X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=856be744d8ea8637b28ea6d7654cfe81be33b31e;hb=a064561d8665ee9db217b17cda826fceac90cbbc;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..856be74 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,25 +1,61 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
+import java.util.Arrays;
+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
 {
+  private static final List<String> CROSS_REFERENCES = Arrays
+          .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
+
   /*
-   * 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 +71,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   public Regex getAccessionValidator()
   {
-    return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+    return ACCESSION_REGEX;
   }
 
   @Override
@@ -45,15 +81,17 @@ 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);
   }
 
   /**
@@ -64,10 +102,10 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   protected boolean identifiesSequence(SequenceFeature sf, String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.EXON))
+    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+            SequenceOntologyI.EXON))
     {
-      String parentFeature = (String) sf.getValue("Parent");
+      String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))
       {
         return true;
@@ -76,4 +114,12 @@ public class EnsemblCdna extends EnsemblSeqProxy
     return false;
   }
 
+  @Override
+  protected List<String> getCrossReferenceDatabases()
+  {
+    return CROSS_REFERENCES;
+    // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
+    // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
+  }
+
 }