X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=0d1b5540c9728a4fbb47f71ff5aa3c5f2307344f;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=eb8f90ee738dcb1391137e6d0e755284df00bdf4;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index eb8f90e..0d1b554 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -20,28 +20,40 @@
  */
 package jalview.ext.ensembl;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLociI;
+import jalview.util.MapList;
 
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.function.Function;
 
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 /**
- * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
- * identifier given a transcript identifier.
+ * A client for the Ensembl lookup REST endpoint
  * 
  * @author gmcarstairs
- *
  */
 public class EnsemblLookup extends EnsemblRestClient
 {
+  private static final String SPECIES = "species";
+
+  private static final String PARENT = "Parent";
+
+  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
+  private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+  private static final String ID = "id";
+  private static final String OBJECT_TYPE_GENE = "Gene";
+  private static final String OBJECT_TYPE = "object_type";
 
   /**
    * Default constructor (to use rest.ensembl.org)
@@ -87,7 +99,7 @@ public class EnsemblLookup extends EnsemblRestClient
   protected URL getUrl(String identifier)
   {
     String url = getDomain() + "/lookup/id/" + identifier
-            + "?content-type=application/json";
+            + CONTENT_TYPE_JSON;
     try
     {
       return new URL(url);
@@ -116,13 +128,44 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
+   * Calls the Ensembl lookup REST endpoint and returns
+   * <ul>
+   * <li>the 'id' for the identifier if its type is "Gene"</li>
+   * <li>the 'Parent' if its type is 'Transcript'</li>
+   * <ul>
+   * If the type is 'Translation', does a recursive call to this method, passing
+   * in the 'Parent' (transcript id).
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getGeneId(String identifier)
+  {
+    return (String) getResult(identifier, br -> parseGeneId(br));
+  }
+
+  /**
+   * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
    * given identifier, or null if not found
    * 
    * @param identifier
    * @return
    */
-  public String getParent(String identifier)
+  public String getSpecies(String identifier)
+  {
+    return (String) getResult(identifier, br -> getAttribute(br, SPECIES));
+  }
+
+  /**
+   * Calls the /lookup/id rest service and delegates parsing of the JSON
+   * response to the supplied parser
+   * 
+   * @param identifier
+   * @param parser
+   * @return
+   */
+  protected Object getResult(String identifier,
+          Function<BufferedReader, Object> parser)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
@@ -134,7 +177,7 @@ public class EnsemblLookup extends EnsemblRestClient
       {
         br = getHttpResponse(url, ids);
       }
-      return (parseResponse(br));
+      return br == null ? null : parser.apply(br);
     } catch (IOException e)
     {
       // ignore
@@ -155,26 +198,151 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Parses "Parent" from the JSON response and returns the value, or null if
-   * not found
+   * Answers the value of 'attribute' from the JSON response, or null if not
+   * found
    * 
    * @param br
+   * @param attribute
    * @return
-   * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  protected String getAttribute(BufferedReader br, String attribute)
   {
-    String parent = null;
+    String value = null;
     JSONParser jp = new JSONParser();
     try
     {
       JSONObject val = (JSONObject) jp.parse(br);
-      parent = val.get("Parent").toString();
-    } catch (ParseException e)
+      value = val.get(attribute).toString();
+    } catch (ParseException | NullPointerException | IOException e)
+    {
+      // ignore
+    }
+    return value;
+  }
+
+  /**
+   * Parses the JSON response and returns the gene identifier, or null if not
+   * found. If the returned object_type is Gene, returns the id, if Transcript
+   * returns the Parent. If it is Translation (peptide identifier), then the
+   * Parent is the transcript identifier, so we redo the search with this value.
+   * 
+   * @param br
+   * @return
+   */
+  protected String parseGeneId(BufferedReader br)
+  {
+    String geneId = null;
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      String type = val.get(OBJECT_TYPE).toString();
+      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+      {
+        geneId = val.get(ID).toString();
+      }
+      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+      {
+        geneId = val.get(PARENT).toString();
+      }
+      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+      {
+        String transcriptId = val.get(PARENT).toString();
+        try
+        {
+          geneId = getGeneId(transcriptId);
+        } catch (StackOverflowError e)
+        {
+          /*
+           * unlikely data condition error!
+           */
+          System.err
+                  .println("** Ensembl lookup "
+                          + getUrl(transcriptId).toString()
+                          + " looping on Parent!");
+        }
+      }
+    } catch (ParseException | IOException e)
     {
       // ignore
     }
-    return parent;
+    return geneId;
+  }
+
+  /**
+   * Calls the /lookup/id rest service for the given id, and if successful,
+   * parses and returns the gene's chromosomal coordinates
+   * 
+   * @param geneId
+   * @return
+   */
+  public GeneLociI getGeneLoci(String geneId)
+  {
+    return (GeneLociI) getResult(geneId, br -> parseGeneLoci(br));
+  }
+
+  /**
+   * Parses the /lookup/id response for species, asssembly_name,
+   * seq_region_name, start, end and returns an object that wraps them, or null
+   * if unsuccessful
+   * 
+   * @param br
+   * @return
+   */
+  GeneLociI parseGeneLoci(BufferedReader br)
+  {
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      final String species = val.get("species").toString();
+      final String assembly = val.get("assembly_name").toString();
+      final String chromosome = val.get("seq_region_name").toString();
+      String strand = val.get("strand").toString();
+      int start = Integer.parseInt(val.get("start").toString());
+      int end = Integer.parseInt(val.get("end").toString());
+      int fromEnd = end - start + 1;
+      boolean reverseStrand = "-1".equals(strand);
+      int toStart = reverseStrand ? end : start;
+      int toEnd = reverseStrand ? start : end;
+      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+          fromEnd });
+      List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+          toEnd });
+      final MapList map = new MapList(fromRange, toRange, 1, 1);
+      return new GeneLociI()
+      {
+
+        @Override
+        public String getSpeciesId()
+        {
+          return species == null ? "" : species;
+        }
+
+        @Override
+        public String getAssemblyId()
+        {
+          return assembly;
+        }
+
+        @Override
+        public String getChromosomeId()
+        {
+          return chromosome;
+        }
+
+        @Override
+        public MapList getMap()
+        {
+          return map;
+        }
+      };
+    } catch (ParseException | NullPointerException | IOException
+            | NumberFormatException | ClassCastException e)
+    {
+      Cache.log.error("Error looking up gene loci: " + e.getMessage());
+    }
+    return null;
   }
 
 }