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 8a57a16..0facbb5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -2,16 +2,45 @@ package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
 
+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
 {
+  /*
+   * 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(
+          "(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()
   {
@@ -47,8 +76,7 @@ public class EnsemblProtein extends EnsemblSeqProxy
    * applicable to the protein product sequence
    */
   @Override
-  protected void addFeaturesAndProduct(String accId, AlignmentI alignment,
-          SequenceI genomicSequence)
+  protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
   {
   }
 
@@ -66,4 +94,34 @@ public class EnsemblProtein extends EnsemblSeqProxy
     return false;
   }
 
+  @Override
+  public Regex getAccessionValidator()
+  {
+    return ACCESSION_REGEX;
+  }
+
+  /**
+   * Returns an accession id for a query, including conversion of ENST* to
+   * ENSP*. This supports querying for the protein sequence for a transcript
+   * (ENST identifier) and returning the ENSP identifier.
+   */
+  @Override
+  public String getAccessionIdFromQuery(String query)
+  {
+    String accId = super.getAccessionIdFromQuery(query);
+
+    /*
+     * ensure last character before (11) digits is P
+     * ENST00000288602 -> ENSP00000288602
+     * ENSMUST00000288602 -> ENSMUSP00000288602
+     */
+    if (accId != null && accId.length() >= 12)
+    {
+      char[] chars = accId.toCharArray();
+      chars[chars.length - 12] = 'P';
+      accId = new String(chars);
+    }
+    return accId;
+  }
+
 }