File FeatureSettingsTest.java

Branches:

Statements:

109

Methods:

Classes:

LOC:

299

NCLOC:

192

Total complexity:

Complexity density:

0.08

Statements/Method:

13.62

Methods/Class:

Average method complexity:

1.12

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureSettingsTest	54	109	9	0.9915966499.2%

Class FeatureSettingsTest

Class FeatureSettingsTest	Line # 54	Total Statements 109	Complexity 9	TOTAL Coverage 0.9915966499.2%
setUpBeforeClass() : void setUpBeforeClass() : void	5656	2.02	1.01	1.0 1.0100%
tearDown() : void tearDown() : void	6666	2.02	2.02	0.75 0.7575%
testSaveLoad() : void testSaveLoad() : void	7878	78.078	1.01	1.0 1.0100%
addFeatures(SequenceI,String,int) : void addFeatures(SequenceI,String,int) : void	219219	2.02	1.01	1.0 1.0100%
<init>, line 232() <init>, line 232()	232232	1.01	1.01	1.0 1.0100%
addFeature(SequenceI,String,int) : void addFeature(SequenceI,String,int) : void	225225	4.04	1.01	1.0 1.0100%
testGetColorTooltip() : void testGetColorTooltip() : void	243243	16.016	1.01	1.0 1.0100%
testIdentifyFeatureSettingsFile() : void testIdentifyFeatureSettingsFile() : void	288288	4.04	1.01	1.0 1.0100%

Contributing tests

This file is covered by 3 tests. .

Contributing tests

Test contribution	Test	Result
0.7478992	jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad	1PASS
0.14285715	jalview.gui.FeatureSettingsTest.testGetColorTooltipjalview.gui.FeatureSettingsTest.testGetColorTooltip	1PASS
0.042016808	jalview.gui.FeatureSettingsTest.testIdentifyFeatureSettingsFilejalview.gui.FeatureSettingsTest.testIdentifyFeatureSettingsFile	1PASS

Source view

* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

* Copyright (C) $$Year-Rel$$ The Jalview Authors

* This file is part of Jalview.

* Jalview is free software: you can redistribute it and/or

* modify it under the terms of the GNU General Public License

* as published by the Free Software Foundation, either version 3

* of the License, or (at your option) any later version.

* Jalview is distributed in the hope that it will be useful, but

* WITHOUT ANY WARRANTY; without even the implied warranty

* of MERCHANTABILITY or FITNESS FOR A PARTICULAR

* PURPOSE. See the GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with Jalview. If not, see <http://www.gnu.org/licenses/>.

* The Jalview Authors are detailed in the 'AUTHORS' file.

package jalview.gui;

import static org.testng.Assert.assertEquals;

import static org.testng.Assert.assertNull;

import static org.testng.Assert.assertTrue;

import java.awt.Color;

import java.io.File;

import java.io.IOException;

import java.util.HashMap;

import org.testng.annotations.AfterMethod;

import org.testng.annotations.BeforeClass;

import org.testng.annotations.Test;

import jalview.api.FeatureColourI;

import jalview.bin.Cache;

import jalview.bin.Jalview;

import jalview.datamodel.SequenceFeature;

import jalview.datamodel.SequenceI;

import jalview.datamodel.features.FeatureMatcher;

import jalview.datamodel.features.FeatureMatcherSet;

import jalview.datamodel.features.FeatureMatcherSetI;

import jalview.io.DataSourceType;

import jalview.io.FileFormat;

import jalview.io.FileFormatI;

import jalview.io.FileLoader;

import jalview.io.IdentifyFile;

import jalview.schemes.FeatureColour;

import jalview.schemes.FeatureColourTest;

import jalview.util.matcher.Condition;

import jalview.viewmodel.seqfeatures.FeatureRendererModel;

public class FeatureSettingsTest

{

@BeforeClass(alwaysRun = true)

public static void setUpBeforeClass() throws Exception

{

* use read-only test properties file

Cache.loadProperties("test/jalview/io/testProps.jvprops");

Jalview.main(new String[] { "--nonews" });

}

@AfterMethod(alwaysRun = true)

public void tearDown()

{

if (Desktop.instance != null)

Desktop.instance.closeAll_actionPerformed(null);

}

/**

* Test a roundtrip of save and reload of feature colours and filters as XML

* @throws IOException

@Test(groups = "Functional")

public void testSaveLoad() throws IOException

{

AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(

">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);

SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);

* add some features to the sequence

int score = 1;

addFeatures(seq1, "type1", score++);

addFeatures(seq1, "type2", score++);

addFeatures(seq1, "type3", score++);

addFeatures(seq1, "type4", score++);

addFeatures(seq1, "type5", score++);

* set colour schemes for features

FeatureRendererModel fr = af.getFeatureRenderer();

100

// type1: red

101

fr.setColour("type1", new FeatureColour(Color.red));

102

103

// type2: by label

104

FeatureColourI byLabel = new FeatureColour();

105

byLabel.setColourByLabel(true);

106

fr.setColour("type2", byLabel);

107

108

// type3: by score above threshold

109

FeatureColourI byScore = new FeatureColour(null, Color.BLACK,

110

Color.BLUE, null, 1, 10);

111

byScore.setAboveThreshold(true);

112

byScore.setThreshold(2f);

113

fr.setColour("type3", byScore);

114

115

// type4: by attribute AF

116

FeatureColourI byAF = new FeatureColour();

117

byAF.setColourByLabel(true);

118

byAF.setAttributeName("AF");

119

fr.setColour("type4", byAF);

120

121

// type5: by attribute CSQ:PolyPhen below threshold

122

FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,

123

Color.BLUE, null, 1, 10);

124

byPolyPhen.setBelowThreshold(true);

125

byPolyPhen.setThreshold(3f);

