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JAL-3253 JAL-3260 SwingJS-3.2.9.v1e and tests
[jalview.git]
/
src
/
jalview
/
ext
/
paradise
/
Annotate3D.java
diff --git
a/src/jalview/ext/paradise/Annotate3D.java
b/src/jalview/ext/paradise/Annotate3D.java
index
5b75206
..
3b7044b
100644
(file)
--- a/
src/jalview/ext/paradise/Annotate3D.java
+++ b/
src/jalview/ext/paradise/Annotate3D.java
@@
-20,6
+20,7
@@
*/
package jalview.ext.paradise;
*/
package jalview.ext.paradise;
+import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
@@
-32,11
+33,10
@@
import java.net.URL;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import org.apache.http.NameValuePair;
import org.apache.http.message.BasicNameValuePair;
import org.apache.http.NameValuePair;
import org.apache.http.message.BasicNameValuePair;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
@@
-94,8
+94,8
@@
public class Annotate3D
}
@Override
}
@Override
- public boolean startObjectEntry(String key) throws ParseException,
- IOException
+ public boolean startObjectEntry(String key)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
{
// TODO Auto-generated method stub
return false;
@@
-123,8
+123,8
@@
public class Annotate3D
}
@Override
}
@Override
- public boolean primitive(Object value) throws ParseException,
- IOException
+ public boolean primitive(Object value)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
{
// TODO Auto-generated method stub
return false;
@@
-144,21
+144,26
@@
public class Annotate3D
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
- final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
- twoDtoolsURL, vals, 0, 0);
+ final BufferedReader postResponse = HttpClientUtils
+ .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
return readers.iterator();
}
readers.add(postResponse);
return readers.iterator();
}
+ /**
+ * @param respons
+ * @return
+ * @throws Exception
+ */
public static Iterator<Reader> processJsonResponseFor(Reader respons)
throws Exception
{
public static Iterator<Reader> processJsonResponseFor(Reader respons)
throws Exception
{
- org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+ // BH 2019 never called?
try
{
try
{
- final JSONArray responses = (JSONArray) jp.parse(respons);
- final Iterator rvals = responses.iterator();
+ @SuppressWarnings("unchecked")
+ final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
return new Iterator<Reader>()
{
@Override
return new Iterator<Reader>()
{
@Override
@@
-167,10
+172,11
@@
public class Annotate3D
return rvals.hasNext();
}
return rvals.hasNext();
}
- @Override
+ @SuppressWarnings("unchecked")
+ @Override
public Reader next()
{
public Reader next()
{
- JSONObject val = (JSONObject) rvals.next();
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
Object sval = null;
try
Object sval = null;
try
@@
-183,15
+189,13
@@
public class Annotate3D
;
if (sval == null)
{
;
if (sval == null)
{
- System.err
- .println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ System.err.println(
+ "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ val.toString());
sval = "";
}
+ val.toString());
sval = "";
}
- return new StringReader(
- (sval instanceof JSONObject) ? ((JSONObject) sval)
- .toString() : sval.toString());
+ return new StringReader(sval.toString());
}
}
@@
-228,9
+232,8
@@
public class Annotate3D
};
} catch (Exception foo)
{
};
} catch (Exception foo)
{
- throw new Exception(
- MessageManager
- .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+ throw new Exception(MessageManager.getString(
+ "exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
foo);
}