Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureSettingsTest	27	101	5	1.0100%	Show methods

Class FeatureSettingsTest

Class FeatureSettingsTest	Line # 27	Total Statements 101	Complexity 5	TOTAL Coverage 1.0100%
testSaveLoad() : void   testSaveLoad() : void	3434	78.078	1.01	1.0 1.0100%
addFeatures(SequenceI,String,int) : void   addFeatures(SequenceI,String,int) : void	174174	2.02	1.01	1.0 1.0100%
<init>, line 187()   <init>, line 187()	187187	1.01	1.01	1.0 1.0100%
addFeature(SequenceI,String,int) : void   addFeature(SequenceI,String,int) : void	180180	4.04	1.01	1.0 1.0100%
testGetColorTooltip() : void   testGetColorTooltip() : void	198198	16.016	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	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 java.awt.Color;
8		import java.io.File;
9		import java.io.IOException;
10		import java.util.HashMap;
11
12		import org.testng.annotations.Test;
13
14		import jalview.api.FeatureColourI;
15		import jalview.datamodel.SequenceFeature;
16		import jalview.datamodel.SequenceI;
17		import jalview.datamodel.features.FeatureMatcher;
18		import jalview.datamodel.features.FeatureMatcherSet;
19		import jalview.datamodel.features.FeatureMatcherSetI;
20		import jalview.io.DataSourceType;
21		import jalview.io.FileLoader;
22		import jalview.schemes.FeatureColour;
23		import jalview.schemes.FeatureColourTest;
24		import jalview.util.matcher.Condition;
25		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
26
		100% Uncovered Elements: 0 (106) Complexity: 5 Complexity Density: 0.05
27		public class FeatureSettingsTest
28		{
29		/**
30		* Test a roundtrip of save and reload of feature colours and filters as XML
31		*
32		* @throws IOException
33		*/
		100% Uncovered Elements: 0 (78) Complexity: 1 Complexity Density: 0.01 1PASS
34	1	@Test(groups = "Functional")...
35		public void testSaveLoad() throws IOException
36		{
37	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
38		">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
39	1	SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
40
41		/*
42		* add some features to the sequence
43		*/
44	1	int score = 1;
45	1	addFeatures(seq1, "type1", score++);
46	1	addFeatures(seq1, "type2", score++);
47	1	addFeatures(seq1, "type3", score++);
48	1	addFeatures(seq1, "type4", score++);
49	1	addFeatures(seq1, "type5", score++);
50
51		/*
52		* set colour schemes for features
53		*/
54	1	FeatureRendererModel fr = af.getFeatureRenderer();
55
56		// type1: red
57	1	fr.setColour("type1", new FeatureColour(Color.red));
58
59		// type2: by label
60	1	FeatureColourI byLabel = new FeatureColour();
61	1	byLabel.setColourByLabel(true);
62	1	fr.setColour("type2", byLabel);
63
64		// type3: by score above threshold
65	1	FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
66		Color.BLUE, null, 1, 10);
67	1	byScore.setAboveThreshold(true);
68	1	byScore.setThreshold(2f);
69	1	fr.setColour("type3", byScore);
70
71		// type4: by attribute AF
72	1	FeatureColourI byAF = new FeatureColour();
73	1	byAF.setColourByLabel(true);
74	1	byAF.setAttributeName("AF");
75	1	fr.setColour("type4", byAF);
76
77		// type5: by attribute CSQ:PolyPhen below threshold
78	1	FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
79		Color.BLUE, null, 1, 10);
80	1	byPolyPhen.setBelowThreshold(true);
81	1	byPolyPhen.setThreshold(3f);
82	1	byPolyPhen.setAttributeName("CSQ", "PolyPhen");
83	1	fr.setColour("type5", byPolyPhen);
84
85		/*
86		* set filters for feature types
87		*/
88
89		// filter type1 features by (label contains "x")
90	1	FeatureMatcherSetI filterByX = new FeatureMatcherSet();
91	1	filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
92	1	fr.setFeatureFilter("type1", filterByX);
93
94		// filter type2 features by (score <= 2.4 and score > 1.1)
95	1	FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
96	1	filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
97	1	filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
98	1	fr.setFeatureFilter("type2", filterByScore);
99
100		// filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
101	1	FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
102	1	filterByXY
103		.and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
104	1	filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
105		"PolyPhen"));
106	1	fr.setFeatureFilter("type3", filterByXY);
107
108		/*
109		* save colours and filters to an XML file
110		*/
111	1	File coloursFile = File.createTempFile("testSaveLoad", ".fc");
112	1	coloursFile.deleteOnExit();
113	1	FeatureSettings fs = new FeatureSettings(af);
114	1	fs.save(coloursFile);
