+/*
+ * 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 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)
protected URL getUrl(String identifier)
{
String url = getDomain() + "/lookup/id/" + identifier
- + "?content-type=application/json";
+ + CONTENT_TYPE_JSON;
try
{
return new URL(url);
}
/**
- * 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 });
-
+
BufferedReader br = null;
try
{
{
br = getHttpResponse(url, ids);
}
- return (parseResponse(br));
+ return br == null ? null : parser.apply(br);
} catch (IOException e)
{
// ignore
}
/**
- * 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 parent;
+ 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 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;
}
}