Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AverageDistanceEngineTest	52	33	5	0.87587.5%	Show methods

Class AverageDistanceEngineTest

Class AverageDistanceEngineTest	Line # 52	Total Statements 33	Complexity 5	TOTAL Coverage 0.87587.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5555	2.02	1.01	1.0 1.0100%
loadProperties() : void   loadProperties() : void	6262	1.01	1.01	1.0 1.0100%
testUPGMAEngine() : void   testUPGMAEngine() : void	6868	30.030	3.03	0.85294116 0.8529411685.3%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.75	jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine	1PASS

 

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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.analysis;
22
23		import java.io.File;
24		import java.io.FileInputStream;
25		import java.io.IOException;
26		import java.io.InputStream;
27		import java.util.ArrayList;
28		import java.util.List;
29		import java.util.Map;
30
31		import org.junit.Assert;
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.BeforeMethod;
34		import org.testng.annotations.Test;
35
36		import jalview.bin.Cache;
37		import jalview.bin.Console;
38		import jalview.datamodel.AlignmentAnnotation;
39		import jalview.datamodel.AlignmentI;
40		import jalview.datamodel.BinaryNode;
41		import jalview.datamodel.ContactMatrixI;
42		import jalview.datamodel.SequenceI;
43		import jalview.gui.AlignFrame;
44		import jalview.gui.JvOptionPane;
45		import jalview.io.DataSourceType;
46		import jalview.io.FastaFile;
47		import jalview.io.FileLoader;
48		import jalview.io.FormatAdapter;
49		import jalview.util.Platform;
50		import jalview.ws.datamodel.alphafold.PAEContactMatrix;
51
		87.5% Uncovered Elements: 5 (40) Complexity: 5 Complexity Density: 0.15
52		public class AverageDistanceEngineTest
53		{
54
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
55	1	@BeforeClass(alwaysRun = true)...
56		public void setUpJvOptionPane()
57		{
58	1	JvOptionPane.setInteractiveMode(false);
59	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60		}
61
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
62	1	@BeforeMethod(alwaysRun = true)...
63		public void loadProperties()
64		{
65	1	Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
66		}
67
		85.3% Uncovered Elements: 5 (34) Complexity: 3 Complexity Density: 0.1 1PASS
68	1	@Test(groups = { "Functional" })...
69		public void testUPGMAEngine() throws Exception
70		{
71	1	AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
72		"examples/test_fab41.result/sample.a3m", DataSourceType.FILE);
73	1	AlignmentI seqs = af.getViewport().getAlignment();
74	1	SequenceI target = seqs.getSequenceAt(0);
75	1	File testPAE = new File(
76		"examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
77	1	List<Object> pae_obj = (List<Object>) Platform
78		.parseJSON(new FileInputStream(testPAE));
79	1	if (pae_obj == null)
80		{
81	0	Assert.fail("JSON PAE file did not parse properly.");
82		}
83	1	ContactMatrixI matrix = new PAEContactMatrix(target,
84		(Map<String, Object>) pae_obj.get(0));
85	1	AlignmentAnnotation aa = target.addContactList(matrix);
86	1	System.out.println("Matrix has max=" + matrix.getMax() + " and min="
87		+ matrix.getMin());
88	1	long start = System.currentTimeMillis();
89	1	AverageDistanceEngine clusterer = new AverageDistanceEngine(
90		af.getViewport(), null, matrix, false);
91	1	System.out.println("built a tree in "
92		+ (System.currentTimeMillis() - start) * 0.001 + " seconds.");
93	1	StringBuffer sb = new StringBuffer();
94	1	System.out.println("Newick string\n"
95		+ new jalview.io.NewickFile(clusterer.getTopNode(), true, true)
96		.print());
97
98	1	double height = clusterer.findHeight(clusterer.getTopNode());
99		// compute height fraction to cut
100		// PAE matrixes are absolute measure in angstrom, so
101		// cluster all regions within threshold (e.g. 2A) - if height above
102		// threshold. Otherwise all nodes are in one cluster
103	1	double thr = .2;
104	1	List<BinaryNode> groups;
105	1	if (height > thr)
106		{
107	1	float cut = (float) (thr / height);
108	1	System.out.println("Threshold " + cut + " for height=" + height);
109	1	groups = clusterer.groupNodes(cut);
110		}
111		else
112		{
113	0	groups = new ArrayList<BinaryNode>();
114	0	groups.add(clusterer.getTopNode());
115		}
116	1	int n = 1;
117	1	for (BinaryNode root : groups)
118		{
119	2	System.out.println("Cluster " + n++);
120	2	for (BinaryNode leaf : clusterer.findLeaves(root))
121		{
122	59	System.out.print(" " + leaf.getName());
123		}
124	2	System.out.println("\\");
125		}
126		}
127
128		}