1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.gui

File FeatureSettingsTest.java

 

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Class
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Actions
FeatureSettingsTest 54 109 9
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Contributing tests

This file is covered by 3 tests. .

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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.gui;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertNull;
25    import static org.testng.Assert.assertTrue;
26   
27    import java.awt.Color;
28    import java.io.File;
29    import java.io.IOException;
30    import java.util.HashMap;
31   
32    import org.testng.annotations.AfterMethod;
33    import org.testng.annotations.BeforeClass;
34    import org.testng.annotations.Test;
35   
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.FileFormat;
46    import jalview.io.FileFormatI;
47    import jalview.io.FileLoader;
48    import jalview.io.IdentifyFile;
49    import jalview.schemes.FeatureColour;
50    import jalview.schemes.FeatureColourTest;
51    import jalview.util.matcher.Condition;
52    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
53   
 
54    public class FeatureSettingsTest
55    {
 
56  1 toggle @BeforeClass(alwaysRun = true)
57    public static void setUpBeforeClass() throws Exception
58    {
59    /*
60    * use read-only test properties file
61    */
62  1 Cache.loadProperties("test/jalview/io/testProps.jvprops");
63  1 Jalview.main(new String[] { "--nonews" });
64    }
65   
 
66  3 toggle @AfterMethod(alwaysRun = true)
67    public void tearDown()
68    {
69  3 if (Desktop.instance != null)
70  3 Desktop.instance.closeAll_actionPerformed(null);
71    }
72   
73    /**
74    * Test a roundtrip of save and reload of feature colours and filters as XML
75    *
76    * @throws IOException
77    */
 
78  1 toggle @Test(groups = "Functional")
79    public void testSaveLoad() throws IOException
80    {
81  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
82    ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
83  1 SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
84   
85    /*
86    * add some features to the sequence
87    */
88  1 int score = 1;
89  1 addFeatures(seq1, "type1", score++);
90  1 addFeatures(seq1, "type2", score++);
91  1 addFeatures(seq1, "type3", score++);
92  1 addFeatures(seq1, "type4", score++);
93  1 addFeatures(seq1, "type5", score++);
94   
95    /*
96    * set colour schemes for features
97    */
98  1 FeatureRendererModel fr = af.getFeatureRenderer();
99   
100    // type1: red
101  1 fr.setColour("type1", new FeatureColour(Color.red));
102   
103    // type2: by label
104  1 FeatureColourI byLabel = new FeatureColour();
105  1 byLabel.setColourByLabel(true);
106  1 fr.setColour("type2", byLabel);
107   
108    // type3: by score above threshold
109  1 FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
110    Color.BLUE, null, 1, 10);
111  1 byScore.setAboveThreshold(true);
112  1 byScore.setThreshold(2f);
113  1 fr.setColour("type3", byScore);
114   
115    // type4: by attribute AF
116  1 FeatureColourI byAF = new FeatureColour();
117  1 byAF.setColourByLabel(true);
118  1 byAF.setAttributeName("AF");
119  1 fr.setColour("type4", byAF);
120   
121    // type5: by attribute CSQ:PolyPhen below threshold
122  1 FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
123    Color.BLUE, null, 1, 10);
124  1 byPolyPhen.setBelowThreshold(true);
125  1 byPolyPhen.setThreshold(3f);
126  1 byPolyPhen.setAttributeName("CSQ", "PolyPhen");
127  1 fr.setColour("type5", byPolyPhen);
128   
129    /*
130    * set filters for feature types
131    */
132   
133    // filter type1 features by (label contains "x")
134  1 FeatureMatcherSetI filterByX = new FeatureMatcherSet();
135  1 filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
136  1 fr.setFeatureFilter("type1", filterByX);
137   
138    // filter type2 features by (score <= 2.4 and score > 1.1)
139  1 FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
140  1 filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
141  1 filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
142  1 fr.setFeatureFilter("type2", filterByScore);
143   
144    // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
145  1 FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
146  1 filterByXY
147    .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
148  1 filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
149    "PolyPhen"));
150  1 fr.setFeatureFilter("type3", filterByXY);
151   
152    /*
153    * save colours and filters to an XML file
154    */
155  1 File coloursFile = File.createTempFile("testSaveLoad", ".fc");
156  1 coloursFile.deleteOnExit();
157  1 FeatureSettings fs = new FeatureSettings(af);
158  1 fs.save(coloursFile);
159   
160    /*
161    * change feature colours and filters
162    */
163  1 FeatureColourI pink = new FeatureColour(Color.pink);
164  1 fr.setColour("type1", pink);
165  1 fr.setColour("type2", pink);
166  1 fr.setColour("type3", pink);
167  1 fr.setColour("type4", pink);
168  1 fr.setColour("type5", pink);
169   
170  1 FeatureMatcherSetI filter2 = new FeatureMatcherSet();
171  1 filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
172  1 fr.setFeatureFilter("type1", filter2);
173  1 fr.setFeatureFilter("type2", filter2);
174  1 fr.setFeatureFilter("type3", filter2);
175  1 fr.setFeatureFilter("type4", filter2);
176  1 fr.setFeatureFilter("type5", filter2);
177   
178    /*
179    * reload colours and filters from file and verify they are restored
180    */
181  1 fs.load(coloursFile);
182  1 FeatureColourI fc = fr.getFeatureStyle("type1");
183  1 assertTrue(fc.isSimpleColour());
184  1 assertEquals(fc.getColour(), Color.red);
185  1 fc = fr.getFeatureStyle("type2");
186  1 assertTrue(fc.isColourByLabel());
187  1 fc = fr.getFeatureStyle("type3");
188  1 assertTrue(fc.isGraduatedColour());
189  1 assertNull(fc.getAttributeName());
190  1 assertTrue(fc.isAboveThreshold());
191  1 assertEquals(fc.getThreshold(), 2f);
192  1 fc = fr.getFeatureStyle("type4");
193  1 assertTrue(fc.isColourByLabel());
194  1 assertTrue(fc.isColourByAttribute());
195  1 assertEquals(fc.getAttributeName(), new String[] { "AF" });
196  1 fc = fr.getFeatureStyle("type5");
197  1 assertTrue(fc.isGraduatedColour());
198  1 assertTrue(fc.isColourByAttribute());
199  1 assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
200  1 assertTrue(fc.isBelowThreshold());
201  1 assertEquals(fc.getThreshold(), 3f);
202   
203  1 assertEquals(fr.getFeatureFilter("type1").toStableString(),
204    "Label Contains x");
205  1 assertEquals(fr.getFeatureFilter("type2").toStableString(),
206    "(Score LE 2.4) AND (Score GT 1.1)");
207  1 assertEquals(fr.getFeatureFilter("type3").toStableString(),
208    "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
209    }
210   
211    /**
212    * 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"
214    *
215    * @param seq
216    * @param featureType
217    * @param score
218    */
 
