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  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.io

File NewickFileTests.java

 

Code metrics

12
49
7
1
188
140
14
0.29
7
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Classes

Class Line # Actions
NewickFileTests 48 49 14
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.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    */
 
48    public class NewickFileTests
49    {
50   
 
51  0 toggle @BeforeClass(alwaysRun = true)
52    public void setUpJvOptionPane()
53    {
54  0 JvOptionPane.setInteractiveMode(false);
55  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56    }
57   
 
58  0 toggle @Factory
59    public static Object[] factoryData()
60    {
61  0 return wrapDataProvider(NewickFileTests.class, data());
62    }
63   
 
64  0 toggle @Parameters
65    public static Collection data()
66    {
67  0 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   
 
82  0 toggle public NewickFileTests(String _name, String _testTree)
83    {
84  0 this.name = _name;
85  0 this.testTree = _testTree;
86    }
87   
88    /**
89    * @throws java.lang.Exception
90    */
 
91  0 toggle @BeforeClass(alwaysRun = true)
92    public static void setUpBeforeClass() throws Exception
93    {
94    }
95   
 
96  0 toggle @Test(groups = { "Functional" })
97    public void testTreeIO() throws Exception
98    {
99  0 String stage = "Init", treename = " '" + name + "' :";
100  0 try
101    {
102  0 stage = "Parsing testTree " + treename;
103  0 System.out.println(treename + "\n" + testTree);
104  0 NewickFile nf = new NewickFile(testTree, DataSourceType.PASTE);
105  0 nf.parse();
106  0 AssertJUnit.assertTrue(
107    stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
108    nf.isValid());
109  0 BinaryNode tree = nf.getTree();
110  0 AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
111  0 stage = "Creating newick file from testTree " + treename;
112  0 String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
113    nf.HasDistances());
114  0 AssertJUnit.assertTrue(stage + "Empty string generated",
115    gentree != null && gentree.trim().length() > 0);
116  0 stage = "Parsing regenerated testTree " + treename;
117  0 NewickFile nf_regen = new NewickFile(gentree, DataSourceType.PASTE);
118  0 nf_regen.parse();
119  0 AssertJUnit.assertTrue(
120    stage + "Newick file is invalid ('"
121    + nf_regen.getWarningMessage() + "')",
122    nf_regen.isValid());
123  0 BinaryNode tree_regen = nf.getTree();
124  0 AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
125  0 stage = "Compare original and generated tree" + treename;
126   
127  0 Vector<BinaryNode> oseqs, nseqs;
128  0 oseqs = new TreeModel(new SequenceI[0], null, nf)
129    .findLeaves(nf.getTree());
130  0 AssertJUnit.assertTrue(stage + "No nodes in original tree.",
131    oseqs.size() > 0);
132  0 SequenceI[] olsqs = new SequenceI[oseqs.size()];
133  0 for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
134    {
135  0 olsqs[i] = (SequenceI) oseqs.get(i).element();
136    }
137  0 nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
138    .findLeaves(nf_regen.getTree());
139  0 AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
140    nseqs.size() > 0);
141  0 SequenceI[] nsqs = new SequenceI[nseqs.size()];
142  0 for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
143    {
144  0 nsqs[i] = (SequenceI) nseqs.get(i).element();
145    }
146  0 AssertJUnit.assertTrue(
147    stage + " Different number of leaves (original "
148    + olsqs.length + " and regen " + nsqs.length + ")",
149    olsqs.length == nsqs.length);
150  0 SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs),
151    nmatcher = new SequenceIdMatcher(nsqs);
152   
153  0 SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
154  0 SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
155  0 String warns = "";
156  0 for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
157    {
158  0 if (nsmatches[i] == null)
159    {
160  0 warns += "\noriginal sequence ID '" + olsqs[i].getName()
161    + "' wasn't found in regenerated set.";
162    }
163  0 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  0 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    */
 
183  0 toggle @AfterClass(alwaysRun = true)
184    public static void tearDownAfterClass() throws Exception
185    {
186    }
187   
188    }