/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.paradise;
-import jalview.util.MessageManager;
-import jalview.ws.HttpClientUtils;
-
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
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.json.simple.JSONArray;
-import org.json.simple.JSONObject;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
+import jalview.ws.HttpClientUtils;
+
/**
* simple methods for calling the various paradise RNA tools
*
}
@Override
- public boolean startObjectEntry(String key) throws ParseException,
- IOException
+ public boolean startObjectEntry(String key)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
}
@Override
- public boolean primitive(Object value) throws ParseException,
- IOException
+ public boolean primitive(Object value)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
throws Exception
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("data", pdbfile));
vals.add(new BasicNameValuePair("output", "rnaml"));
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
- ArrayList<Reader> readers = new ArrayList<Reader>();
- final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
- twoDtoolsURL, vals, 0, 0);
+ ArrayList<Reader> readers = new ArrayList<>();
+ final BufferedReader postResponse = HttpClientUtils
+ .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
return readers.iterator();
org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
try
{
- final JSONArray responses = (JSONArray) jp.parse(respons);
- final Iterator rvals = responses.iterator();
- return new Iterator<Reader>()
- {
- @Override
- public boolean hasNext()
- {
- return rvals.hasNext();
- }
-
- @Override
- public Reader next()
- {
- JSONObject val = (JSONObject) rvals.next();
-
- Object sval = null;
- try
- {
- sval = val.get("2D");
- } catch (Exception x)
- {
- x.printStackTrace();
- }
- ;
- 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 :"
- + val.toString());
-
- sval = "";
- }
- return new StringReader(
- (sval instanceof JSONObject) ? ((JSONObject) sval)
- .toString() : sval.toString());
-
- }
-
- @Override
- public void remove()
- {
- throw new Error(
- MessageManager.getString("error.not_implemented_remove"));
-
- }
-
- @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);
- }
-
- @Override
- protected void finalize() throws Throwable
- {
- while (rvals.hasNext())
- {
- rvals.next();
- }
- super.finalize();
- }
- };
+ final RvalsIterator rvals = new RvalsIterator(respons);
+ return rvals;
} 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);
}
public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
throws Exception
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("pdbid", pdbid));
vals.add(new BasicNameValuePair("output", "rnaml"));
+ pdbid + "&output=rnaml");
// return processJsonResponseFor(new
// InputStreamReader(geturl.openStream()));
- ArrayList<Reader> readers = new ArrayList<Reader>();
+ ArrayList<Reader> readers = new ArrayList<>();
readers.add(new InputStreamReader(geturl.openStream()));
return readers.iterator();
}
}
+
+class RvalsIterator implements Iterator, AutoCloseable
+{
+ private Iterator<Object> rvals;
+
+ @SuppressWarnings("unchecked")
+ protected RvalsIterator(Reader respons) throws IOException, ParseException
+ {
+ /*
+ * as in 2.11.1 (pre-JalviewJS)
+ */
+ // final JSONArray responses = (JSONArray) jp.parse(respons);
+ // this.rvals = responses.iterator();
+
+ /*
+ * as in JalviewJS (with comment that this code is never called)
+ */
+ this.rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @Override
+ public Reader next()
+ {
+ // JSONObject val = (JSONObject) rvals.next(); // 2.11.1
+ @SuppressWarnings("unchecked")
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+
+ Object sval = null;
+ try
+ {
+ sval = val.get("2D");
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+
+ 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 :"
+ + val.toString());
+
+ sval = "";
+ }
+ // 2.11.1:
+ // return new StringReader(
+ // (sval instanceof JSONObject) ? ((JSONObject) sval).toString()
+ // : sval.toString());
+ return new StringReader(sval.toString());
+
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new Error(
+ MessageManager.getString("error.not_implemented_remove"));
+
+ }
+
+ @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);
+ }
+
+ @Override
+ public void close()
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff