2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertNull;
25 import static org.testng.Assert.assertTrue;
27 import java.awt.Color;
29 import java.io.IOException;
30 import java.util.HashMap;
32 import org.testng.annotations.AfterMethod;
33 import org.testng.annotations.BeforeClass;
34 import org.testng.annotations.Test;
36 import jalview.api.FeatureColourI;
37 import jalview.bin.Cache;
38 import jalview.bin.Jalview;
39 import jalview.datamodel.SequenceFeature;
40 import jalview.datamodel.SequenceI;
41 import jalview.datamodel.features.FeatureMatcher;
42 import jalview.datamodel.features.FeatureMatcherSet;
43 import jalview.datamodel.features.FeatureMatcherSetI;
44 import jalview.io.DataSourceType;
45 import jalview.io.FileLoader;
46 import jalview.schemes.FeatureColour;
47 import jalview.schemes.FeatureColourTest;
48 import jalview.util.matcher.Condition;
49 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
51 public class FeatureSettingsTest
53 @BeforeClass(alwaysRun = true)
54 public static void setUpBeforeClass() throws Exception
57 * use read-only test properties file
59 Cache.loadProperties("test/jalview/io/testProps.jvprops");
60 Jalview.main(new String[] { "-nonews" });
63 @AfterMethod(alwaysRun = true)
64 public void tearDown()
66 Desktop.instance.closeAll_actionPerformed(null);
70 * Test a roundtrip of save and reload of feature colours and filters as XML
74 @Test(groups = "Functional")
75 public void testSaveLoad() throws IOException
77 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
78 ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
79 SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
82 * add some features to the sequence
85 addFeatures(seq1, "type1", score++);
86 addFeatures(seq1, "type2", score++);
87 addFeatures(seq1, "type3", score++);
88 addFeatures(seq1, "type4", score++);
89 addFeatures(seq1, "type5", score++);
92 * set colour schemes for features
94 FeatureRendererModel fr = af.getFeatureRenderer();
97 fr.setColour("type1", new FeatureColour(Color.red));
100 FeatureColourI byLabel = new FeatureColour();
101 byLabel.setColourByLabel(true);
102 fr.setColour("type2", byLabel);
104 // type3: by score above threshold
105 FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
106 Color.BLUE, null, 1, 10);
107 byScore.setAboveThreshold(true);
108 byScore.setThreshold(2f);
109 fr.setColour("type3", byScore);
111 // type4: by attribute AF
112 FeatureColourI byAF = new FeatureColour();
113 byAF.setColourByLabel(true);
114 byAF.setAttributeName("AF");
115 fr.setColour("type4", byAF);
117 // type5: by attribute CSQ:PolyPhen below threshold
118 FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
119 Color.BLUE, null, 1, 10);
120 byPolyPhen.setBelowThreshold(true);
121 byPolyPhen.setThreshold(3f);
122 byPolyPhen.setAttributeName("CSQ", "PolyPhen");
123 fr.setColour("type5", byPolyPhen);
126 * set filters for feature types
129 // filter type1 features by (label contains "x")
130 FeatureMatcherSetI filterByX = new FeatureMatcherSet();
131 filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
132 fr.setFeatureFilter("type1", filterByX);
134 // filter type2 features by (score <= 2.4 and score > 1.1)
135 FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
136 filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
137 filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
138 fr.setFeatureFilter("type2", filterByScore);
140 // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
141 FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
143 .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
144 filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
146 fr.setFeatureFilter("type3", filterByXY);
149 * save colours and filters to an XML file
151 File coloursFile = File.createTempFile("testSaveLoad", ".fc");
152 coloursFile.deleteOnExit();
