+++ /dev/null
-package jalview.renderer.seqfeatures;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotEquals;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-
-import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.FeatureRenderer;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import jalview.schemes.FeatureColour;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-
-import java.awt.Color;
-import java.util.List;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-/**
- * Unit tests for feature colour determination, including but not limited to
- * <ul>
- * <li>gap position</li>
- * <li>no features present</li>
- * <li>features present but show features turned off</li>
- * <li>features displayed but selected feature turned off</li>
- * <li>features displayed but feature group turned off</li>
- * <li>feature displayed but none at the specified position</li>
- * <li>multiple features at position, with no transparency</li>
- * <li>multiple features at position, with transparency</li>
- * <li>score graduated feature colour</li>
- * <li>contact feature start at the selected position</li>
- * <li>contact feature end at the selected position</li>
- * <li>contact feature straddling the selected position (not shown)</li>
- * </ul>
- */
-public class FeatureColourFinderTest
-{
- private AlignViewport av;
-
- private SequenceI seq;
-
- private FeatureColourFinder finder;
-
- private AlignFrame af;
-
- private FeatureRenderer fr;
-
- @BeforeTest(alwaysRun = true)
- public void setUp()
- {
- Cache.initLogger();
- // aligned column 8 is sequence position 6
- String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
- af = new FileLoader().LoadFileWaitTillLoaded(s,
- DataSourceType.PASTE);
- av = af.getViewport();
- seq = av.getAlignment().getSequenceAt(0);
- fr = af.getFeatureRenderer();
- finder = new FeatureColourFinder(fr);
- }
-
- /**
- * Clear down any sequence features before each test (not as easy as it
- * sounds...)
- */
- @BeforeMethod(alwaysRun = true)
- public void setUpBeforeTest()
- {
- List<SequenceFeature> sfs = seq.getSequenceFeatures();
- for (SequenceFeature sf : sfs)
- {
- seq.deleteFeature(sf);
- }
- fr.findAllFeatures(true);
-
- /*
- * reset all feature groups to visible
- */
- for (String group : fr.getGroups(false))
- {
- fr.setGroupVisibility(group, true);
- }
-
- fr.clearRenderOrder();
- av.setShowSequenceFeatures(true);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_noFeatures()
- {
- av.setShowSequenceFeatures(false);
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
-
- av.setShowSequenceFeatures(true);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_noFeaturesShown()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- fr.featuresAdded();
- av.setShowSequenceFeatures(false);
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_singleFeatureAtPosition()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- fr.setColour("Metal", new FeatureColour(Color.red));
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
- }
-
- /**
- * feature colour at a gap is null (not white) - a user defined colour scheme
- * can then provide a bespoke gap colour if configured to do so
- */
- @Test(groups = "Functional")
- public void testFindFeatureColour_gapPosition()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
- null));
- fr.setColour("Metal", new FeatureColour(Color.red));
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
- Color c = finder.findFeatureColour(null, seq, 6);
- assertNull(c);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
- {
- /*
- * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
- * new features 'on top' (but reverses the order of any added features)
- */
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
- Float.NaN, "DomainGroup"));
- FeatureColour green = new FeatureColour(Color.green);
- fr.setColour("Domain", green);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * expect Domain (green) to be rendered above Metal (red)
- */
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.green);
-
- /*
- * now promote Metal above Domain
- * - currently no way other than mimicking reordering of
- * table in Feature Settings
- */
- FeatureSettingsBean[] data = new FeatureSettingsBean[2];
- data[0] = new FeatureSettingsBean("Metal", red, null, true);
- data[1] = new FeatureSettingsBean("Domain", green, null, true);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
-
- /*
- * ..and turn off display of Metal
- */
- data[0] = new FeatureSettingsBean("Metal", red, null, false);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.green);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_singleFeatureNotAtPosition()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
- Float.NaN, "MetalGroup"));
- fr.setColour("Metal", new FeatureColour(Color.red));
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
- // column 2 = sequence position 3
- Color c = finder.findFeatureColour(Color.blue, seq, 2);
- assertEquals(c, Color.blue);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_featureTypeNotDisplayed()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
-
- /*
- * turn off display of Metal - is this the easiest way to do it??
