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package jalview.renderer.seqfeatures; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertFalse; |
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import static org.testng.Assert.assertNull; |
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import static org.testng.Assert.assertTrue; |
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import jalview.api.AlignViewportI; |
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import jalview.api.FeatureColourI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.FeatureMatcher; |
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import jalview.datamodel.features.FeatureMatcherSet; |
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import jalview.datamodel.features.FeatureMatcherSetI; |
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import jalview.gui.AlignFrame; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.schemes.FeatureColour; |
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import jalview.util.matcher.Condition; |
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import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (267) |
Complexity: 4 |
Complexity Density: 0.02 |
|
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public class FeatureRendererTest |
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{ |
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| 100% |
Uncovered Elements: 0 (61) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testFindAllFeatures() |
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{ |
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String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n"; |
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AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, |
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DataSourceType.PASTE); |
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AlignViewportI av = af.getViewport(); |
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FeatureRenderer fr = new FeatureRenderer(av); |
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1 |
fr.findAllFeatures(true); |
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assertTrue(fr.getRenderOrder().isEmpty()); |
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assertTrue(fr.getFeatureGroups().isEmpty()); |
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List<SequenceI> seqs = av.getAlignment().getSequences(); |
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SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f, |
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"Group"); |
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seqs.get(0).addSequenceFeature(sf1); |
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fr.findAllFeatures(true); |
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|
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List<String> types = fr.getRenderOrder(); |
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List<String> groups = fr.getFeatureGroups(); |
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assertEquals(types.size(), 0); |
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assertFalse(types.contains("Type")); |
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assertEquals(groups.size(), 0); |
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assertFalse(groups.contains("Group")); |
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seqs.get(1).addSequenceFeature( |
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new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup")); |
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seqs.get(2).addSequenceFeature( |
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new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup")); |
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seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9, |
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Float.NaN, "RfamGroup")); |
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seqs.get(3).addSequenceFeature( |
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new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null)); |
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seqs.get(3).addSequenceFeature( |
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new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null)); |
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fr.findAllFeatures(true); |
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types = fr.getRenderOrder(); |
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groups = fr.getFeatureGroups(); |
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assertEquals(types.size(), 3); |
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assertFalse(types.contains("Type")); |
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assertTrue(types.contains("Pfam")); |
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assertTrue(types.contains("Rfam")); |
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assertTrue(types.contains("Scop")); |
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assertEquals(groups.size(), 2); |
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assertFalse(groups.contains("Group")); |
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assertTrue(groups.contains("PfamGroup")); |
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assertTrue(groups.contains("RfamGroup")); |