115
116		/*
117		* change feature colours and filters
118		*/
119	1	FeatureColourI pink = new FeatureColour(Color.pink);
120	1	fr.setColour("type1", pink);
121	1	fr.setColour("type2", pink);
122	1	fr.setColour("type3", pink);
123	1	fr.setColour("type4", pink);
124	1	fr.setColour("type5", pink);
125
126	1	FeatureMatcherSetI filter2 = new FeatureMatcherSet();
127	1	filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
128	1	fr.setFeatureFilter("type1", filter2);
129	1	fr.setFeatureFilter("type2", filter2);
130	1	fr.setFeatureFilter("type3", filter2);
131	1	fr.setFeatureFilter("type4", filter2);
132	1	fr.setFeatureFilter("type5", filter2);
133
134		/*
135		* reload colours and filters from file and verify they are restored
136		*/
137	1	fs.load(coloursFile);
138	1	FeatureColourI fc = fr.getFeatureStyle("type1");
139	1	assertTrue(fc.isSimpleColour());
140	1	assertEquals(fc.getColour(), Color.red);
141	1	fc = fr.getFeatureStyle("type2");
142	1	assertTrue(fc.isColourByLabel());
143	1	fc = fr.getFeatureStyle("type3");
144	1	assertTrue(fc.isGraduatedColour());
145	1	assertNull(fc.getAttributeName());
146	1	assertTrue(fc.isAboveThreshold());
147	1	assertEquals(fc.getThreshold(), 2f);
148	1	fc = fr.getFeatureStyle("type4");
149	1	assertTrue(fc.isColourByLabel());
150	1	assertTrue(fc.isColourByAttribute());
151	1	assertEquals(fc.getAttributeName(), new String[] { "AF" });
152	1	fc = fr.getFeatureStyle("type5");
153	1	assertTrue(fc.isGraduatedColour());
154	1	assertTrue(fc.isColourByAttribute());
155	1	assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
156	1	assertTrue(fc.isBelowThreshold());
157	1	assertEquals(fc.getThreshold(), 3f);
158
159	1	assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
160	1	assertEquals(fr.getFeatureFilter("type2").toStableString(),
161		"(Score LE 2.4) AND (Score GT 1.1)");
162	1	assertEquals(fr.getFeatureFilter("type3").toStableString(),
163		"(AF Contains X) OR (CSQ:PolyPhen NE 0)");
164		}
165
166		/**
167		* Adds two features of the given type to the given sequence, also setting the
168		* score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
169		*
170		* @param seq
171		* @param featureType
172		* @param score
173		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
174	5	private void addFeatures(SequenceI seq, String featureType, int score)...
175		{
176	5	addFeature(seq, featureType, score++);
177	5	addFeature(seq, featureType, score);
178		}
179
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
180	10	private void addFeature(SequenceI seq, String featureType, int score)...
181		{
182	10	SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
183		score, "grp");
184	10	sf.setValue("AF", score);
185	10	sf.setValue("CSQ", new HashMap<String, String>()
186		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
187	10	{...
188	10	put("PolyPhen", Integer.toString(score));
189		}
190		});
191	10	seq.addSequenceFeature(sf);
192		}
193
194		/**
195		* @see FeatureColourTest#testGetDescription()
196		* @throws IOException
197		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
198	1	@Test(groups = "Functional")...
199		public void testGetColorTooltip() throws IOException
200		{
201	1	assertNull(FeatureSettings.getColorTooltip(null, false));
202
203		/*
204		* simple colour
205		*/
206	1	FeatureColourI fc = new FeatureColour(Color.black);
207	1	String simpleTooltip = "Click to edit, right-click for menu";
208	1	assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
209	1	assertNull(FeatureSettings.getColorTooltip(fc, false));
210
211		/*
212		* graduated colour tooltip includes description of colour
213		*/
214	1	fc.setColourByLabel(true);
215	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
216		"<html>By Label</html>");
217	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
218		"<html>By Label<br>" + simpleTooltip + "</br></html>");
219
220		/*
221		* graduated colour with threshold is html-encoded
222		*/
223	1	fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
224	1	fc.setBelowThreshold(true);
225	1	fc.setThreshold(4f);
226	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
227		"<html>By Score (&lt; 4.0)</html>");
228	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
229		"<html>By Score (&lt; 4.0)<br>" + simpleTooltip
230		+ "</br></html>");
231
232	1	fc.setAboveThreshold(true);
233	1	assertEquals(FeatureSettings.getColorTooltip(fc, false),
234		"<html>By Score (&gt; 4.0)</html>");
235	1	assertEquals(FeatureSettings.getColorTooltip(fc, true),
236		"<html>By Score (&gt; 4.0)<br>" + simpleTooltip
237		+ "</br></html>");
238		}
239		}