JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[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 fb79ccf..97796a5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -8,6 +8,12 @@ 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
 {
   /*
@@ -21,11 +27,24 @@ public class EnsemblProtein extends EnsemblSeqProxy
   private static final List<String> CROSSREFS = Arrays.asList(new String[] {
       "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
 
+  /**
+   * 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()
   {