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Merge branch 'develop' into trialMerge
[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
b8ba847
..
3c443de
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;
@@
-151,22
+151,25
@@
public class Annotate3D
}
}
+ /**
+ * @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();
try
{
try
{
- final JSONArray responses = (JSONArray) jp.parse(respons);
- final RvalsIterator rvals = new RvalsIterator(responses);
- return rvals;
+ @SuppressWarnings("unchecked")
+ List<Object> responses = (List<Object>) JSONUtils.parse(respons);
+ return new RvalsIterator(responses);
} catch (Exception foo)
{
throw new Exception(MessageManager.getString(
"exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
} catch (Exception foo)
{
throw new Exception(MessageManager.getString(
"exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
-
}
public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
}
public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
@@
-187,11
+190,11
@@
public class Annotate3D
}
}
-class RvalsIterator implements Iterator, AutoCloseable
+class RvalsIterator implements Iterator<Reader>, AutoCloseable
{
{
- private Iterator rvals;
+ private Iterator<Object> rvals;
- protected RvalsIterator(JSONArray responses)
+ protected RvalsIterator(List<Object> responses)
{
this.rvals = responses.iterator();
}
{
this.rvals = responses.iterator();
}
@@
-205,7
+208,7
@@
class RvalsIterator implements Iterator, AutoCloseable
@Override
public Reader next()
{
@Override
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
@@
-215,7
+218,6
@@
class RvalsIterator implements Iterator, AutoCloseable
{
x.printStackTrace();
}
{
x.printStackTrace();
}
- ;
if (sval == null)
{
System.err.println(
if (sval == null)
{
System.err.println(
@@
-224,31
+226,19
@@
class RvalsIterator implements Iterator, AutoCloseable
sval = "";
}
sval = "";
}
- return new StringReader(
- (sval instanceof JSONObject) ? ((JSONObject) sval).toString()
- : sval.toString());
-
+ return new StringReader(sval.toString());
}
@Override
public void remove()
{
}
@Override
public void remove()
{
- throw new Error(
- MessageManager.getString("error.not_implemented_remove"));
-
+ throw new UnsupportedOperationException();
}
@Override
protected Object clone() throws CloneNotSupportedException
{
}
@Override
protected Object clone() throws CloneNotSupportedException
{
- throw new CloneNotSupportedException(
- MessageManager.getString("error.not_implemented_clone"));
- }
-
- @Override
- public boolean equals(Object obj)
- {
- return super.equals(obj);
+ throw new UnsupportedOperationException();
}
@Override
}
@Override