126

byPolyPhen.setAttributeName("CSQ", "PolyPhen");

127

fr.setColour("type5", byPolyPhen);

128

129

130

* set filters for feature types

131

132

133

// filter type1 features by (label contains "x")

134

FeatureMatcherSetI filterByX = new FeatureMatcherSet();

135

filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));

136

fr.setFeatureFilter("type1", filterByX);

137

138

// filter type2 features by (score <= 2.4 and score > 1.1)

139

FeatureMatcherSetI filterByScore = new FeatureMatcherSet();

140

filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));

141

filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));

142

fr.setFeatureFilter("type2", filterByScore);

143

144

// filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)

145

FeatureMatcherSetI filterByXY = new FeatureMatcherSet();

146

filterByXY

147

.and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));

148

filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",

149

"PolyPhen"));

150

fr.setFeatureFilter("type3", filterByXY);

151

152

153

* save colours and filters to an XML file

154

155

File coloursFile = File.createTempFile("testSaveLoad", ".fc");

156

coloursFile.deleteOnExit();

157

FeatureSettings fs = new FeatureSettings(af);

158

fs.save(coloursFile);

159

160

161

* change feature colours and filters

162

163

FeatureColourI pink = new FeatureColour(Color.pink);

164

fr.setColour("type1", pink);

165

fr.setColour("type2", pink);

166

fr.setColour("type3", pink);

167

fr.setColour("type4", pink);

168

fr.setColour("type5", pink);

169

170

FeatureMatcherSetI filter2 = new FeatureMatcherSet();

171

filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));

172

fr.setFeatureFilter("type1", filter2);

173

fr.setFeatureFilter("type2", filter2);

174

fr.setFeatureFilter("type3", filter2);

175

fr.setFeatureFilter("type4", filter2);

176

fr.setFeatureFilter("type5", filter2);

177

178

179

* reload colours and filters from file and verify they are restored

180

181

fs.load(coloursFile);

182

FeatureColourI fc = fr.getFeatureStyle("type1");

183

assertTrue(fc.isSimpleColour());

184

assertEquals(fc.getColour(), Color.red);

185

fc = fr.getFeatureStyle("type2");

186

assertTrue(fc.isColourByLabel());

187

fc = fr.getFeatureStyle("type3");

188

assertTrue(fc.isGraduatedColour());

189

assertNull(fc.getAttributeName());

190

assertTrue(fc.isAboveThreshold());

191

assertEquals(fc.getThreshold(), 2f);

192

fc = fr.getFeatureStyle("type4");

193

assertTrue(fc.isColourByLabel());

194

assertTrue(fc.isColourByAttribute());

195

assertEquals(fc.getAttributeName(), new String[] { "AF" });

196

fc = fr.getFeatureStyle("type5");

197

assertTrue(fc.isGraduatedColour());

198

assertTrue(fc.isColourByAttribute());

199

assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });

200

assertTrue(fc.isBelowThreshold());

201

assertEquals(fc.getThreshold(), 3f);

202

203

assertEquals(fr.getFeatureFilter("type1").toStableString(),

204

"Label Contains x");

205

assertEquals(fr.getFeatureFilter("type2").toStableString(),

206

"(Score LE 2.4) AND (Score GT 1.1)");

207

assertEquals(fr.getFeatureFilter("type3").toStableString(),

208

"(AF Contains X) OR (CSQ:PolyPhen NE 0)");

}

/**

* Adds two features of the given type to the given sequence, also setting the

213

* score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"

* @param seq

* @param featureType

* @param score

private void addFeatures(SequenceI seq, String featureType, int score)

220

{

221

addFeature(seq, featureType, score++);

222

addFeature(seq, featureType, score);

223

}

224

225

private void addFeature(SequenceI seq, String featureType, int score)

226

{

227

SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,

228

score, "grp");

229

sf.setValue("AF", score);

230

sf.setValue("CSQ", new HashMap<String, String>()

231

{

232

{

233

put("PolyPhen", Integer.toString(score));

234

}

235

});

236

seq.addSequenceFeature(sf);

}

/**

* @see FeatureColourTest#testGetDescription()

241

* @throws IOException

242

243

@Test(groups = "Functional")

244

public void testGetColorTooltip() throws IOException

245

{

246

assertNull(FeatureSettings.getColorTooltip(null, false));

* simple colour

FeatureColourI fc = new FeatureColour(Color.black);

252

String simpleTooltip = "Click to edit, right-click for menu";

253

assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);

254

assertNull(FeatureSettings.getColorTooltip(fc, false));

255

256

257

* graduated colour tooltip includes description of colour

258

259

fc.setColourByLabel(true);

260

assertEquals(FeatureSettings.getColorTooltip(fc, false),

261

"<html>By Label</html>");

262

assertEquals(FeatureSettings.getColorTooltip(fc, true),

263

"<html>By Label " + simpleTooltip + "</html>");

264

265

266

* graduated colour with threshold is html-encoded

267

268

fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);

269

fc.setBelowThreshold(true);

270

fc.setThreshold(4f);

271

assertEquals(FeatureSettings.getColorTooltip(fc, false),

272

"<html>By Score (< 4.0)</html>");

273

assertEquals(FeatureSettings.getColorTooltip(fc, true),

274

"<html>By Score (< 4.0) " + simpleTooltip

275

+ "</html>");

276

277

fc.setAboveThreshold(true);

278

assertEquals(FeatureSettings.getColorTooltip(fc, false),

279

"<html>By Score (> 4.0)</html>");

280

assertEquals(FeatureSettings.getColorTooltip(fc, true),

281

"<html>By Score (> 4.0) " + simpleTooltip

+ "</html>");

}

String fsfile = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">",

286

fsfile2 = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n<ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">";

287