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assertFalse(groups.contains(null)); |
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Map<String, float[][]> minMax = fr.getMinMax(); |
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assertEquals(minMax.size(), 1); |
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assertEquals(minMax.get("Pfam")[0][0], 1f); |
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assertEquals(minMax.get("Pfam")[0][1], 2f); |
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seqs.get(0).addSequenceFeature( |
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new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup")); |
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seqs.get(1).addSequenceFeature( |
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new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup")); |
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fr.findAllFeatures(true); |
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assertEquals(minMax.size(), 2); |
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assertEquals(minMax.get("Pfam")[0][0], 1f); |
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assertEquals(minMax.get("Pfam")[0][1], 8f); |
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assertEquals(minMax.get("Rfam")[0][0], 6f); |
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assertEquals(minMax.get("Rfam")[0][1], 6f); |
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List<String> renderOrder = fr.getRenderOrder(); |
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assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam")); |
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FeatureSettingsBean[] data = new FeatureSettingsBean[3]; |
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FeatureColourI colour = new FeatureColour(Color.RED); |
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data[0] = new FeatureSettingsBean("Rfam", colour, null, true); |
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data[1] = new FeatureSettingsBean("Pfam", colour, null, false); |
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data[2] = new FeatureSettingsBean("Scop", colour, null, false); |
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fr.setFeaturePriority(data); |
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assertEquals(fr.getRenderOrder(), |
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Arrays.asList("Scop", "Pfam", "Rfam")); |
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assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam")); |
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seqs.get(2).addSequenceFeature( |
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new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup")); |
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fr.findAllFeatures(true); |
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assertEquals(fr.getRenderOrder(), |
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Arrays.asList("Scop", "Pfam", "Rfam", "Metal")); |
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assertEquals(fr.getDisplayedFeatureTypes(), |
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Arrays.asList("Rfam", "Metal")); |
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} |
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| 100% |
Uncovered Elements: 0 (82) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testFindFeaturesAtColumn() |
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{ |
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String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n"; |
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AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, |
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DataSourceType.PASTE); |
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AlignViewportI av = af.getViewport(); |
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FeatureRenderer fr = new FeatureRenderer(av); |
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SequenceI seq = av.getAlignment().getSequenceAt(0); |
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List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3); |
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assertTrue(features.isEmpty()); |
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SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f, |
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"Group"); |
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seq.addSequenceFeature(sf1); |
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SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f, |
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"Group1"); |
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seq.addSequenceFeature(sf2); |
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SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f, |
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"Group2"); |
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seq.addSequenceFeature(sf3); |
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SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f, |
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null); |
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seq.addSequenceFeature(sf4); |
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SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7, |
