import java.util.Iterator;
import java.util.List;
import java.util.StringTokenizer;
-import java.util.Vector;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
public class IdentifiersUrlProvider extends UrlProviderImpl
{
+ private static final String LOCAL_KEY = "Local";
+
+ private static final String ID_ORG_KEY = "identifiers.org";
+
// map of string ids to urls
private HashMap<String, UrlLink> urls;
try
{
FileReader reader = new FileReader(idFileName);
+ String key = "";
+ JSONObject obj = (JSONObject) parser.parse(reader);
+ if (obj.containsKey(ID_ORG_KEY))
+ {
+ key = ID_ORG_KEY;
+ }
+ else if (obj.containsKey(LOCAL_KEY))
+ {
+ key = LOCAL_KEY;
+ }
+ else
+ {
+ System.out
+ .println("Unexpected key returned from identifiers jalview service");
+ return idData;
+ }
- JSONArray jsonarray = (JSONArray) parser.parse(reader);
+ JSONArray jsonarray = (JSONArray) obj.get(key);
// loop over each entry in JSON array and build HashMap entry
for (int i = 0; i < jsonarray.size(); i++)
String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
+ DELIM;
- UrlLink link = new UrlLink((String) item.get("name") + SEP + url);
+ UrlLink link = new UrlLink((String) item.get("name"), url,
+ (String) item.get("prefix"));
idData.put((String) item.get("id"), link);
}
} catch (FileNotFoundException e)
{
e.printStackTrace();
+ idData.clear();
} catch (IOException e)
{
e.printStackTrace();
+ idData.clear();
} catch (ParseException e)
{
e.printStackTrace();
+ idData.clear();
}
return idData;
}
}
// reset defaultUrl in case it is no longer selected
- setDefaultUrl(defaultUrl);
+ setPrimaryUrl(primaryUrl);
}
@Override
- public boolean setDefaultUrl(String id)
+ public boolean setPrimaryUrl(String id)
{
- if (selectedUrls.contains(id))
+ if (urls.containsKey(id))
{
- defaultUrl = id;
+ primaryUrl = id;
}
else
{
- defaultUrl = null;
+ primaryUrl = null;
}
- return selectedUrls.contains(id);
+
+ return urls.containsKey(id);
}
@Override
}
@Override
- public Vector<String> getLinksForMenu()
+ public List<String> getLinksForMenu()
{
- Vector<String> links = new Vector<String>();
+ List<String> links = new ArrayList<String>();
for (String key : selectedUrls)
{
- links.add(urls.get(key).toString());
+ links.add(urls.get(key).toStringWithTarget());
}
return links;
}
if (isMiriamId(link.getId()))
{
// select/deselect links accordingly and set default url
-
- if (link.getIsSelected())
+ if (urls.containsKey(link.getId()))
{
- if (urls.containsKey(link.getId()))
+ if (link.getIsSelected())
{
selectedUrls.add(link.getId());
}
- if (link.getIsDefault())
+ if (link.getIsPrimary())
{
- setDefaultUrl(link.getId());
+ setPrimaryUrl(link.getId());
}
-
}
}
-
}
}
@Override
- public String getDefaultUrl(String seqid)
+ public String getPrimaryUrl(String seqid)
{
- return super.getDefaultUrl(seqid, urls);
+ return super.getPrimaryUrl(seqid, urls);
}
@Override
- public String getDefaultUrlId()
+ public String getPrimaryUrlId()
{
- return defaultUrl;
+ return primaryUrl;
}
@Override
- public String getDefaultTarget(String seqid)
+ public String getPrimaryTarget(String seqid)
{
- // TODO Auto-generated method stub
return null;
}
@Override
- public String chooseDefaultUrl()
+ public String choosePrimaryUrl()
{
- // TODO Auto-generated method stub
return null;
}
+ @Override
+ public boolean contains(String id)
+ {
+ return (urls.containsKey(id));
+ }
}