Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Annotate3D	58	30	14	0.00%	Show methods
RvalsIterator	190	16	10	0.00%	Show methods

Class Annotate3D

Class Annotate3D	Line # 58	Total Statements 30	Complexity 14	TOTAL Coverage 0.00%
startJSON() : void   startJSON() : void	6969	0.00	1.01	-1.0 -1.0 -
endJSON() : void   endJSON() : void	7676	0.00	1.01	-1.0 -1.0 -
startObject() : boolean   startObject() : boolean	8383	1.01	1.01	0.0 0.00%
endObject() : boolean   endObject() : boolean	9090	1.01	1.01	0.0 0.00%
startObjectEntry(String) : boolean   startObjectEntry(String) : boolean	9797	1.01	1.01	0.0 0.00%
endObjectEntry() : boolean   endObjectEntry() : boolean	105105	1.01	1.01	0.0 0.00%
startArray() : boolean   startArray() : boolean	112112	1.01	1.01	0.0 0.00%
endArray() : boolean   endArray() : boolean	119119	1.01	1.01	0.0 0.00%
primitive(Object) : boolean   primitive(Object) : boolean	126126	1.01	1.01	0.0 0.00%
createContentHandler() : ContentHandler   createContentHandler() : ContentHandler	6464	2.02	1.01	0.0 0.00%
getRNAMLForPDBFileAsString(String) : Iterator<Reader>   getRNAMLForPDBFileAsString(String) : Iterator<Reader>	138138	8.08	1.01	0.0 0.00%
processJsonResponseFor(Reader) : Iterator<Reader>   processJsonResponseFor(Reader) : Iterator<Reader>	155155	5.05	2.02	0.0 0.00%
getRNAMLForPDBId(String) : Iterator<Reader>   getRNAMLForPDBId(String) : Iterator<Reader>	172172	8.08	1.01	0.0 0.00%

 

Class RvalsIterator

Class RvalsIterator	Line # 190	Total Statements 16	Complexity 10	TOTAL Coverage 0.00%
RvalsIterator(Reader)   RvalsIterator(Reader)	194194	1.01	1.01	0.0 0.00%
hasNext() : boolean   hasNext() : boolean	209209	1.01	1.01	0.0 0.00%
next() : Reader   next() : Reader	215215	9.09	3.03	0.0 0.00%
remove() : void   remove() : void	247247	1.01	1.01	0.0 0.00%
clone() : Object   clone() : Object	255255	1.01	1.01	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	262262	1.01	1.01	0.0 0.00%
close() : void   close() : void	268268	2.02	2.02	0.0 0.00%

 