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15, 1f, "Group1"); |
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seq.addSequenceFeature(sf5); |
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SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7, |
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15, 1f, "Group2"); |
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seq.addSequenceFeature(sf6); |
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SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7, |
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15, 1f, null); |
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seq.addSequenceFeature(sf7); |
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SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f, |
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"Group"); |
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seq.addSequenceFeature(sf8); |
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SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5, |
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6, 1f, "Group"); |
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seq.addSequenceFeature(sf9); |
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fr.findAllFeatures(true); |
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features = fr.findFeaturesAtColumn(seq, 15); |
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assertEquals(features.size(), 6); |
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assertTrue(features.contains(sf2)); |
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assertTrue(features.contains(sf3)); |
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assertTrue(features.contains(sf4)); |
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assertTrue(features.contains(sf5)); |
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assertTrue(features.contains(sf6)); |
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assertTrue(features.contains(sf7)); |
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238 |
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features = fr.findFeaturesAtColumn(seq, 14); |
239 |
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assertEquals(features.size(), 3); |
240 |
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assertTrue(features.contains(sf2)); |
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1 |
assertTrue(features.contains(sf3)); |
242 |
1 |
assertTrue(features.contains(sf4)); |
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247 |
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FeatureColourI colour = new FeatureColour(Color.RED); |
248 |
1 |
FeatureSettingsBean[] data = new FeatureSettingsBean[4]; |
249 |
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data[0] = new FeatureSettingsBean("Type1", colour, null, true); |
250 |
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data[1] = new FeatureSettingsBean("Type2", colour, null, false); |
251 |
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data[2] = new FeatureSettingsBean("Type3", colour, null, true); |
252 |
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data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null, |
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true); |
254 |
1 |
fr.setFeaturePriority(data); |
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|
256 |
1 |
features = fr.findFeaturesAtColumn(seq, 15); |
257 |
1 |
assertEquals(features.size(), 5); |
258 |
1 |
assertTrue(features.contains(sf3)); |
259 |
1 |
assertTrue(features.contains(sf4)); |
260 |
1 |
assertTrue(features.contains(sf5)); |
261 |
1 |
assertTrue(features.contains(sf6)); |
262 |
1 |
assertTrue(features.contains(sf7)); |
263 |
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264 |
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265 |
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266 |
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267 |
1 |
fr.setGroupVisibility("Group2", false); |
268 |
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269 |
1 |
features = fr.findFeaturesAtColumn(seq, 15); |
270 |
1 |
assertEquals(features.size(), 3); |
271 |
1 |
assertTrue(features.contains(sf4)); |
272 |
1 |
assertTrue(features.contains(sf5)); |
273 |
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assertTrue(features.contains(sf7)); |
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276 |
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277 |
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features = fr.findFeaturesAtColumn(seq, 4); |
278 |
1 |
assertEquals(features.size(), 1); |
279 |
1 |
assertTrue(features.contains(sf8)); |
280 |
1 |
features = fr.findFeaturesAtColumn(seq, 5); |
281 |
1 |
assertEquals(features.size(), 1); |
282 |
1 |
assertTrue(features.contains(sf8)); |
283 |
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286 |
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287 |
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288 |
1 |
FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f, |
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10f); |
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fr.getFeatureColours().put("Type3", gc); |
291 |
1 |
features = fr.findFeaturesAtColumn(seq, 8); |
292 |
1 |
assertTrue(features.contains(sf4)); |
293 |
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1 |
gc.setAboveThreshold(true); |
295 |
1 |
gc.setThreshold(2f); |
