X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSymbol.java;h=411a244f4c245a3fd0c2a908f0493a5e0cf5ae48;hb=916c073172d5e374f7375ec718420455472dfcb3;hp=7763f29cc93d560a03ece621b0c138d87a19a914;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 7763f29..411a244 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import java.io.BufferedReader;
@@ -5,6 +25,7 @@ import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -22,6 +43,11 @@ import org.json.simple.parser.ParseException;
  */
 public class EnsemblSymbol extends EnsemblXref
 {
+  private static final String COLON = ":";
+  private static final String GENE = "gene";
+  private static final String TYPE = "type";
+  private static final String ID = "id";
+
   /**
    * Constructor given the target domain to fetch data from
    * 
@@ -42,8 +68,7 @@ public class EnsemblSymbol extends EnsemblXref
    * @return
    * @throws IOException
    */
-  protected String parseSymbolResponse(BufferedReader br)
-          throws IOException
+  protected String parseSymbolResponse(BufferedReader br) throws IOException
   {
     JSONParser jp = new JSONParser();
     String result = null;
@@ -54,8 +79,9 @@ public class EnsemblSymbol extends EnsemblXref
       while (rvals.hasNext())
       {
         JSONObject val = (JSONObject) rvals.next();
-        String id = val.get("id").toString();
-        if (id != null && isGeneIdentifier(id))
+        String id = val.get(ID).toString();
+        String type = val.get(TYPE).toString();
+        if (id != null && GENE.equals(type))
         {
           result = id;
           break;
@@ -68,12 +94,30 @@ public class EnsemblSymbol extends EnsemblXref
     return result;
   }
 
-  protected URL getUrl(String id, Species species)
+  /**
+   * Constructs the URL for the REST symbol endpoint
+   * 
+   * @param id
+   *          the accession id (Ensembl or external)
+   * @param species
+   *          a species name recognisable by Ensembl
+   * @param type
+   *          an optional type to filter the response (gene, transcript,
+   *          translation)
+   * @return
+   */
+  protected URL getUrl(String id, String species, String... type)
   {
-    String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
-            + id + "?content-type=application/json";
+    StringBuilder sb = new StringBuilder();
+    sb.append(getDomain()).append("/xrefs/symbol/").append(species)
+            .append("/").append(id).append(CONTENT_TYPE_JSON);
+    for (String t : type)
+    {
+      sb.append("&object_type=").append(t);
+    }
     try
     {
+      String url = sb.toString();
       return new URL(url);
     } catch (MalformedURLException e)
     {
@@ -82,41 +126,40 @@ public class EnsemblSymbol extends EnsemblXref
   }
 
   /**
-   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
-   * for the given identifier, for any known model organisms
+   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves gene id(s) for
+   * the given identifier. If the identifier has the format species:symbol then
+   * the gene id for the specified species is returned, else any matched gene ids
+   * for model organisms. If lookup fails, the returned list is empty.
    * 
    * @param identifier
    * @return
    */
-  public List<String> getIds(String identifier)
+  public List<String> getGeneIds(String identifier)
   {
-    List<String> result = new ArrayList<String>();
-    List<String> ids = new ArrayList<String>();
-    ids.add(identifier);
+    List<String> result = new ArrayList<>();
+    List<String> ids = Collections.<String> emptyList();
+    List<String> species = getSpecies(identifier);
 
-    String[] queries = identifier.split(getAccessionSeparator());
+    String symbol = identifier.substring(identifier.indexOf(COLON) + 1);
     BufferedReader br = null;
     try
     {
-      for (String query : queries)
-      {
-        for (Species taxon : Species.values())
+      for (String taxon : species)
         {
-          if (taxon.isModelOrganism())
+        URL url = getUrl(symbol, taxon, GENE);
+          if (url != null)
           {
-            URL url = getUrl(query, taxon);
-            if (url != null)
-            {
-              br = getHttpResponse(url, ids);
-            }
-            String geneId = parseSymbolResponse(br);
-            if (geneId != null)
+            br = getHttpResponse(url, ids);
+            if (br != null)
             {
-              result.add(geneId);
+              String geneId = parseSymbolResponse(br);
+              if (geneId != null && !result.contains(geneId))
+              {
+                result.add(geneId);
+              }
             }
           }
         }
-      }
     } catch (IOException e)
     {
       // ignore
@@ -136,4 +179,27 @@ public class EnsemblSymbol extends EnsemblXref
     return result;
   }
 
+  /**
+   * Answers a list of species names which is
+   * <ul>
+   * <li>the species in the identifier if it is of the form species:symbol</li>
+   * <li>else a fixed list of 'model organism' species</li>
+   * </ul>
+   * 
+   * @param identifier
+   * @return
+   */
+  private List<String> getSpecies(String identifier)
+  {
+    int pos = identifier.indexOf(COLON);
+    if (pos > 0)
+    {
+      return Collections.singletonList(identifier.substring(0, pos));
+    }
+    else
+    {
+      return Species.getModelOrganisms();
+    }
+  }
+
 }