Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureSettingsTest	26	101	5	0	1.0100%	Show methods

Class FeatureSettingsTest

Class FeatureSettingsTest	Line # 26	Total Statements 101	Complexity 5	Uncovered Elements 0	TOTAL Coverage 1.0100%
testSaveLoad() : void   testSaveLoad() : void	3333	78.078	1.01	0.00	1.0 1.0100%
addFeatures(SequenceI,String,int) : void   addFeatures(SequenceI,String,int) : void	173173	2.02	1.01	0.00	1.0 1.0100%
<init>, line 186()   <init>, line 186()	186186	1.01	1.01	0.00	1.0 1.0100%
addFeature(SequenceI,String,int) : void   addFeature(SequenceI,String,int) : void	179179	4.04	1.01	0.00	1.0 1.0100%
testGetColorTooltip() : void   testGetColorTooltip() : void	197197	16.016	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8396226	jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad	1PASS
	0.16037735	jalview.gui.FeatureSettingsTest.testGetColorTooltipjalview.gui.FeatureSettingsTest.testGetColorTooltip	1PASS

 

Source view

1		package jalview.gui;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertNull;
5		import static org.testng.Assert.assertTrue;
6
7		import jalview.api.FeatureColourI;
8		import jalview.datamodel.SequenceFeature;
9		import jalview.datamodel.SequenceI;
10		import jalview.datamodel.features.FeatureMatcher;
11		import jalview.datamodel.features.FeatureMatcherSet;
12		import jalview.datamodel.features.FeatureMatcherSetI;
13		import jalview.io.DataSourceType;
14		import jalview.io.FileLoader;
15		import jalview.schemes.FeatureColour;
16		import jalview.schemes.FeatureColourTest;
17		import jalview.util.matcher.Condition;
18
19		import java.awt.Color;
20		import java.io.File;
21		import java.io.IOException;
22		import java.util.HashMap;
23
24		import org.testng.annotations.Test;
25
		100% Uncovered Elements: 0 (106) Complexity: 5 Complexity Density: 0.05
26		public class FeatureSettingsTest
27		{
28		/**
29		* Test a roundtrip of save and reload of feature colours and filters as XML
30		*
31		* @throws IOException
32		*/
		100% Uncovered Elements: 0 (78) Complexity: 1 Complexity Density: 0.01 1PASS
33	1	@Test(groups = "Functional")...
34		public void testSaveLoad() throws IOException
35		{
36	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
37		">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
38	1	SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
39
40		/*
41		* add some features to the sequence
42		*/
43	1	int score = 1;
44	1	addFeatures(seq1, "type1", score++);
45	1	addFeatures(seq1, "type2", score++);
46	1	addFeatures(seq1, "type3", score++);
47	1	addFeatures(seq1, "type4", score++);
48	1	addFeatures(seq1, "type5", score++);
49
50		/*
51		* set colour schemes for features
52		*/
53	1	FeatureRenderer fr = af.getFeatureRenderer();
54
55		// type1: red
56	1	fr.setColour("type1", new FeatureColour(Color.red));
57
58		// type2: by label
59	1	FeatureColourI byLabel = new FeatureColour();
60	1	byLabel.setColourByLabel(true);
61	1	fr.setColour("type2", byLabel);
62
63		// type3: by score above threshold
64	1	FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
65		10);
66	1	byScore.setAboveThreshold(true);
67	1	byScore.setThreshold(2f);
68	1	fr.setColour("type3", byScore);
69
70		// type4: by attribute AF
71	1	FeatureColourI byAF = new FeatureColour();
72	1	byAF.setColourByLabel(true);
73	1	byAF.setAttributeName("AF");
74	1	fr.setColour("type4", byAF);
75
76		// type5: by attribute CSQ:PolyPhen below threshold
77	1	FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
78		1, 10);
79	1	byPolyPhen.setBelowThreshold(true);
80	1	byPolyPhen.setThreshold(3f);
81	1	byPolyPhen.setAttributeName("CSQ", "PolyPhen");
82	1	fr.setColour("type5", byPolyPhen);
83
84		/*
85		* set filters for feature types
86		*/
87
88		// filter type1 features by (label contains "x")
89	1	FeatureMatcherSetI filterByX = new FeatureMatcherSet();
90	1	filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
91	1	fr.setFeatureFilter("type1", filterByX);
92
93		// filter type2 features by (score <= 2.4 and score > 1.1)
94	1	FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
95	1	filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
96	1	filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
97	1	fr.setFeatureFilter("type2", filterByScore);
98
99		// filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
100	1	FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
101	1	filterByXY
102		.and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
103	1	filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
104		"PolyPhen"));
105	1	fr.setFeatureFilter("type3", filterByXY);
106
107		/*
108		* save colours and filters to an XML file
109		*/
110	1	File coloursFile = File.createTempFile("testSaveLoad", ".fc");