296 |
1 |
features = fr.findFeaturesAtColumn(seq, 8); |
297 |
1 |
assertFalse(features.contains(sf4)); |
298 |
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299 |
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300 |
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301 |
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302 |
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303 |
1 |
gc.setAttributeName("AF"); |
304 |
1 |
features = fr.findFeaturesAtColumn(seq, 8); |
305 |
1 |
assertFalse(features.contains(sf4)); |
306 |
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|
307 |
1 |
sf4.setValue("AF", "2.4"); |
308 |
1 |
features = fr.findFeaturesAtColumn(seq, 8); |
309 |
1 |
assertTrue(features.contains(sf4)); |
310 |
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|
311 |
1 |
sf4.setValue("AF", "1.4"); |
312 |
1 |
features = fr.findFeaturesAtColumn(seq, 8); |
313 |
1 |
assertFalse(features.contains(sf4)); |
314 |
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} |
315 |
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| 100% |
Uncovered Elements: 0 (46) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
316 |
1 |
@Test(groups = "Functional")... |
317 |
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public void testFilterFeaturesForDisplay() |
318 |
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{ |
319 |
1 |
String seqData = ">s1\nabcdef\n"; |
320 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, |
321 |
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DataSourceType.PASTE); |
322 |
1 |
AlignViewportI av = af.getViewport(); |
323 |
1 |
FeatureRenderer fr = new FeatureRenderer(av); |
324 |
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|
325 |
1 |
List<SequenceFeature> features = new ArrayList<>(); |
326 |
1 |
fr.filterFeaturesForDisplay(features); |
327 |
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328 |
1 |
SequenceI seq = av.getAlignment().getSequenceAt(0); |
329 |
1 |
SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN, |
330 |
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"group1"); |
331 |
1 |
seq.addSequenceFeature(sf1); |
332 |
1 |
SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f, |
333 |
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"group2"); |
334 |
1 |
seq.addSequenceFeature(sf2); |
335 |
1 |
SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f, |
336 |
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"group3"); |
337 |
1 |
seq.addSequenceFeature(sf3); |
338 |
1 |
SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f, |
339 |
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"group4"); |
340 |
1 |
seq.addSequenceFeature(sf4); |
341 |
1 |
SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f, |
342 |
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"group4"); |
343 |
1 |
seq.addSequenceFeature(sf5); |
344 |
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|
345 |
1 |
fr.findAllFeatures(true); |
346 |
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|
347 |
1 |
features = seq.getSequenceFeatures(); |
348 |
1 |
assertEquals(features.size(), 5); |
349 |
1 |
assertTrue(features.contains(sf1)); |
350 |
1 |
assertTrue(features.contains(sf2)); |
351 |
1 |
assertTrue(features.contains(sf3)); |
352 |
1 |
assertTrue(features.contains(sf4)); |
353 |
1 |
assertTrue(features.contains(sf5)); |
354 |
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355 |
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356 |
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357 |
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358 |
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359 |
1 |
fr.filterFeaturesForDisplay(features); |
360 |
1 |
assertEquals(features.size(), 3); |
361 |
1 |
assertTrue(features.contains(sf1) || features.contains(sf4)); |
362 |
1 |
assertFalse(features.contains(sf1) && features.contains(sf4)); |
363 |
1 |
assertTrue(features.contains(sf2) || features.contains(sf3)); |
364 |
1 |
assertFalse(features.contains(sf2) && features.contains(sf3)); |
365 |
1 |
assertTrue(features.contains(sf5)); |
366 |
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|
367 |
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|
368 |
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|
369 |
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|
370 |
1 |
fr.setGroupVisibility("group2", false); |
371 |
1 |
fr.setGroupVisibility("group3", false); |
372 |
1 |
features = seq.getSequenceFeatures(); |
373 |
1 |
fr.filterFeaturesForDisplay(features); |
374 |
1 |
assertEquals(features.size(), 3); |
375 |
1 |
assertTrue(features.contains(sf1) || features.contains(sf4)); |
376 |
1 |
assertFalse(features.contains(sf1) && features.contains(sf4)); |
377 |
1 |
assertTrue(features.contains(sf2) || features.contains(sf3)); |
378 |
1 |
assertFalse(features.contains(sf2) && features.contains(sf3)); |
379 |
1 |
assertTrue(features.contains(sf5)); |
380 |
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|
381 |
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|
382 |
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|
383 |
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|
384 |
1 |
fr.setTransparency(0.5f); |
385 |
1 |
features = seq.getSequenceFeatures(); |
386 |
1 |
fr.filterFeaturesForDisplay(features); |
387 |
1 |
assertEquals(features.size(), 5); |
388 |
|
} |
389 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (74) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
|
|
390 |
1 |
