X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblInfo.java;h=e2d2725e371c81950f1bf806288eb79083d78f66;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=de55a536430b7a62e8b809b1c37e24999a0c0fca;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index de55a53..e2d2725 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,7 +1,30 @@
+/*
+ * 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.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
+import jalview.util.JSONUtils;
import java.io.BufferedReader;
import java.io.IOException;
@@ -13,8 +36,6 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.json.simple.JSONArray;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
public class EnsemblInfo extends EnsemblRestClient
@@ -61,18 +82,6 @@ public class EnsemblInfo extends EnsemblRestClient
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Answers the domain (http://rest.ensembl.org or
* http://rest.ensemblgenomes.org) for the given division, or null if not
@@ -87,7 +96,7 @@ public class EnsemblInfo extends EnsemblRestClient
{
fetchDivisions();
}
- return divisions.get(division.toUpperCase());
+ return divisions.get(division.toUpperCase(Locale.ROOT));
}
/**
@@ -101,54 +110,17 @@ public class EnsemblInfo extends EnsemblRestClient
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST);
-
- BufferedReader br = null;
- try
- {
- URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST);
- if (url != null)
- {
- br = getHttpResponse(url, null);
- }
- parseResponse(br, ENSEMBL_GENOMES_REST);
- } catch (IOException e)
- {
- // ignore
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
-
- /**
- * Parses the JSON response to /info/divisions, and add each to the lookup map
- *
- * @param br
- * @param domain
- */
- void parseResponse(BufferedReader br, String domain)
- {
- JSONParser jp = new JSONParser();
-
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), ensemblDomain);
try
{
- JSONArray parsed = (JSONArray) jp.parse(br);
-
- Iterator rvals = parsed.iterator();
+ @SuppressWarnings("unchecked")
+ Iterator