JAL-1941 added test URL and notes about PyRNA restclient

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

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 29c7eda..0facbb5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -3,25 +3,44 @@ package jalview.ext.ensembl;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 
-import java.util.Arrays;
 import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
+/**
+ * A client to fetch protein translated sequence for an Ensembl identifier
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblProtein extends EnsemblSeqProxy
 {
-  // TODO modify to accept other species e.g. ENSMUSPnnn
+  /*
+   * accepts ENSP with 11 digits
+   * or ENSMUSP or similar for other species
+   * or CCDSnnnnn.nn with at least 3 digits
+   */
   private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENSP|CCDS)[0-9.]{3,}$");
-
-  private static final List<String> CROSSREFS = Arrays.asList(new String[] {
-      "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
+          "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
   public EnsemblProtein()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblProtein(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -76,12 +95,6 @@ public class EnsemblProtein extends EnsemblSeqProxy
   }
 
   @Override
-  protected List<String> getCrossReferenceDatabases()
-  {
-    return CROSSREFS;
-  }
-
-  @Override
   public Regex getAccessionValidator()
   {
     return ACCESSION_REGEX;