JAL-3193 removal of rest.ensemblgenomes.org

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

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 6d031b7..d6d3f3a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -21,11 +21,11 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
+import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyI;
 
-import java.util.HashMap;
-import java.util.Map;
+import java.util.ArrayList;
+import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
@@ -47,13 +47,6 @@ public class EnsemblCdna extends EnsemblSeqProxy
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
-  private static Map<String, String> params = new HashMap<String, String>();
-
-  static
-  {
-    params.put("object_type", "transcript");
-  }
-
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
@@ -70,16 +63,6 @@ public class EnsemblCdna extends EnsemblSeqProxy
     super();
   }
 
-  /**
-   * Constructor given the target domain to fetch data from
-   * 
-   * @param d
-   */
-  public EnsemblCdna(String d)
-  {
-    super(d);
-  }
-
   @Override
   public String getDbName()
   {
@@ -119,33 +102,37 @@ public class EnsemblCdna extends EnsemblSeqProxy
   }
 
   /**
-   * Answers true if the sequence feature type is 'exon' (or a subtype of exon
-   * in the Sequence Ontology), and the Parent of the feature is the transcript
-   * we are retrieving
+   * Answers a list of sequence features (if any) whose type is 'exon' (or a
+   * subtype of exon in the Sequence Ontology), and whose Parent is the
+   * transcript we are retrieving
    */
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
-            SequenceOntologyI.EXON))
+    List<SequenceFeature> result = new ArrayList<>();
+    List<SequenceFeature> sfs = seq.getFeatures()
+            .getFeaturesByOntology(SequenceOntologyI.EXON);
+    for (SequenceFeature sf : sfs)
     {
       String parentFeature = (String) sf.getValue(PARENT);
-      if (("transcript:" + accId).equals(parentFeature))
+      if (accId.equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+
+    return result;
   }
 
   /**
-   * Parameter object_type=cdna added to ensure cdna and not peptide is returned
-   * (JAL-2529)
+   * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+   * returned (JAL-2529)
    */
   @Override
-  protected Map<String, String> getAdditionalParameters()
+  protected String getObjectType()
   {
-    return params;
+    return OBJECT_TYPE_TRANSCRIPT;
   }
 
 }