Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
NewickFileTests	47	49	14	7	0.8970588489.7%	Show methods

Class NewickFileTests

Class NewickFileTests	Line # 47	Total Statements 49	Complexity 14	Uncovered Elements 7	TOTAL Coverage 0.8970588489.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.00	1.0 1.0100%
factoryData() : Object[]   factoryData() : Object[]	5757	1.01	1.01	0.00	1.0 1.0100%
data() : Collection   data() : Collection	6363	1.01	1.01	0.00	1.0 1.0100%
NewickFileTests(String,String)   NewickFileTests(String,String)	8282	2.02	1.01	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	9191	0.00	1.01	0.00	-1.0 -1.0 -
testTreeIO() : void   testTreeIO() : void	9696	43.043	8.08	7.07	0.8727273 0.872727387.3%
tearDownAfterClass() : void   tearDownAfterClass() : void	184184	0.00	1.01	0.00	-1.0 -1.0 -

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7205882	jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO	1PASS
	0.7205882	jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO	1PASS
	0.7205882	jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO	1PASS

 

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.io;
22
23		import static org.testng.ConversionUtils.wrapDataProvider;
24
25		import jalview.analysis.SequenceIdMatcher;
26		import jalview.analysis.TreeModel;
27		import jalview.datamodel.SequenceI;
28		import jalview.datamodel.SequenceNode;
29		import jalview.gui.JvOptionPane;
30
31		import java.util.Arrays;
32		import java.util.Collection;
33		import java.util.Vector;
34
35		import org.junit.runners.Parameterized.Parameters;
36		import org.testng.Assert;
37		import org.testng.AssertJUnit;
38		import org.testng.annotations.AfterClass;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Factory;
41		import org.testng.annotations.Test;
42
43		/**
44		* @author jimp
45		*
46		*/
		89.7% Uncovered Elements: 7 (68) Complexity: 14 Complexity Density: 0.29
47		public class NewickFileTests
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	3	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	3	JvOptionPane.setInteractiveMode(false);
54	3	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
57	1	@Factory...
58		public static Object[] factoryData()
59		{
60	1	return wrapDataProvider(NewickFileTests.class, data());
61		}
62
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
63	1	@Parameters...
64		public static Collection data()
65		{
66	1	return Arrays
67		.asList(new Object[][] {
68
69		new String[] {
70		"Simple uniref50 newick",
71		"(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" },
72		new String[] {
73		"Tree with quotes",
74		"('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" },
75		new String[] {
76		"Tree with double escaped comma in node",
77		"('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } });
78		};
79
80		String name, testTree;
81
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
82	3	public NewickFileTests(String _name, String _testTree)...
83		{
84	3	this.name = _name;
85	3	this.testTree = _testTree;
86		}
87
88		/**
89		* @throws java.lang.Exception
90		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
91	3	@BeforeClass(alwaysRun = true)...
92		public static void setUpBeforeClass() throws Exception
93		{
94		}
95
		87.3% Uncovered Elements: 7 (55) Complexity: 8 Complexity Density: 0.19 1PASS
96	3	@Test(groups = { "Functional" })...
97		public void testTreeIO() throws Exception
98		{
99	3	String stage = "Init", treename = " '" + name + "' :";
100	3	try
101		{
102	3	stage = "Parsing testTree " + treename;
103	3	System.out.println(treename + "\n" + testTree);
104	3	NewickFile nf = new NewickFile(testTree, DataSourceType.PASTE);
105	3	nf.parse();
106	3	AssertJUnit.assertTrue(
107		stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
108		nf.isValid());
109	3	SequenceNode tree = nf.getTree();
110	3	AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
111	3	stage = "Creating newick file from testTree " + treename;
112	3	String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
113		nf.HasDistances());
114	3	AssertJUnit.assertTrue(stage + "Empty string generated",
115		gentree != null && gentree.trim().length() > 0);
116	3	stage = "Parsing regenerated testTree " + treename;
117	3	NewickFile nf_regen = new NewickFile(gentree, DataSourceType.PASTE);
118	3	nf_regen.parse();
119	3	AssertJUnit.assertTrue(
120		stage + "Newick file is invalid ('"
121		+ nf_regen.getWarningMessage() + "')",
122		nf_regen.isValid());
123	3	SequenceNode tree_regen = nf.getTree();
124	3	AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
125	3	stage = "Compare original and generated tree" + treename;
126
127	3	Vector<SequenceNode> oseqs, nseqs;
128	3	oseqs = new TreeModel(new SequenceI[0], null, nf).findLeaves(nf
129		.getTree());
130	3	AssertJUnit.assertTrue(stage + "No nodes in original tree.",
131		oseqs.size() > 0);
132	3	SequenceI[] olsqs = new SequenceI[oseqs.size()];
133	22	for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
134		{
135	19	olsqs[i] = (SequenceI) oseqs.get(i).element();
136		}
137	3	nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
138		.findLeaves(nf_regen
139		.getTree());
140	3	AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
141		nseqs.size() > 0);
142	3	SequenceI[] nsqs = new SequenceI[nseqs.size()];
143	22	for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
144		{
145	19	nsqs[i] = (SequenceI) nseqs.get(i).element();
146		}
147	3	AssertJUnit.assertTrue(stage
148		+ " Different number of leaves (original " + olsqs.length
149		+ " and regen " + nsqs.length + ")",
150		olsqs.length == nsqs.length);
151	3	SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
152		nsqs);
153
154	3	SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
155	3	SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
156	3	String warns = "";
157	22	for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
158		{
159	19	if (nsmatches[i] == null)
160		{
161	0	warns += "\noriginal sequence ID '" + olsqs[i].getName()
162		+ "' wasn't found in regenerated set.";
163		}
164	19	if (osmatches[i] == null)
165		{
166	0	warns += "\nregenerated sequence ID '" + nsqs[i].getName()
167		+ "' wasn't found in original set.";
168		}
169		}
170
171	3	if (warns.length() > 0)
172		{
173	0	Assert.fail(stage + warns);
174		}
175		} catch (Exception x)
176		{
177	0	throw (new Exception(stage + "Exception raised", x));
178		}
179		}
180
181		/**
182		* @throws java.lang.Exception
183		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
184	3	@AfterClass(alwaysRun = true)...
185		public static void tearDownAfterClass() throws Exception
186		{
187		}
188
189		}