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.AlignViewportI;
import jalview.api.FeatureColourI;
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;
*/
public class FeatureColourFinderTest
{
- private AlignViewport av;
+ private AlignViewportI av;
private SequenceI seq;
@BeforeMethod(alwaysRun = true)
public void setUpBeforeTest()
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs != null)
+ List<SequenceFeature> sfs = seq.getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- for (SequenceFeature sf : sfs)
- {
- seq.deleteFeature(sf);
- }
+ seq.deleteFeature(sf);
}
fr.findAllFeatures(true);
* - currently no way other than mimicking reordering of
* table in Feature Settings
*/
- Object[][] data = new Object[2][];
- data[0] = new Object[] { "Metal", red, true };
- data[1] = new Object[] { "Domain", green, true };
+ 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][2] = false;
+ data[0] = new FeatureSettingsBean("Metal", red, null, false);
fr.setFeaturePriority(data);
c = finder.findFeatureColour(Color.blue, seq, 10);
assertEquals(c, Color.green);
/*
* turn off display of Metal - is this the easiest way to do it??
*/
- Object[][] data = new Object[1][];
- data[0] = new Object[] { "Metal", red, false };
+ 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 Object[] { "Metal", red, true };
+ 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 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,
*/
Color min = new Color(100, 50, 150);
Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fr.setColour("kd", fc);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
* 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
*/
- Object[][] data = new Object[2][];
- data[0] = new Object[] { "Metal", red, true };
- data[1] = new Object[] { "Domain", green, true };
+ 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));
* Domain (green) above background (pink)
* 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
*/
- data[0][2] = false;
+ 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));
/*
* turn off display of Metal
*/
- Object[][] data = new Object[1][];
- data[0] = new Object[] { "Metal", red, false };
+ FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+ data[0] = new FeatureSettingsBean("Metal", red, null, false);
fr.setFeaturePriority(data);
assertTrue(finder.noFeaturesDisplayed());
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