Contributing tests

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ext.paradise;
22
23		import java.io.BufferedReader;
24		import java.io.IOException;
25		import java.io.InputStreamReader;
26		import java.io.Reader;
27		import java.io.StringReader;
28		import java.net.URL;
29		import java.util.ArrayList;
30		import java.util.Iterator;
31		import java.util.List;
32		import java.util.Map;
33
34		import org.apache.http.NameValuePair;
35		import org.apache.http.message.BasicNameValuePair;
36		import org.json.simple.parser.ContentHandler;
37		import org.json.simple.parser.ParseException;
38
39		import jalview.util.HttpUtils;
40		import jalview.util.JSONUtils;
41		import jalview.util.MessageManager;
42		import jalview.ws.HttpClientUtils;
43
44		/**
45		* simple methods for calling the various paradise RNA tools
46		*
47		* @author jimp
48		*
49		* @version v1.0 revised from original due to refactoring of
50		* paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
51		* http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/>
52		* See also testing URL from fjossinet:<br/>
53		* http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/>
54		* If in doubt, check against the REST client at:
55		* https://github.com/fjossinet/RNA-Science
56		* -Toolbox/blob/master/pyrna/restclient.py
57		*/
		0% Uncovered Elements: 43 (43) Complexity: 14 Complexity Density: 0.47
58		public class Annotate3D
59		{
60		// also test with
61		// "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d";
62		private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview";
63
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
64	0	private static ContentHandler createContentHandler()...
65		{
66	0	ContentHandler ch = new ContentHandler()
67		{
68
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
69	0	@Override...
70		public void startJSON() throws ParseException, IOException
71		{
72		// TODO Auto-generated method stub
73
74		}
75
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
76	0	@Override...
77		public void endJSON() throws ParseException, IOException
78		{
79		// TODO Auto-generated method stub
80
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public boolean startObject() throws ParseException, IOException
85		{
86		// TODO Auto-generated method stub
87	0	return false;
88		}
89
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
90	0	@Override...
91		public boolean endObject() throws ParseException, IOException
92		{
93		// TODO Auto-generated method stub
94	0	return false;
95		}
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	@Override...
98		public boolean startObjectEntry(String key)
99		throws ParseException, IOException
100		{
101		// TODO Auto-generated method stub
102	0	return false;
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	@Override...
106		public boolean endObjectEntry() throws ParseException, IOException
107		{
108		// TODO Auto-generated method stub
109	0	return false;
110		}
111
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	@Override...
113		public boolean startArray() throws ParseException, IOException
114		{
115		// TODO Auto-generated method stub
116	0	return false;
117		}
118
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
119	0	@Override...
120		public boolean endArray() throws ParseException, IOException
121		{
122		// TODO Auto-generated method stub
123	0	return false;
124		}
125
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	@Override...
127		public boolean primitive(Object value)
128		throws ParseException, IOException
129		{
130		// TODO Auto-generated method stub
131	0	return false;
132		}
133
134		};
135	0	return ch;
136		}
137
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
138	0	public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)...
139		throws Exception
140		{
141	0	List<NameValuePair> vals = new ArrayList<>();
142	0	vals.add(new BasicNameValuePair("tool", "rnaview"));
143	0	vals.add(new BasicNameValuePair("data", pdbfile));
144	0	vals.add(new BasicNameValuePair("output", "rnaml"));
145		// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
146		// vals));
147	0	ArrayList<Reader> readers = new ArrayList<>();
148	0	final BufferedReader postResponse = HttpClientUtils
149		.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
150	0	readers.add(postResponse);
151	0	return readers.iterator();
152
153		}
154
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.4
155	0	public static Iterator<Reader> processJsonResponseFor(Reader respons)...
156		throws Exception
157		{
158	0	org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
159	0	try
160		{
161	0	final RvalsIterator rvals = new RvalsIterator(respons);
162	0	return rvals;
163		} catch (Exception foo)
164		{
165	0	throw new Exception(MessageManager.getString(
166		"exception.couldnt_parse_responde_from_annotated3d_server"),
167		foo);
168		}
169
170		}
171
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
172	0	public static Iterator<Reader> getRNAMLForPDBId(String pdbid)...
173		throws Exception
174		{
175	0	List<NameValuePair> vals = new ArrayList<>();
176	0	vals.add(new BasicNameValuePair("tool", "rnaview"));
177	0	vals.add(new BasicNameValuePair("pdbid", pdbid));
178	0	vals.add(new BasicNameValuePair("output", "rnaml"));
179	0	java.net.URL geturl = new URL(twoDtoolsURL + "?tool=rnaview&pdbid="
180		+ pdbid + "&output=rnaml");
181		// return processJsonResponseFor(new
182		// InputStreamReader(geturl.openStream()));
183	0	ArrayList<Reader> readers = new ArrayList<>();
184	0	readers.add(new InputStreamReader(HttpUtils.openStream(geturl)));
185	0	return readers.iterator();
186		}
187
188		}
189
		0% Uncovered Elements: 27 (27) Complexity: 10 Complexity Density: 0.62
190		class RvalsIterator implements Iterator, AutoCloseable
191		{
192		private Iterator<Object> rvals;
193
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
194	0	@SuppressWarnings("unchecked")...
195		protected RvalsIterator(Reader respons) throws IOException, ParseException
196		{
197		/*
198		* as in 2.11.1 (pre-JalviewJS)
199		*/
200		// final JSONArray responses = (JSONArray) jp.parse(respons);
201		// this.rvals = responses.iterator();
202
203		/*
204		* as in JalviewJS (with comment that this code is never called)
205		*/
206	0	this.rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
207		}
208
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
209	0	@Override...
210		public boolean hasNext()
211		{
212	0	return rvals.hasNext();
213		}
214
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
215	0	@Override...
216		public Reader next()
217		{
218		// JSONObject val = (JSONObject) rvals.next(); // 2.11.1
219	0	@SuppressWarnings("unchecked")
220		Map<String, Object> val = (Map<String, Object>) rvals.next();
221
222	0	Object sval = null;
223	0	try
224		{
225	0	sval = val.get("2D");
226		} catch (Exception x)
227		{
228	0	x.printStackTrace();
229		}
230
231	0	if (sval == null)
232		{
233	0	jalview.bin.Console.errPrintln(
234		"DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
235		+ val.toString());
236
237	0	sval = "";
238		}
239		// 2.11.1:
240		// return new StringReader(
241		// (sval instanceof JSONObject) ? ((JSONObject) sval).toString()
242		// : sval.toString());
243	0	return new StringReader(sval.toString());
244
245		}
246
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
247	0	@Override...
248		public void remove()
249		{
250	0	throw new Error(
251		MessageManager.getString("error.not_implemented_remove"));
252
253		}
254
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
255	0	@Override...
256		protected Object clone() throws CloneNotSupportedException
257		{
258	0	throw new CloneNotSupportedException(
259		MessageManager.getString("error.not_implemented_clone"));
260		}
261
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
262	0	@Override...
263		public boolean equals(Object obj)
264		{
265	0	return super.equals(obj);
266		}
267
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
268	0	@Override...
269		public void close()
270		{
271	0	while (rvals.hasNext())
272		{
273	0	rvals.next();
274		}
275		}
276		}