219  5 toggle private void addFeatures(SequenceI seq, String featureType, int score)
220    {
221  5 addFeature(seq, featureType, score++);
222  5 addFeature(seq, featureType, score);
223    }
224   
 
225  10 toggle private void addFeature(SequenceI seq, String featureType, int score)
226    {
227  10 SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
228    score, "grp");
229  10 sf.setValue("AF", score);
230  10 sf.setValue("CSQ", new HashMap<String, String>()
231    {
 
232  10 toggle {
233  10 put("PolyPhen", Integer.toString(score));
234    }
235    });
236  10 seq.addSequenceFeature(sf);
237    }
238   
239    /**
240    * @see FeatureColourTest#testGetDescription()
241    * @throws IOException
242    */
 
243  1 toggle @Test(groups = "Functional")
244    public void testGetColorTooltip() throws IOException
245    {
246  1 assertNull(FeatureSettings.getColorTooltip(null, false));
247   
248    /*
249    * simple colour
250    */
251  1 FeatureColourI fc = new FeatureColour(Color.black);
252  1 String simpleTooltip = "Click to edit, right-click for menu";
253  1 assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
254  1 assertNull(FeatureSettings.getColorTooltip(fc, false));
255   
256    /*
257    * graduated colour tooltip includes description of colour
258    */
259  1 fc.setColourByLabel(true);
260  1 assertEquals(FeatureSettings.getColorTooltip(fc, false),
261    "<html>By Label</html>");
262  1 assertEquals(FeatureSettings.getColorTooltip(fc, true),
263    "<html>By Label<br>" + simpleTooltip + "</br></html>");
264   
265    /*
266    * graduated colour with threshold is html-encoded
267    */
268  1 fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
269  1 fc.setBelowThreshold(true);
270  1 fc.setThreshold(4f);
271  1 assertEquals(FeatureSettings.getColorTooltip(fc, false),
272    "<html>By Score (&lt; 4.0)</html>");
273  1 assertEquals(FeatureSettings.getColorTooltip(fc, true),
274    "<html>By Score (&lt; 4.0)<br>" + simpleTooltip
275    + "</br></html>");
276   
277  1 fc.setAboveThreshold(true);
278  1 assertEquals(FeatureSettings.getColorTooltip(fc, false),
279    "<html>By Score (&gt; 4.0)</html>");
280  1 assertEquals(FeatureSettings.getColorTooltip(fc, true),
281    "<html>By Score (&gt; 4.0)<br>" + simpleTooltip
282    + "</br></html>");
283    }
284   
285    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   
 
288  1 toggle @Test(groups = "Functional")
289    public void testIdentifyFeatureSettingsFile() throws Exception
290    {
291  1 FileFormatI type = new IdentifyFile().identify(fsfile,
292    DataSourceType.PASTE);
293  1 assertTrue(FileFormat.FeatureSettings == type,
294    "Feature settings file was identified as " + type);
295  1 type = new IdentifyFile().identify(fsfile2, DataSourceType.PASTE);
296  1 assertTrue(FileFormat.FeatureSettings == type,
297    "Feature settings file with newline was identified as " + type);
298    }
299    }