Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
NewickFileTests	48	49	14	0.8970588489.7%	Show methods

Class NewickFileTests

Class NewickFileTests	Line # 48	Total Statements 49	Complexity 14	TOTAL Coverage 0.8970588489.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5151	2.02	1.01	1.0 1.0100%
factoryData() : Object[]   factoryData() : Object[]	5858	1.01	1.01	1.0 1.0100%
data() : Collection   data() : Collection	6464	1.01	1.01	1.0 1.0100%
NewickFileTests(String,String)   NewickFileTests(String,String)	8282	2.02	1.01	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	9191	0.00	1.01	-1.0 -1.0 -
testTreeIO() : void   testTreeIO() : void	9696	43.043	8.08	0.8727273 0.872727387.3%
tearDownAfterClass() : void   tearDownAfterClass() : void	183183	0.00	1.01	-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.BinaryNode;
28		import jalview.datamodel.SequenceI;
29		import jalview.datamodel.SequenceNode;
30		import jalview.gui.JvOptionPane;
31
32		import java.util.Arrays;
33		import java.util.Collection;
34		import java.util.Vector;
35
36		import org.junit.runners.Parameterized.Parameters;
37		import org.testng.Assert;
38		import org.testng.AssertJUnit;
39		import org.testng.annotations.AfterClass;
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.Factory;
42		import org.testng.annotations.Test;
43
44		/**
45		* @author jimp
46		*
47		*/
		89.7% Uncovered Elements: 7 (68) Complexity: 14 Complexity Density: 0.29
48		public class NewickFileTests
49		{
50
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
51	3	@BeforeClass(alwaysRun = true)...
52		public void setUpJvOptionPane()
53		{
54	3	JvOptionPane.setInteractiveMode(false);
55	3	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56		}
57
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
58	4	@Factory...
59		public static Object[] factoryData()
60		{
61	4	return wrapDataProvider(NewickFileTests.class, data());
62		}
63
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	4	@Parameters...
65		public static Collection data()
66		{
67	4	return Arrays.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	12	public NewickFileTests(String _name, String _testTree)...
83		{
84	12	this.name = _name;
85	12	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	BinaryNode 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	BinaryNode 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<BinaryNode> oseqs, nseqs;
128	3	oseqs = new TreeModel(new SequenceI[0], null, nf,null)
129		.findLeaves(nf.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,null)
138		.findLeaves(nf_regen.getTree());
139	3	AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
140		nseqs.size() > 0);
141	3	SequenceI[] nsqs = new SequenceI[nseqs.size()];
142	22	for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
143		{
144	19	nsqs[i] = (SequenceI) nseqs.get(i).element();
145		}
146	3	AssertJUnit.assertTrue(
147		stage + " Different number of leaves (original "
148		+ olsqs.length + " and regen " + nsqs.length + ")",
149		olsqs.length == nsqs.length);
150	3	SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs),
151		nmatcher = new SequenceIdMatcher(nsqs);
152
153	3	SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
154	3	SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
155	3	String warns = "";
156	22	for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
157		{
158	19	if (nsmatches[i] == null)
159		{
160	0	warns += "\noriginal sequence ID '" + olsqs[i].getName()
161		+ "' wasn't found in regenerated set.";
162		}
163	19	if (osmatches[i] == null)
164		{
165	0	warns += "\nregenerated sequence ID '" + nsqs[i].getName()
166		+ "' wasn't found in original set.";
167		}
168		}
169
170	3	if (warns.length() > 0)
171		{
172	0	Assert.fail(stage + warns);
173		}
174		} catch (Exception x)
175		{
176	0	throw (new Exception(stage + "Exception raised", x));
177		}
178		}
179
180		/**
181		* @throws java.lang.Exception
182		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
183	3	@AfterClass(alwaysRun = true)...
184		public static void tearDownAfterClass() throws Exception
185		{
186		}
187
188		}