Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Annotate3D	41	42	13	0.00%	Show methods

Class Annotate3D

Class Annotate3D	Line # 41	Total Statements 42	Complexity 13	TOTAL Coverage 0.00%
Annotate3D()   Annotate3D()	4646	1.01	1.01	0.0 0.00%
getRNAMLFor(FileParse) : AlignmentI   getRNAMLFor(FileParse) : AlignmentI	6969	20.020	7.07	0.0 0.00%
Annotate3D(String)   Annotate3D(String)	119119	21.021	5.05	0.0 0.00%

 

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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.ws.jws1;
22
23		import java.io.BufferedReader;
24		import java.io.FileReader;
25		import java.io.IOException;
26		import java.io.InputStreamReader;
27		import java.io.Reader;
28		import java.net.MalformedURLException;
29		import java.net.URL;
30		import java.net.URLEncoder;
31		import java.util.Iterator;
32
33		import jalview.datamodel.AlignmentI;
34		import jalview.io.FileFormat;
35		import jalview.io.FileParse;
36		import jalview.io.FormatAdapter;
37		import jalview.io.InputStreamParser;
38		import jalview.util.HttpUtils;
39		import jalview.util.MessageManager;
40
		0% Uncovered Elements: 59 (59) Complexity: 13 Complexity Density: 0.31
41		public class Annotate3D
42		{
43		// protected BufferedReader in;
44		// protected BufferedWriter out;
45
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public Annotate3D()...
47		{
48	0	jalview.bin.Console.outPrintln("Annotate3D");
49		// try {
50		// Create a URL for the desired page
51		// String id = "1HR2";
52		// URL url = new
53		// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
54		// in = new BufferedReader(new InputStreamReader(url.openStream()));
55		// String str;
56		// OutputStream out1 = null;
57		// out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
58		// while ((str = in.readLine()) != null) {
59		// jalview.bin.Console.outPrintln(str);
60		// out.write(str);
61		// }
62		// in.close();
63		// out.close();
64		// } catch (MalformedURLException e) {
65		// } catch (IOException e) {
66		// }
67		}
68
		0% Uncovered Elements: 30 (30) Complexity: 7 Complexity Density: 0.35
69	0	public AlignmentI getRNAMLFor(final FileParse source) throws IOException...
70		{
71	0	try
72		{
73	0	StringBuffer sb = new StringBuffer();
74
75	0	Reader fpr = source.getReader();
76	0	int p = 0;
77	0	char[] cbuff = new char[2048];
78	0	while ((p = fpr.read(cbuff)) > 0)
79		{
80	0	for (int i = 0; i < p; i++)
81		{
82	0	sb.append(cbuff[i]);
83		}
84		}
85	0	Iterator<Reader> r = jalview.ext.paradise.Annotate3D
86		.getRNAMLForPDBFileAsString(sb.toString());
87	0	AlignmentI al = null;
88	0	while (r.hasNext())
89		{
90	0	FileParse fp = new InputStreamParser(r.next(),
91		source.getDataName());
92	0	AlignmentI nal = new FormatAdapter().readFromFile(fp,
93		FileFormat.Rnaml);
94	0	if (al == null)
95		{
96	0	al = nal;
97		}
98		else
99		{
100	0	al.append(nal);
101		}
102		}
103	0	return al;
104		} catch (Throwable x)
105		{
106	0	if (x instanceof IOException)
107		{
108	0	throw ((IOException) x);
109		}
110		else
111		{
112	0	throw new IOException(MessageManager.getString(
113		"exception.unexpected_handling_rnaml_translation_for_pdb"),
114		x);
115		}
116		}
117		}
118
		0% Uncovered Elements: 25 (25) Complexity: 5 Complexity Density: 0.24
119	0	public Annotate3D(String path) throws InterruptedException...
120		{
121	0	jalview.bin.Console.outPrintln("Annotate3D");
122	0	try
123		{
124		// //URL url = new
125		// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
126		// jalview.bin.Console.outPrintln("Step1");
127		// FileReader r = new FileReader(inFile);
128		// BufferedReader in = new BufferedReader(r);
129		// StringBuffer content = new StringBuffer();
130		// jalview.bin.Console.outPrintln("Step2");
131		// while(in.readLine()!=null){
132		// content.append(in.readLine());
133		// //jalview.bin.Console.outPrintln("Step3"+in.readLine());
134		// }
135		//
136		// String data = URLEncoder.encode("data", "UTF-8") + "=" +
137		// URLEncoder.encode(content.toString(), "UTF-8");
138		// for (int i=0;i<data.length();i++)
139		// {
140		// System.out.print(data.charAt(i));
141		// }
142
143		// String data = "width=50&height=100";
144
145		// // Send the request
146		// FileReader r = new FileReader(path);
147		// BufferedReader in = new BufferedReader(r);
