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JAL-2112 optimisation of EMBL CDS parsing
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSymbol.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSymbol.java
b/src/jalview/ext/ensembl/EnsemblSymbol.java
index
5b3baa1
..
1c47f11
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/
src/jalview/ext/ensembl/EnsemblSymbol.java
@@
-13,9
+13,26
@@
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+/**
+ * A client for the Ensembl xrefs/symbol REST service;
+ *
+ * @see http://rest.ensembl.org/documentation/info/xref_external
+ * @author gmcarstairs
+ *
+ */
public class EnsemblSymbol extends EnsemblXref
{
/**
public class EnsemblSymbol extends EnsemblXref
{
/**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblSymbol(String d)
+ {
+ super(d);
+ }
+
+ /**
* Returns the first "id" value in gene identifier format from the JSON
* response, or null if none found
*
* Returns the first "id" value in gene identifier format from the JSON
* response, or null if none found
*
@@
-23,7
+40,7
@@
public class EnsemblSymbol extends EnsemblXref
* @return
* @throws IOException
*/
* @return
* @throws IOException
*/
- protected String parseResponse(BufferedReader br)
+ protected String parseSymbolResponse(BufferedReader br)
throws IOException
{
JSONParser jp = new JSONParser();
throws IOException
{
JSONParser jp = new JSONParser();
@@
-51,7
+68,7
@@
public class EnsemblSymbol extends EnsemblXref
protected URL getUrl(String id, Species species)
{
protected URL getUrl(String id, Species species)
{
- String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
+ String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
+ id
+ "?content-type=application/json";
try
+ id
+ "?content-type=application/json";
try
@@
-91,7
+108,7
@@
public class EnsemblSymbol extends EnsemblXref
{
br = getHttpResponse(url, ids);
}
{
br = getHttpResponse(url, ids);
}
- String geneId = parseResponse(br);
+ String geneId = parseSymbolResponse(br);
if (geneId != null)
{
result.add(geneId);
if (geneId != null)
{
result.add(geneId);