X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=e01ad17eaee377a850713e5af6e8fd47582859f1;hb=8d0d4cb4f21a2f15d61b90b0eb764041c664c81d;hp=b8c9c3ff5502b374732ef4c758c332fd95a26722;hpb=b03ec66ae6238b44bd20d2403d1157cadc5f0e01;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index b8c9c3f..e01ad17 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,25 +1,78 @@
+/*
+ * 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;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+
+import java.util.ArrayList;
+import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
+/**
+ * A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
+ * sequence that is transcribed to RNA, but not necessarily translated to
+ * protein)
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblCdna extends EnsemblSeqProxy
 {
   /*
-   * fetch exon features on genomic sequence (to identify the cdnaregions)
+   * accepts ENST or ENSTG with 11 digits
+   * or ENSMUST or similar for other species
+   * or CCDSnnnnn.nn with at least 3 digits
+   */
+  private static final Regex ACCESSION_REGEX = new Regex(
+          "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+
+  /*
+   * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
   public EnsemblCdna()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblCdna(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -35,7 +88,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   public Regex getAccessionValidator()
   {
-    return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+    return ACCESSION_REGEX;
   }
 
   @Override
@@ -45,35 +98,51 @@ public class EnsemblCdna extends EnsemblSeqProxy
   }
 
   /**
-   * Answers true unless the feature type is 'exon' (or a sub-type of exon in
-   * the Sequence Ontology). Exon features are only retrieved in order to
-   * identify the exon sequence range, and are redundant information on the exon
-   * sequence itself.
+   * Answers true unless the feature type is 'transcript' (or a sub-type in the
+   * Sequence Ontology).
    */
   @Override
-  protected boolean retainFeature(String type)
+  protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    return !SequenceOntology.getInstance().isA(type, SequenceOntology.EXON);
+    if (isTranscript(sf.getType()))
+    {
+      return false;
+    }
+    return featureMayBelong(sf, accessionId);
   }
 
   /**
-   * 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 (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.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))
+      String parentFeature = (String) sf.getValue(PARENT);
+      if (accId.equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+
+    return result;
+  }
+
+  /**
+   * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+   * returned (JAL-2529)
+   */
+  @Override
+  protected String getObjectType()
+  {
+    return OBJECT_TYPE_TRANSCRIPT;
   }
 
 }