Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParsePropertiesTest	39	81	5	1.0100%	Show methods

Class ParsePropertiesTest

Class ParsePropertiesTest	Line # 39	Total Statements 81	Complexity 5	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5656	7.07	1.01	1.0 1.0100%
testGetScoresFromDescription() : void   testGetScoresFromDescription() : void	7979	20.020	1.01	1.0 1.0100%
testGetScoresFromDescription_twoScores() : void   testGetScoresFromDescription_twoScores() : void	115115	29.029	1.01	1.0 1.0100%
testGetScoresFromDescription_wordBoundaries() : void   testGetScoresFromDescription_wordBoundaries() : void	177177	23.023	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3488372	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_twoScoresjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_twoScores	1PASS
	0.27906978	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_wordBoundariesjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_wordBoundaries	1PASS
	0.24418604	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescriptionjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription	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 static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import jalview.datamodel.Alignment;
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceI;
30		import jalview.gui.AlignFrame;
31		import jalview.gui.JvOptionPane;
32
33		import java.util.List;
34
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.BeforeMethod;
37		import org.testng.annotations.Test;
38
		100% Uncovered Elements: 0 (86) Complexity: 5 Complexity Density: 0.06
39		public class ParsePropertiesTest
40		{
41
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	1	JvOptionPane.setInteractiveMode(false);
46	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
49		private Alignment al;
50
51		private ParseProperties pp;
52
53		/**
54		* Construct an alignment with 4 sequences with varying description format
55		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
56	3	@BeforeMethod(alwaysRun = true)...
57		public void setUp()
58		{
59	3	SequenceI[] seqs = new SequenceI[] {
60		new Sequence("sq1", "THISISAPLACEHOLDER"),
61		new Sequence("sq2", "THISISAPLACEHOLDER"),
62		new Sequence("sq3", "THISISAPLACEHOLDER"),
63		new Sequence("sq4", "THISISAPLACEHOLDER") };
64	3	seqs[0].setDescription("1 mydescription1");
65	3	seqs[1].setDescription("mydescription2");
66	3	seqs[2].setDescription("2. 0.1 mydescription+3");
67	3	seqs[3].setDescription("3 0.01 mydescription4");
68	3	al = new Alignment(seqs);
69
70	3	pp = new ParseProperties(al);
71
72		}
73
74		/**
75		* Test with a description pattern that matches any string ending in one or
76		* more 'number characters' (0-9+.), i.e. greedily matches any trailing
77		* numeric part of the string
78		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
79	1	@Test(groups = { "Functional" })...
80		public void testGetScoresFromDescription()
81		{
82	1	String regex = ".*([-0-9.+]+)";
83	1	final int count = pp.getScoresFromDescription("my Score",
84		"my Score Description", regex, true);
85	1	System.out.println("Matched " + count + " for " + regex);
86	1	assertEquals(4, count);
87
88		/*
89		* Verify values 1/2/3/4 have been parsed from sequence descriptions
90		*/
91	1	AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
92	1	assertEquals(1, anns.length);
93	1	assertEquals(1d, anns[0].getScore(), 0.001d);
94	1	assertEquals("my Score Description", anns[0].description);
95	1	assertEquals("my Score", anns[0].label);
96	1	anns = al.getSequenceAt(1).getAnnotation();
97	1	assertEquals(1, anns.length);
98	1	assertEquals(2d, anns[0].getScore(), 0.001d);
99	1	assertEquals("my Score Description", anns[0].description);
100	1	assertEquals("my Score", anns[0].label);
101	1	anns = al.getSequenceAt(2).getAnnotation();
102	1	assertEquals(1, anns.length);
103	1	assertEquals(3d, anns[0].getScore(), 0.001d);
104	1	anns = al.getSequenceAt(3).getAnnotation();
105	1	assertEquals(1, anns.length);
106	1	assertEquals(4d, anns[0].getScore(), 0.001d);
107		}
108
109		/**
110		* Test with a description pattern that matches any string (or none), followed
111		* by a 'number character' (0-9+.), followed by at least one separator
112		* character, followed by at least one 'number character', then any trailing
113		* characters.
114		*/
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
115	1	@Test(groups = { "Functional" })...
