   */
   @Override
   public String getDescription()
   {
@@ -915,10 +915,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
   /**
    * Answers true if the feature type is either 'NMD_transcript_variant' or
-   * 'transcript' or one of its sub-types in the Sequence Ontology. This is
-   * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+   * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
+   * because NMD_transcript_variant behaves like 'transcript' in Ensembl
    * although strictly speaking it is not (it is a sub-type of
    * sequence_variant).
+   * <p>
+   * (This test was needed when fetching transcript features as GFF. As we are
+   * now fetching as JSON, all features have type 'transcript' so the check for
+   * NMD_transcript_variant is redundant. Left in for any future case arising.)
    * 
    * @param featureType
    * @return