148		// StringBuffer content = new StringBuffer();
149		// jalview.bin.Console.outPrintln("Step1");
150		// while(in.readLine()!=null){
151		// content.append(in.readLine());
152		//
153		// }
154		// jalview.bin.Console.outPrintln("Step2");
155		// String data = URLEncoder.encode("data", "UTF-8") + "=" +
156		// URLEncoder.encode(content.toString(), "UTF-8");
157		// jalview.bin.Console.outPrintln("Step2");
158		// URL url = new
159		// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
160		// DataInputStream is = new DataInputStream(url.openStream());
161		// String str;
162		// while ((str = is.readLine()) != null) {
163		// jalview.bin.Console.outPrintln(str);
164		// //out.write(str);
165		// }
166	0	FileReader r = new FileReader(path);
167	0	BufferedReader in = new BufferedReader(r);
168	0	String content = "";
169	0	String str;
170
171	0	while ((str = in.readLine()) != null)
172		{
173		// jalview.bin.Console.outPrintln(str);
174
175	0	content = content + str;
176		}
177	0	jalview.bin.Console.outPrintln("pdbfile=" + content.toString());
178	0	jalview.bin.Console.outPrintln("capacité=" + content.length());
179	0	String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
180	0	jalview.bin.Console.outPrintln("param=" + paramfile);
181	0	URL url = new URL(
182		"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
183		+ content);
184	0	BufferedReader is = new BufferedReader(
185		new InputStreamReader(HttpUtils.openStream(url)));
186	0	String str4;
187	0	while ((str4 = is.readLine()) != null)
188		{
189	0	jalview.bin.Console.outPrintln(str4);
190		// out.write(str);
191		}
192	0	in.close();
193	0	is.close();
194
195		// HttpURLConnection connection = (HttpURLConnection)url.openConnection();
196		// connection.setRequestMethod("POST" );
197		// connection.setRequestProperty("data", path );
198		// //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
199		// BufferedReader input = new BufferedReader(new
200		// InputStreamReader(connection.getInputStream()));
201		// //DataInputStream input = new
202		// DataInputStream(connection.getInputStream());
203		// String c;
204		// while((c=input.readLine())!=null){
205		// System.out.print(c);
206		// }
207		// input.close();
208		// BufferedReader in1 = new BufferedReader(is);
209
210		// OutputStream out1 = null;
211		// jalview.bin.Console.outPrintln("Step3");
212		// BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
213		// "temp.rnaml"));
214		//
215		// in.close();
216		// out.close();
217
218		// return;
219
220		// jalview.bin.Console.outPrintln(data.length());
221		// jalview.bin.Console.outPrintln("step2");
222		// URL url = new
223		// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
224		// jalview.bin.Console.outPrintln("step3");
225		// URLConnection conn = url.openConnection();
226		// conn.setDoOutput(true);
227		// OutputStreamWriter writer = new
228		// OutputStreamWriter(conn.getOutputStream());
229
230		// write parameters
231		// writer.write(data);
232		// writer.flush();
233
234		// Get the response
235		// StringBuffer answer = new StringBuffer();
236		// //BufferedReader reader = new BufferedReader(new
237		// InputStreamReader(conn.getInputStream()));
238		// //String line;
239		// while ((line = reader.readLine()) != null) {
240		// answer.append(line);
241		// jalview.bin.Console.outPrintln(line);
242		// }
243		// writer.close();
244		// reader.close();
245
246		// Output the response
247
248		} catch (MalformedURLException ex)
249		{
250	0	ex.printStackTrace();
251		} catch (IOException ex)
252		{
253	0	ex.printStackTrace();
254		}
255		}
256
257		// in = new BufferedReader(new InputStreamReader(url.openStream()));
258
259		// String str;
260
261		// out = new FileOutputStream("temp.rnaml");
262		// out = new BufferedWriter(new FileWriter("temp.rnaml"));
263
264		// while ((str = in.readLine()) != null) {
265		// jalview.bin.Console.outPrintln(str);
266		// out.write(str);
267		// jalview.bin.Console.outPrintln(str);
268		// in.close();
269
270		// out.close();
271		// } catch (MalformedURLException e) {
272		// } catch (IOException e) {
273		// }
274		//
275		// }
276
277		// public BufferedWriter getReader()
278		// {
279		// jalview.bin.Console.outPrintln("The buffer");
280
281		// return out;
282
283		// }
284
285		}