import static jalview.util.UrlConstants.DELIM;
import static jalview.util.UrlConstants.SEP;
+import jalview.util.JSONUtils;
import jalview.util.UrlLink;
-import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
* name of identifiers.org download file
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
- private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+ @SuppressWarnings("unchecked")
+private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
- JSONParser parser = new JSONParser();
-
// identifiers.org data
HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
String errorMessage = null;
try
{
+ // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+
FileReader reader = new FileReader(idFileName);
String key = "";
- JSONObject obj = (JSONObject) parser.parse(reader);
+ Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
if (obj.containsKey(ID_ORG_KEY))
{
key = ID_ORG_KEY;
return idData;
}
- JSONArray jsonarray = (JSONArray) obj.get(key);
+ List<Object> jsonarray = (List<Object>) obj.get(key);
// loop over each entry in JSON array and build HashMap entry
for (int i = 0; i < jsonarray.size(); i++)
{
- JSONObject item = (JSONObject) jsonarray.get(i);
+ Map<String, Object> item = (Map<String, Object>) jsonarray.get(i);
String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
+ DELIM;