153 FeatureSettings fs = new FeatureSettings(af);
154 fs.save(coloursFile);
157 * change feature colours and filters
159 FeatureColourI pink = new FeatureColour(Color.pink);
160 fr.setColour("type1", pink);
161 fr.setColour("type2", pink);
162 fr.setColour("type3", pink);
163 fr.setColour("type4", pink);
164 fr.setColour("type5", pink);
166 FeatureMatcherSetI filter2 = new FeatureMatcherSet();
167 filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
168 fr.setFeatureFilter("type1", filter2);
169 fr.setFeatureFilter("type2", filter2);
170 fr.setFeatureFilter("type3", filter2);
171 fr.setFeatureFilter("type4", filter2);
172 fr.setFeatureFilter("type5", filter2);
175 * reload colours and filters from file and verify they are restored
177 fs.load(coloursFile);
178 FeatureColourI fc = fr.getFeatureStyle("type1");
179 assertTrue(fc.isSimpleColour());
180 assertEquals(fc.getColour(), Color.red);
181 fc = fr.getFeatureStyle("type2");
182 assertTrue(fc.isColourByLabel());
183 fc = fr.getFeatureStyle("type3");
184 assertTrue(fc.isGraduatedColour());
185 assertNull(fc.getAttributeName());
186 assertTrue(fc.isAboveThreshold());
187 assertEquals(fc.getThreshold(), 2f);
188 fc = fr.getFeatureStyle("type4");
189 assertTrue(fc.isColourByLabel());
190 assertTrue(fc.isColourByAttribute());
191 assertEquals(fc.getAttributeName(), new String[] { "AF" });
192 fc = fr.getFeatureStyle("type5");
193 assertTrue(fc.isGraduatedColour());
194 assertTrue(fc.isColourByAttribute());
195 assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
196 assertTrue(fc.isBelowThreshold());
197 assertEquals(fc.getThreshold(), 3f);
199 assertEquals(fr.getFeatureFilter("type1").toStableString(),
201 assertEquals(fr.getFeatureFilter("type2").toStableString(),
202 "(Score LE 2.4) AND (Score GT 1.1)");
203 assertEquals(fr.getFeatureFilter("type3").toStableString(),
204 "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
208 * Adds two features of the given type to the given sequence, also setting the
209 * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
215 private void addFeatures(SequenceI seq, String featureType, int score)
217 addFeature(seq, featureType, score++);
218 addFeature(seq, featureType, score);
221 private void addFeature(SequenceI seq, String featureType, int score)
223 SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
225 sf.setValue("AF", score);
226 sf.setValue("CSQ", new HashMap<String, String>()
229 put("PolyPhen", Integer.toString(score));
232 seq.addSequenceFeature(sf);
236 * @see FeatureColourTest#testGetDescription()
237 * @throws IOException
239 @Test(groups = "Functional")
240 public void testGetColorTooltip() throws IOException
242 assertNull(FeatureSettings.getColorTooltip(null, false));
247 FeatureColourI fc = new FeatureColour(Color.black);
248 String simpleTooltip = "Click to edit, right-click for menu";
249 assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
250 assertNull(FeatureSettings.getColorTooltip(fc, false));
253 * graduated colour tooltip includes description of colour
255 fc.setColourByLabel(true);
256 assertEquals(FeatureSettings.getColorTooltip(fc, false),
257 "<html>By Label</html>");
258 assertEquals(FeatureSettings.getColorTooltip(fc, true),
259 "<html>By Label<br>" + simpleTooltip + "</br></html>");
262 * graduated colour with threshold is html-encoded
264 fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
265 fc.setBelowThreshold(true);
267 assertEquals(FeatureSettings.getColorTooltip(fc, false),
268 "<html>By Score (< 4.0)</html>");
269 assertEquals(FeatureSettings.getColorTooltip(fc, true),
270 "<html>By Score (< 4.0)<br>" + simpleTooltip
273 fc.setAboveThreshold(true);
274 assertEquals(FeatureSettings.getColorTooltip(fc, false),
275 "<html>By Score (> 4.0)</html>");
276 assertEquals(FeatureSettings.getColorTooltip(fc, true),
277 "<html>By Score (> 4.0)<br>" + simpleTooltip