X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=e141db4b172d18876ba472a4eefc2baf788bdea2;hb=d547268f85f377f14dbeb169072caebad45f9e2b;hp=f60125b94b97bdef9237ed8a57e017a463680d52;hpb=ef9282b464dc189faf9ce40a4b7420a204266668;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index f60125b..e141db4 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -4,15 +4,25 @@ import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
-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
 {
-  // TODO modify to accept other species e.g. ENSMUSPnnn
+  /*
+   * 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(
-          "(ENST|ENSG|CCDS)[0-9.]{3,}$");
+          "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
   
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
@@ -22,11 +32,24 @@ public class EnsemblCdna extends EnsemblSeqProxy
       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()
   {
@@ -85,12 +108,4 @@ public class EnsemblCdna extends EnsemblSeqProxy
     return false;
   }
 
-  @Override
-  protected List<String> getCrossReferenceDatabases()
-  {
-    return super.getCrossReferenceDatabases();
-    // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
-    // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
-  }
-
 }