X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSymbol.java;h=ef79d72df4b7a33f1c8863d4d1ca7b42e9e59118;hb=3b74463d9ba726384240d7707b6ea416a24c6b59;hp=1c47f11ff81a0b9b5361384ad3b3fcf9ed4234af;hpb=a61896507a80dd6dcafaee02a872678022afe943;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 1c47f11..ef79d72 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -1,16 +1,33 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
-import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
@@ -22,57 +39,60 @@ import org.json.simple.parser.ParseException;
*/
public class EnsemblSymbol extends EnsemblXref
{
+ private static final String GENE = "gene";
+
+ private static final String TYPE = "type";
+
/**
* Constructor given the target domain to fetch data from
*
- * @param d
+ * @param domain
+ * @param dbName
+ * @param dbVersion
*/
- public EnsemblSymbol(String d)
+ public EnsemblSymbol(String domain, String dbName, String dbVersion)
{
- super(d);
+ super(domain, dbName, dbVersion);
}
+ // /**
+ // * Returns the first "id" value in gene identifier format from the JSON
+ // * response, or null if none found
+ // *
+ // * @param br
+ // * @return
+ // * @throws IOException
+ // */
+ // @SuppressWarnings("unchecked")
+ // protected String parseSymbolResponse(BufferedReader br) throws IOException
+ // {
+ // }
+
/**
- * Returns the first "id" value in gene identifier format from the JSON
- * response, or null if none found
+ * Constructs the URL for the REST symbol endpoint
*
- * @param br
+ * @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
- * @throws IOException
*/
- protected String parseSymbolResponse(BufferedReader br)
- throws IOException
+ protected URL getUrl(String id, Species species, String... type)
{
- JSONParser jp = new JSONParser();
- String result = null;
- try
+ StringBuilder sb = new StringBuilder();
+ sb.append(getDomain()).append("/xrefs/symbol/")
+ .append(species.toString()).append("/").append(id)
+ .append(CONTENT_TYPE_JSON);
+ for (String t : type)
{
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
- {
- JSONObject val = (JSONObject) rvals.next();
- String id = val.get("id").toString();
- if (id != null && isGeneIdentifier(id))
- {
- result = id;
- break;
- }
- }
- } catch (ParseException e)
- {
- // ignore
+ sb.append("&object_type=").append(t);
}
- return result;
- }
-
- protected URL getUrl(String id, Species species)
- {
- String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
- + id
- + "?content-type=application/json";
try
{
+ String url = sb.toString();
return new URL(url);
} catch (MalformedURLException e)
{
@@ -87,50 +107,53 @@ public class EnsemblSymbol extends EnsemblXref
* @param identifier
* @return
*/
- public List getIds(String identifier)
+ @SuppressWarnings("unchecked")
+ public List getGeneIds(String identifier)
{
List result = new ArrayList();
List ids = new ArrayList();
ids.add(identifier);
-
+
String[] queries = identifier.split(getAccessionSeparator());
- BufferedReader br = null;
try
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
- if (taxon.isModelOrganism())
+ String geneId = null;/// parseSymbolResponse(br);
+ try
{
- URL url = getUrl(query, taxon);
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- }
- String geneId = parseSymbolResponse(br);
- if (geneId != null)
+ Iterator