JAL-2738 lookup GRCh38/37 gene mapping

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

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
new file mode 100644 (file)
index 0000000..d522ea8
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -0,0 +1,152 @@
+package jalview.ext.ensembl;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Iterator;
+import java.util.List;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblMap extends EnsemblRestClient
+{
+
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblMap()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param
+   */
+  public EnsemblMap(String domain)
+  {
+    super(domain);
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return DBRefSource.ENSEMBL;
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null; // not used
+  }
+
+  protected URL getUrl(String species, String chromosome, String fromRef,
+          String toRef, int startPos, int endPos)
+          throws MalformedURLException
+  {
+    String url = getDomain() + "/map/" + species + "/" + fromRef + "/"
+            + chromosome + ":" + startPos + ".." + endPos + ":1/" + toRef
+            + "?content-type=application/json";
+    try
+    {
+      return new URL(url);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
+  @Override
+  protected boolean useGetRequest()
+  {
+    return true;
+  }
+
+  @Override
+  protected String getRequestMimeType(boolean multipleIds)
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected URL getUrl(List<String> ids) throws MalformedURLException
+  {
+    return null; // not used
+  }
+
+  public int[] getMapping(String species, String chromosome,
+          String fromRef, String toRef, int[] queryRange)
+  {
+    URL url = null;
+    BufferedReader br = null;
+
+    try
+    {
+      url = getUrl(species, chromosome, fromRef, toRef, queryRange[0],
+              queryRange[1]);
+      br = getHttpResponse(url, null);
+      return (parseResponse(br));
+    } catch (Throwable t)
+    {
+      System.out.println("Error calling " + url + ": " + t.getMessage());
+      return null;
+    }
+  }
+
+  /**
+   * Parses the JSON response from the /map REST service. The format is (with
+   * some fields omitted)
+   * 
+   * <pre>
+   *  {"mappings": 
+   *    [{
+   *       "original": {"end":45109016,"start":45051610},
+   *       "mapped"  : {"end":43186384,"start":43128978} 
+   *  }] }
+   * </pre>
+   * 
+   * @param br
+   * @return
+   */
+  protected int[] parseResponse(BufferedReader br)
+  {
+    int[] result = null;
+    JSONParser jp = new JSONParser();
+
+    try
+    {
+      JSONObject parsed = (JSONObject) jp.parse(br);
+      JSONArray mappings = (JSONArray) parsed.get("mappings");
+
+      Iterator rvals = mappings.iterator();
+      while (rvals.hasNext())
+      {
+        // todo check for "mapped"
+        JSONObject val = (JSONObject) rvals.next();
+        JSONObject mapped = (JSONObject) val.get("mapped");
+        String start = mapped.get("start").toString();
+        String end = mapped.get("end").toString();
+        result = new int[] { Integer.parseInt(start), Integer.parseInt(end) };
+      }
+    } catch (IOException | ParseException | NumberFormatException e)
+    {
+      // ignore
+    }
+    return result;
+  }
+
+}