X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=856be744d8ea8637b28ea6d7654cfe81be33b31e;hb=a064561d8665ee9db217b17cda826fceac90cbbc;hp=d4d1c08ef7fbf6e5b71f6a661be1ca0f2dd4ddea;hpb=46b2bc114452c0e30463214b3e82eb0a5c98d23f;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index d4d1c08..856be74 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -4,14 +4,31 @@ import jalview.datamodel.SequenceFeature;
 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
 {
-  // TODO modify to accept other species e.g. ENSMUSPnnn
-  private static final Regex ACCESSION_REGEX = new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+  private static final List<String> CROSS_REFERENCES = Arrays
+          .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
+
+  /*
+   * 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)
@@ -21,11 +38,24 @@ 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()
   {
@@ -87,7 +117,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   protected List<String> getCrossReferenceDatabases()
   {
-    return super.getCrossReferenceDatabases();
+    return CROSS_REFERENCES;
     // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
     // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
   }