111	1	coloursFile.deleteOnExit();
112	1	FeatureSettings fs = new FeatureSettings(af);
113	1	fs.save(coloursFile);
114
115		/*
116		* change feature colours and filters
117		*/
118	1	FeatureColourI pink = new FeatureColour(Color.pink);
119	1	fr.setColour("type1", pink);
120	1	fr.setColour("type2", pink);
121	1	fr.setColour("type3", pink);
122	1	fr.setColour("type4", pink);
123	1	fr.setColour("type5", pink);
124
125	1	FeatureMatcherSetI filter2 = new FeatureMatcherSet();
126	1	filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
127	1	fr.setFeatureFilter("type1", filter2);
128	1	fr.setFeatureFilter("type2", filter2);
129	1	fr.setFeatureFilter("type3", filter2);
130	1	fr.setFeatureFilter("type4", filter2);
131	1	fr.setFeatureFilter("type5", filter2);
132
133		/*
134		* reload colours and filters from file and verify they are restored
135		*/
136	1	fs.load(coloursFile);
137	1	FeatureColourI fc = fr.getFeatureStyle("type1");
138	1	assertTrue(fc.isSimpleColour());
139	1	assertEquals(fc.getColour(), Color.red);
140	1	fc = fr.getFeatureStyle("type2");
141	1	assertTrue(fc.isColourByLabel());
142	1	fc = fr.getFeatureStyle("type3");
143	1	assertTrue(fc.isGraduatedColour());
144	1	assertNull(fc.getAttributeName());
145	1	assertTrue(fc.isAboveThreshold());
146	1	assertEquals(fc.getThreshold(), 2f);
147	1	fc = fr.getFeatureStyle("type4");
148	1	assertTrue(fc.isColourByLabel());
149	1	assertTrue(fc.isColourByAttribute());
150	1	assertEquals(fc.getAttributeName(), new String[] { "AF" });
151	1	fc = fr.getFeatureStyle("type5");
152	1	assertTrue(fc.isGraduatedColour());
153	1	assertTrue(fc.isColourByAttribute());
154	1	assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
155	1	assertTrue(fc.isBelowThreshold());
156	1	assertEquals(fc.getThreshold(), 3f);
157
158	1	assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
159	1	assertEquals(fr.getFeatureFilter("type2").toStableString(),
160		"(Score LE 2.4) AND (Score GT 1.1)");
161	1	assertEquals(fr.getFeatureFilter("type3").toStableString(),
162		"(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
163		}
164
165		/**
166		* Adds two features of the given type to the given sequence, also setting the
167		* score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
168		*
169		* @param seq
170		* @param featureType
171		* @param score
172		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
173	5	private void addFeatures(SequenceI seq, String featureType, int score)...
174		{
175	5	addFeature(seq, featureType, score++);
176	5	addFeature(seq, featureType, score);
177		}
178
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
179	10	private void addFeature(SequenceI seq, String featureType, int score)...
180		{
181	10	SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
182		score, "grp");
183	10	sf.setValue("AF", score);
184	10	sf.setValue("CSQ", new HashMap<String, String>()
185		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
186	10	{...
187	10	put("PolyPhen", Integer.toString(score));
188		}
189		});
190	10	seq.addSequenceFeature(sf);
191		}
192
193		/**
194		* @see FeatureColourTest#testGetDescription()
195		* @throws IOException
196		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
197	1	@Test(groups = "Functional")...
198		public void testGetColorTooltip() throws IOException
199		{
200	1	assertNull(FeatureSettings.getColorTooltip(null, false));
201
202		/*
203		* simple colour
204		*/
205	1	FeatureColourI fc = new FeatureColour(Color.black);
206	1	String simpleTooltip = "Click to edit, right-click for menu";
207	1	assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
208	1	assertNull(FeatureSettings.getColorTooltip(fc, false));
209
210		/*
211		* graduated colour tooltip includes description of colour
212		*/
213	1	fc.setColourByLabel(true);
214	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
215		"<html>By Label</html>");
216	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
217		"<html>By Label<br>" + simpleTooltip + "</br></html>");
218
219		/*
220		* graduated colour with threshold is html-encoded
221		*/
222	1	fc = new FeatureColour(Color.red, Color.blue, 2f, 10f);
223	1	fc.setBelowThreshold(true);
224	1	fc.setThreshold(4f);
225	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
226		"<html>By Score (&lt; 4.0)</html>");
227	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
228		"<html>By Score (&lt; 4.0)<br>" + simpleTooltip
229		+ "</br></html>");
230
231	1	fc.setAboveThreshold(true);
232	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
233		"<html>By Score (&gt; 4.0)</html>");
234	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
235		"<html>By Score (&gt; 4.0)<br>" + simpleTooltip
236		+ "</br></html>");
237		}
238		}