JAL-2679 use object_type=Transcript for lookup of Parent for Protein

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

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 6b4a1f6..bde3c0f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,8 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
 
+/**
+ * A client to fetch genomic sequence from Ensembl
+ * 
+ * TODO: not currently used - delete?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblGenome extends EnsemblSeqProxy
 {
   /*
@@ -13,15 +40,28 @@ public class EnsemblGenome extends EnsemblSeqProxy
       EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
       EnsemblFeatureType.cds, EnsemblFeatureType.variation };
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
   public EnsemblGenome()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblGenome(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (Genome)";
+    return "ENSEMBL (Genomic)";
   }
 
   @Override
@@ -38,15 +78,19 @@ public class EnsemblGenome extends EnsemblSeqProxy
 
   /**
    * Answers true unless the feature type is 'transcript' (or a sub-type of
-   * transcript in the Sequence Ontology). Transcript features are only
-   * retrieved in order to identify the transcript sequence range, and are
-   * redundant information on the transcript sequence itself.
+   * transcript in the Sequence Ontology), or has a parent other than the given
+   * accession id. Transcript features are only retrieved in order to identify
+   * the transcript sequence range, and are redundant information on the
+   * transcript sequence itself.
    */
   @Override
-  protected boolean retainFeature(String type)
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    return !SequenceOntology.getInstance().isA(type,
-            SequenceOntology.TRANSCRIPT);
+    if (isTranscript(sf.getType()))
+    {
+      return false;
+    }
+    return featureMayBelong(sf, accessionId);
   }
 
   /**
@@ -57,11 +101,10 @@ public class EnsemblGenome extends EnsemblSeqProxy
   @Override
   protected boolean identifiesSequence(SequenceFeature sf, String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.TRANSCRIPT))
+    if (isTranscript(sf.getType()))
     {
-      String parentFeature = (String) sf.getValue("ID");
-      if (("transcript:" + accId).equals(parentFeature))
+      String id = (String) sf.getValue("ID");
+      if (("transcript:" + accId).equals(id))
       {
         return true;
       }