116		public void testGetScoresFromDescription_twoScores()
117		{
118	1	String regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
119	1	final int count = pp.getScoresFromDescription("my Score",
120		"my Score Description", regex, true);
121	1	System.out.println("Matched " + count + " for " + regex);
122	1	assertEquals(3, count);
123
124		/*
125		* Seq1 has two score values parsed out
126		*/
127	1	AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
128	1	assertEquals(2, anns.length);
129	1	assertEquals(1d, anns[0].getScore(), 0.001d);
130	1	assertEquals("my Score Description", anns[0].description);
131	1	assertEquals("my Score", anns[0].label);
132	1	assertEquals(1d, anns[1].getScore(), 0.001d);
133	1	assertEquals("my Score Description (column 1)", anns[1].description);
134	1	assertEquals("my Score_1", anns[1].label);
135
136		/*
137		* Seq2 has no score parsed out (is this right?)
138		*/
139	1	assertNull(al.getSequenceAt(1).getAnnotation());
140
141		/*
142		* Seq3 has two score values parsed out
143		*/
144		// TODO parsed values (1.0 and 3.0) look wrong v description
145		// would expect 2.0 and 0.1
146		// undesired 'greedy' behaviour of regex?
147	1	anns = al.getSequenceAt(2).getAnnotation();
148	1	assertEquals(2, anns.length);
149	1	assertEquals(1d, anns[0].getScore(), 0.001d);
150	1	assertEquals("my Score Description", anns[0].description);
151	1	assertEquals("my Score", anns[0].label);
152	1	assertEquals(3d, anns[1].getScore(), 0.001d);
153	1	assertEquals("my Score Description (column 1)", anns[1].description);
154	1	assertEquals("my Score_1", anns[1].label);
155
156		/*
157		* Seq3 has two score values parsed out
158		*/
159		// TODO parsed values (1.0 and 4.0) look wrong v description
160		// would expect 3 and 0.01
161	1	anns = al.getSequenceAt(3).getAnnotation();
162	1	assertEquals(2, anns.length);
163	1	assertEquals(1d, anns[0].getScore(), 0.001d);
164	1	assertEquals("my Score Description", anns[0].description);
165	1	assertEquals("my Score", anns[0].label);
166	1	assertEquals(4d, anns[1].getScore(), 0.001d);
167	1	assertEquals("my Score Description (column 1)", anns[1].description);
168	1	assertEquals("my Score_1", anns[1].label);
169		}
170
171		/**
172		* Test with a regex that looks for numbers separated by words - as currently
173		* used in Jalview (May 2015)
174		*
175		* @see AlignFrame.extractScores_actionPerformed
176		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
177	1	@Test(groups = { "Functional" })...
178		public void testGetScoresFromDescription_wordBoundaries()
179		{
180	1	String regex = "\\W*([-+eE0-9.]+)";
181	1	List<SequenceI> seqs = al.getSequences();
182	1	seqs.get(0).setDescription("Ferredoxin");
183	1	seqs.get(1).setDescription(" Ferredoxin-1, chloroplast precursor");
184	1	seqs.get(2).setDescription("GH28E30p");
185	1	seqs.get(3).setDescription("At1g10960/T19D16_12");
186	1	final int count = pp.getScoresFromDescription("description column",
187		"score in description column ", regex, true);
188	1	assertEquals(3, count);
189
190		/*
191		* No score parsable from seq1 description
192		*/
193	1	AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation();
194	1	assertNull(anns);
195
196		/*
197		* Seq2 description has a '1' in it
198		*/
199	1	anns = al.getSequenceAt(1).getAnnotation();
200	1	assertEquals(1, anns.length);
201	1	assertEquals(1d, anns[0].getScore(), 0.001d);
202
203		/*
204		* Seq3 description has '28E30' in it
205		*
206		* Note: 1.8E308 or larger would result in 'Infinity'
207		*/
208	1	anns = al.getSequenceAt(2).getAnnotation();
209	1	assertEquals(1, anns.length);
210	1	assertEquals(2.8E31d, anns[0].getScore(), 0.001d);
211
212		/*
213		* Seq4 description has several numbers in it
214		*/
215	1	anns = al.getSequenceAt(3).getAnnotation();
216	1	assertEquals(5, anns.length);
217	1	assertEquals(1d, anns[0].getScore(), 0.001d);
218	1	assertEquals(10960d, anns[1].getScore(), 0.001d);
219	1	assertEquals(19d, anns[2].getScore(), 0.001d);
220	1	assertEquals(16d, anns[3].getScore(), 0.001d);
221	1	assertEquals(12d, anns[4].getScore(), 0.001d);
222		}
223		}