Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JmolVsJalviewPDBParserEndToEndTest	46	41	8	0.00%	Show methods

Class JmolVsJalviewPDBParserEndToEndTest

Class JmolVsJalviewPDBParserEndToEndTest	Line # 46	Total Statements 41	Complexity 8	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	0.0 0.00%
main(String[]) : void   main(String[]) : void	6161	8.08	3.03	0.0 0.00%
testFileParser(String,String[]) : void   testFileParser(String,String[]) : void	7878	31.031	4.04	0.0 0.00%

 

Contributing tests

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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.jmol;
22
23		import jalview.datamodel.SequenceI;
24		import jalview.gui.JvOptionPane;
25		import jalview.io.DataSourceType;
26
27		import java.io.File;
28		import java.io.IOException;
29		import java.util.HashSet;
30		import java.util.Set;
31		import java.util.Vector;
32
33		import org.testng.annotations.BeforeClass;
34
35		import mc_view.PDBfile;
36
37		/**
38		* This is not a unit test, rather it is a bulk End-to-End scan for sequences
39		* consistency for PDB files parsed with JmolParser vs. Jalview's PDBfile
40		* parser. The directory of PDB files to test must be provided in the launch
41		* args.
42		*
43		* @author tcnofoegbu
44		*
45		*/
		0% Uncovered Elements: 48 (48) Complexity: 8 Complexity Density: 0.2
46		public class JmolVsJalviewPDBParserEndToEndTest
47		{
48
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
49	0	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	0	JvOptionPane.setInteractiveMode(false);
53	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		/**
57		*
58		* @param args
59		* @j2sIgnore
60		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
61	0	public static void main(String[] args)...
62		{
63	0	if (args == null || args[0] == null)
64		{
65	0	System.err
66		.println("You must provide a PDB directory in the launch argument");
67	0	return;
68		}
69
70		// args[0] must provide the directory of PDB files to run the test with
71	0	String testDir = args[0];
72	0	System.out.println("PDB directory : " + testDir);
73	0	File pdbDir = new File(testDir);
74	0	String testFiles[] = pdbDir.list();
75	0	testFileParser(testDir, testFiles);
76		}
77
		0% Uncovered Elements: 33 (33) Complexity: 4 Complexity Density: 0.13
78	0	public static void testFileParser(String testDir, String[] testFiles)...
79		{
80	0	Set<String> failedFiles = new HashSet<>();
81	0	int totalSeqScanned = 0, totalFail = 0;
82	0	for (String pdbStr : testFiles)
83		{
84	0	String testFile = testDir + "/" + pdbStr;
85	0	PDBfile mctest = null;
86	0	JmolParser jtest = null;
87	0	try
88		{
89	0	mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
90	0	jtest = new JmolParser(testFile, DataSourceType.FILE);
91		} catch (IOException e)
92		{
93	0	System.err.println("Exception thrown while parsing : " + pdbStr);
94		}
95	0	Vector<SequenceI> seqs = jtest.getSeqs();
96	0	Vector<SequenceI> mcseqs = mctest.getSeqs();
97
98	0	for (SequenceI sq : seqs)
99		{
100	0	try
101		{
102	0	String testSeq = mcseqs.remove(0).getSequenceAsString();
103	0	if (!sq.getSequenceAsString().equals(testSeq))
104		{
105	0	++totalFail;
106	0	System.err.println("Test Failed for " + pdbStr + ". Diff:");
107	0	System.err.println(sq.getSequenceAsString());
108	0	System.err.println(testSeq);
109	0	failedFiles.add(pdbStr);
110		}
111	0	++totalSeqScanned;
112		} catch (Exception e)
113		{
114	0	e.printStackTrace();
115		}
116		}
117		}
118	0	int count = 0;
119
120	0	System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
121	0	System.out.println("Total sequence passed : "
122		+ (totalSeqScanned - totalFail));
123	0	System.out.println("Total sequence failed : " + totalFail);
124	0	System.out
125		.println("Success rate: "
126		+ ((totalSeqScanned - totalFail) * 100)
127		/ totalSeqScanned + "%");
128	0	System.out.println("\nList of " + failedFiles.size()
129		+ " file(s) with sequence diffs:");
130	0	for (String problemFile : failedFiles)
131		{
132	0	System.out.println(++count + ". " + problemFile);
133		}
134		}
135		}