- */
- FeatureSettingsBean[] data = new FeatureSettingsBean[1];
- data[0] = new FeatureSettingsBean("Metal", red, null, false);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
-
- /*
- * turn display of Metal back on
- */
- data[0] = new FeatureSettingsBean("Metal", red, null, true);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_featureGroupNotDisplayed()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
-
- /*
- * turn off display of MetalGroup
- */
- fr.setGroupVisibility("MetalGroup", false);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
-
- /*
- * turn display of MetalGroup back on
- */
- fr.setGroupVisibility("MetalGroup", true);
- c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.red);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_contactFeature()
- {
- /*
- * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
- */
- seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
- "Contact", 2, 12, Float.NaN, "Disulphide"));
- fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * Contact positions are residues 2 and 12
- * which are columns 1 and 14
- * positions in between don't count for a contact feature!
- */
- Color c = finder.findFeatureColour(Color.blue, seq, 10);
- assertEquals(c, Color.blue);
- c = finder.findFeatureColour(Color.blue, seq, 8);
- assertEquals(c, Color.blue);
- c = finder.findFeatureColour(Color.blue, seq, 1);
- assertEquals(c, Color.red);
- c = finder.findFeatureColour(Color.blue, seq, 14);
- assertEquals(c, Color.red);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureAtEnd()
- {
- /*
- * terminal residue feature
- */
- seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
- seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
- fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * final column should have PDBRESNUM feature, the others not
- */
- Color c = finder.findFeatureColour(Color.blue, seq,
- seq.getLength() - 2);
- assertNotEquals(c, Color.red);
- c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
- assertEquals(c, Color.red);
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_graduatedFeatureColour()
- {
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
-
- /*
- * graduated colour from 0 to 10
- */
- Color min = new Color(100, 50, 150);
- Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
- fr.setColour("kd", fc);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * position 2, column 1, score 0 - minimum colour in range
- */
- Color c = finder.findFeatureColour(Color.blue, seq, 1);
- assertEquals(c, min);
-
- /*
- * position 7, column 9, score 10 - maximum colour in range
- */
- c = finder.findFeatureColour(Color.blue, seq, 9);
- assertEquals(c, max);
-
- /*
- * position 4, column 3, score 5 - half way from min to max
- */
- c = finder.findFeatureColour(Color.blue, seq, 3);
- assertEquals(c, new Color(150, 25, 125));
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_transparencySingleFeature()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * the FeatureSettings transparency slider has range 0-70 which
- * corresponds to a transparency value of 1 - 0.3
- * A value of 0.4 gives a combination of
- * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
- */
- fr.setTransparency(0.4f);
- Color c = finder.findFeatureColour(Color.cyan, seq, 10);
- assertEquals(c, new Color(102, 153, 153));
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_transparencyTwoFeatures()
- {
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
- Float.NaN, "DomainGroup"));
- FeatureColour green = new FeatureColour(Color.green);
- fr.setColour("Domain", green);
- fr.featuresAdded();
- av.setShowSequenceFeatures(true);
-
- /*
- * Domain (green) rendered above Metal (red) above background (cyan)
- * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
- * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
- */
- fr.setTransparency(0.6f);
- Color c = finder.findFeatureColour(Color.cyan, seq, 10);
- assertEquals(c, new Color(61, 194, 41));
-
- /*
- * now promote Metal above Domain
- * - currently no way other than mimicking reordering of
- * table in Feature Settings
- * Metal (red) rendered above Domain (green) above background (cyan)
- * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
- * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
- */
- FeatureSettingsBean[] data = new FeatureSettingsBean[2];
- data[0] = new FeatureSettingsBean("Metal", red, null, true);
- data[1] = new FeatureSettingsBean("Domain", green, null, true);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.cyan, seq, 10);
- assertEquals(c, new Color(153, 102, 41));
-
- /*
- * ..and turn off display of Metal
- * Domain (green) above background (pink)
- * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
- */
- data[0] = new FeatureSettingsBean("Metal", red, null, false);
- fr.setFeaturePriority(data);
- c = finder.findFeatureColour(Color.pink, seq, 10);
- assertEquals(c, new Color(102, 223, 70));
- }
-
- @Test(groups = "Functional")
- public void testNoFeaturesDisplayed()
- {
- /*
- * no features on alignment to render
- */
- assertTrue(finder.noFeaturesDisplayed());
-
- /*
- * add a feature
- * it will be automatically set visible but we leave
- * the viewport configured not to show features
- */
- av.setShowSequenceFeatures(false);
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
- Float.NaN, "MetalGroup"));
- FeatureColour red = new FeatureColour(Color.red);
- fr.setColour("Metal", red);
- fr.featuresAdded();
- assertTrue(finder.noFeaturesDisplayed());
-
- /*
- * turn on feature display
- */
- av.setShowSequenceFeatures(true);
- assertFalse(finder.noFeaturesDisplayed());
-
- /*
- * turn off display of Metal
- */
- FeatureSettingsBean[] data = new FeatureSettingsBean[1];
- data[0] = new FeatureSettingsBean("Metal", red, null, false);
- fr.setFeaturePriority(data);
- assertTrue(finder.noFeaturesDisplayed());
-
- /*
- * turn display of Metal back on
- */
- fr.setVisible("Metal");
- assertFalse(finder.noFeaturesDisplayed());
-
- /*
- * turn off MetalGroup - has no effect here since the group of a
- * sequence feature instance is independent of its type
- */
- fr.setGroupVisibility("MetalGroup", false);
- assertFalse(finder.noFeaturesDisplayed());
-
- /*
- * a finder with no feature renderer
- */
- FeatureColourFinder finder2 = new FeatureColourFinder(null);
- assertTrue(finder2.noFeaturesDisplayed());
- }
-
- @Test(groups = "Functional")
- public void testFindFeatureColour_graduatedWithThreshold()
- {
- String kdFeature = "kd";
- String metalFeature = "Metal";
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4,
- 5f, "MetalGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
-
- /*
- * kd feature has graduated colour from 0 to 10
- * above threshold value of 5
- */
- Color min = new Color(100, 50, 150);
- Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
- fc.setAboveThreshold(true);
- fc.setThreshold(5f);
- fr.setColour(kdFeature, fc);
- FeatureColour green = new FeatureColour(Color.green);
- fr.setColour(metalFeature, green);
- fr.featuresAdded();
-
- /*
- * render order is kd above Metal
- */
- FeatureSettingsBean[] data = new FeatureSettingsBean[2];
- data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
- data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
- fr.setFeaturePriority(data);
-
- av.setShowSequenceFeatures(true);
-
- /*
- * position 2, column 1, score 0 - below threshold - default colour
- */
- Color c = finder.findFeatureColour(Color.blue, seq, 1);
- assertEquals(c, Color.blue);
-
- /*
- * position 4, column 3, score 5 - at threshold
- * should return Green (colour of Metal feature)
- */
- c = finder.findFeatureColour(Color.blue, seq, 3);
- assertEquals(c, Color.green);
-
- /*
- * position 7, column 9, score 10 - maximum colour in range
- */
- c = finder.findFeatureColour(Color.blue, seq, 9);
- assertEquals(c, max);
-
- /*
- * now colour below threshold of 5
- */
- fc.setBelowThreshold(true);
-
- /*
- * position 2, column 1, score 0 - min colour
- */
- c = finder.findFeatureColour(Color.blue, seq, 1);
- assertEquals(c, min);
-
- /*
- * position 4, column 3, score 5 - at threshold
- * should return Green (colour of Metal feature)
- */
- c = finder.findFeatureColour(Color.blue, seq, 3);
- assertEquals(c, Color.green);
-
- /*
- * position 7, column 9, score 10 - above threshold - default colour
- */
- c = finder.findFeatureColour(Color.blue, seq, 9);
- assertEquals(c, Color.blue);
- }
-}
git://source.jalview.org / jalview.git / blobdiff