@Test(groups = "Functional")... |
391 |
|
public void testGetColour() |
392 |
|
{ |
393 |
1 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n", |
394 |
|
DataSourceType.PASTE); |
395 |
1 |
AlignViewportI av = af.getViewport(); |
396 |
1 |
FeatureRenderer fr = new FeatureRenderer(av); |
397 |
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|
398 |
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|
399 |
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|
400 |
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|
401 |
1 |
FeatureColourI fc = new FeatureColour(Color.red); |
402 |
1 |
fr.getFeatureColours().put("Cath", fc); |
403 |
1 |
SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN, |
404 |
|
"group1"); |
405 |
1 |
assertEquals(fr.getColour(sf1), Color.red); |
406 |
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|
407 |
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|
408 |
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|
409 |
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|
410 |
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|
411 |
1 |
FeatureSettingsBean[] data = new FeatureSettingsBean[1]; |
412 |
1 |
data[0] = new FeatureSettingsBean("Cath", fc, null, false); |
413 |
1 |
fr.setFeaturePriority(data); |
414 |
1 |
assertEquals(fr.getColour(sf1), Color.red); |
415 |
1 |
data[0] = new FeatureSettingsBean("Cath", fc, null, true); |
416 |
1 |
fr.setFeaturePriority(data); |
417 |
1 |
assertEquals(fr.getColour(sf1), Color.red); |
418 |
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|
419 |
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|
420 |
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|
421 |
|
|
422 |
1 |
fr.setGroupVisibility("group1", false); |
423 |
1 |
assertNull(fr.getColour(sf1)); |
424 |
1 |
fr.setGroupVisibility("group1", true); |
425 |
1 |
assertEquals(fr.getColour(sf1), Color.red); |
426 |
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|
427 |
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|
428 |
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|
429 |
|
|
430 |
|
|
431 |
1 |
FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, |
432 |
|
Color.green, 1f, 11f); |
433 |
1 |
fr.getFeatureColours().put("Cath", gc); |
434 |
1 |
assertEquals(fr.getColour(sf1), Color.green); |
435 |
|
|
436 |
|
|
437 |
|
|
438 |
|
|
439 |
1 |
SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f, |
440 |
|
"group1"); |
441 |
|
|
442 |
1 |
Color expected = new Color(255, 128, 0); |
443 |
1 |
assertEquals(fr.getColour(sf2), expected); |
444 |
|
|
445 |
|
|
446 |
|
|
447 |
|
|
448 |
1 |
gc.setAboveThreshold(true); |
449 |
1 |
gc.setThreshold(5f); |
450 |
1 |
assertEquals(fr.getColour(sf2), expected); |
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
|
455 |
|
|
456 |
1 |
gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f); |
457 |
1 |
fr.getFeatureColours().put("Cath", gc); |
458 |
1 |
gc.setAutoScaled(false); |
459 |
1 |
assertEquals(fr.getColour(sf2), new Color(255, 213, 0)); |
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
1 |
gc.setAboveThreshold(true); |
465 |
1 |
gc.setThreshold(7f); |
466 |
1 |
assertNull(fr.getColour(sf2)); |
467 |
|
|
468 |
|
|
469 |
|
|
470 |
|
|
471 |
1 |
gc.setBelowThreshold(true); |
472 |
1 |
gc.setThreshold(3f); |
473 |
1 |
assertNull(fr.getColour(sf2)); |
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
|
479 |
1 |
gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f); |
480 |
1 |
fr.getFeatureColours().put("Cath", gc); |
481 |
1 |
gc.setAttributeName("AF"); |
482 |
1 |
assertEquals(fr.getColour(sf2), Color.green); |
483 |
|
|
484 |
|
|
485 |
1 |
sf2.setValue("AF", "Five"); |
486 |
1 |
assertEquals(fr.getColour(sf2), Color.green); |
487 |
|
|
488 |
|
|
489 |
1 |
sf2.setValue("AF", "6"); |
490 |
1 |
assertEquals(fr.getColour(sf2), expected); |
491 |
|
|
492 |
|
|
493 |
1 |
gc.setAboveThreshold(true); |
494 |
1 |
gc.setThreshold(10f); |
495 |
1 |
assertNull(fr.getColour(sf2)); |
496 |
|
|
497 |
|
|
498 |
1 |
gc.setAboveThreshold(false); |
499 |
1 |
assertEquals(fr.getColour(sf2), expected); |
500 |
1 |
FeatureMatcherSetI filter = new FeatureMatcherSet(); |
501 |
1 |
filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF")); |
502 |
1 |
fr.setFeatureFilter("Cath", filter); |
503 |
1 |
assertNull(fr.getColour(sf2)); |
504 |
|
|
505 |
|
|
506 |
1 |
filter = new FeatureMatcherSet(); |
507 |
1 |
filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense", |
508 |
|
"Consequence")); |
509 |
1 |
fr.setFeatureFilter("Cath", filter); |
510 |
|
|
511 |
1 |
assertNull(fr.getColour(sf2)); |
512 |
|
|
513 |
1 |
sf2.setValue("Consequence", "Synonymous"); |
514 |
1 |
assertNull(fr.getColour(sf2)); |
515 |
|
|
516 |
1 |
sf2.setValue("Consequence", "Missense variant"); |
517 |
1 |
assertEquals(fr.getColour(sf2), expected); |
518 |
|
|
519 |
|
|
520 |
1 |
filter = new FeatureMatcherSet(); |
521 |
1 |
filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234", |
522 |
|
"CSQ", "Feature")); |
523 |
1 |
fr.setFeatureFilter("Cath", filter); |
524 |
|
|
525 |
1 |
assertNull(fr.getColour(sf2)); |
526 |
|
|
527 |
1 |
Map<String, String> csqData = new HashMap<>(); |
528 |
1 |
csqData.put("BIOTYPE", "Transcript"); |
529 |
1 |
sf2.setValue("CSQ", csqData); |
530 |
1 |
assertNull(fr.getColour(sf2)); |
531 |
|
|
532 |
1 |
csqData.put("Feature", "ENST9876"); |
533 |
1 |
assertNull(fr.getColour(sf2)); |
534 |
|
|
535 |
1 |
csqData.put("Feature", "ENST01234"); |
536 |
1 |
assertEquals(fr.getColour(sf2), expected); |
537 |
|
} |
538 |
|
} |