Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TestAnnotate3D	48	51	17	0.00%	Show methods

Class TestAnnotate3D

Class TestAnnotate3D	Line # 48	Total Statements 51	Complexity 17	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5151	2.02	1.01	0.0 0.00%
test1GIDbyId() : void   test1GIDbyId() : void	5858	3.03	1.01	0.0 0.00%
testIdVsContent2GIS() : void   testIdVsContent2GIS() : void	6868	16.016	6.06	0.0 0.00%
testPDBfileVsRNAML() : void   testPDBfileVsRNAML() : void	112112	4.04	1.01	0.0 0.00%
testRNAMLcontent(Iterator<Reader>,PDBfile) : void   testRNAMLcontent(Iterator<Reader>,PDBfile) : void	125125	26.026	8.08	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.ext.paradise;
22
23		import java.util.Locale;
24
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30		import jalview.io.DataSourceType;
31		import jalview.io.FastaFile;
32		import jalview.io.FileFormat;
33		import jalview.io.FormatAdapter;
34
35		import java.io.BufferedReader;
36		import java.io.File;
37		import java.io.Reader;
38		import java.util.Iterator;
39
40		import org.testng.Assert;
41		import org.testng.AssertJUnit;
42		import org.testng.annotations.BeforeClass;
43		import org.testng.annotations.Test;
44
45		import compbio.util.FileUtil;
46		import mc_view.PDBfile;
47
		0% Uncovered Elements: 76 (76) Complexity: 17 Complexity Density: 0.33
48		public class TestAnnotate3D
49		{
50
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
51	0	@BeforeClass(alwaysRun = true)...
52		public void setUpJvOptionPane()
53		{
54	0	JvOptionPane.setInteractiveMode(false);
55	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56		}
57
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33 4-
58	0	@Test(groups = { "Network" }, enabled = true)...
59		public void test1GIDbyId() throws Exception
60		{
61		// use same ID as standard tests given at
62		// https://bitbucket.org/fjossinet/pyrna-rest-clients
63	0	Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
64	0	assertTrue("Didn't retrieve 1GID by id.", ids != null);
65	0	testRNAMLcontent(ids, null);
66		}
67
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.38 4-
68	0	@Test(groups = { "Network" }, enabled = true)...
69		public void testIdVsContent2GIS() throws Exception
70		{
71	0	Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
72	0	assertTrue("Didn't retrieve 2GIS by id.", ids != null);
73	0	Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
74		FileUtil.readFileToString(new File("examples/2GIS.pdb")));
75	0	assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
76	0	int i = 0;
77	0	while (ids.hasNext() && files.hasNext())
78		{
79	0	BufferedReader file = new BufferedReader(files.next()),
80		id = new BufferedReader(ids.next());
81	0	String iline, fline;
82	0	do
83		{
84	0	iline = id.readLine();
85	0	fline = file.readLine();
86	0	if (iline != null)
87		{
88	0	System.out.println(iline);
89		}
90	0	if (fline != null)
91		{
92	0	System.out.println(fline);
93		}
94		// next assert fails for latest RNAview - because the XMLID entries
95		// change between file and ID based RNAML generation.
96	0	assertTrue(
97		"Results differ for ID and file upload based retrieval (chain entry "
98		+ (++i) + ")",
99		((iline == fline && iline == null) || (iline != null
100		&& fline != null && iline.equals(fline))));
101
102	0	} while (iline != null);
103		}
104		}
105
106		/**
107		* test to demonstrate JAL-1142 - compare sequences in RNAML returned from
108		* Annotate3d vs those extracted by Jalview from the originl PDB file
109		*
110		* @throws Exception
111		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
112	0	@Test(groups = { "Network" }, enabled = true)...
113		public void testPDBfileVsRNAML() throws Exception
114		{
115	0	PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
116		DataSourceType.FILE);
117	0	Assert.assertTrue(pdbf.isValid());
118		// Comment - should add new FileParse constructor like new FileParse(Reader
119		// ..). for direct reading
120	0	Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
121		FileUtil.readFileToString(new File("examples/2GIS.pdb")));
122	0	testRNAMLcontent(readers, pdbf);
123		}
124
		0% Uncovered Elements: 38 (38) Complexity: 8 Complexity Density: 0.31
125	0	private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)...
126		throws Exception
127		{
128	0	StringBuffer sb = new StringBuffer();
129	0	int r = 0;
130	0	while (readers.hasNext())
131		{
132	0	System.out.println("Testing RNAML input number " + (++r));
133	0	BufferedReader br = new BufferedReader(readers.next());
134	0	String line;
135	0	while ((line = br.readLine()) != null)
136		{
137	0	sb.append(line + "\n");
138		}
139	0	assertTrue("No data returned by Annotate3D", sb.length() > 0);
140	0	final String lines = sb.toString();
141	0	AlignmentI al = new FormatAdapter().readFile(lines,
142		DataSourceType.PASTE, FileFormat.Rnaml);
143	0	if (al == null || al.getHeight() == 0)
144		{
145	0	System.out.println(lines);
146		}
147	0	assertTrue("No alignment returned.", al != null);
148	0	assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
149	0	if (pdbf != null)
150		{
151	0	for (SequenceI sq : al.getSequences())
152		{
153		{
154	0	SequenceI struseq = null;
155	0	String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
156	0	for (SequenceI _struseq : pdbf.getSeqsAsArray())
157		{
158	0	final String lowerCase = _struseq.getSequenceAsString()
159		.toLowerCase(Locale.ROOT);
160	0	if (lowerCase.equals(sq_))
161		{
162	0	struseq = _struseq;
163	0	break;
164		}
165		}
166	0	if (struseq == null)
167		{
168	0	AssertJUnit.fail(
169		"Couldn't find this sequence in original input:\n"
170		+ new FastaFile().print(new SequenceI[]
171		{ sq }, true) + "\n\nOriginal input:\n"
172		+ new FastaFile().print(pdbf.getSeqsAsArray(),
173		true)
174		+ "\n");
175		}
176		}
177		}
178		}
179		}
180		}
181		}