+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.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;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import java.awt.Color;
+import java.util.List;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
/**
private AlignFrame af;
- private FeatureRenderer fr;
+ private FeatureRendererModel fr;
- @BeforeClass(alwaysRun = true)
+ @BeforeTest(alwaysRun = true)
public void setUp()
{
// aligned column 8 is sequence position 6
String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
- af = new FileLoader().LoadFileWaitTillLoaded(s,
- DataSourceType.PASTE);
+ af = new FileLoader().LoadFileWaitTillLoaded(s, DataSourceType.PASTE);
av = af.getViewport();
seq = av.getAlignment().getSequenceAt(0);
fr = af.getFeatureRenderer();
}
/**
- * Clear down any sequence features before each test
+ * Clear down any sequence features before each test (not as easy as it
+ * sounds...)
*/
@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);
{
fr.setGroupVisibility(group, true);
}
+
+ fr.clearRenderOrder();
+ av.setShowSequenceFeatures(true);
}
@Test(groups = "Functional")
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));
+ 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);
- assertEquals(c, Color.white);
+ assertNull(c);
}
@Test(groups = "Functional")
* - 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);
/*
* currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
*/
- seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
- "Contact", 2, 12, Float.NaN, "Disulphide"));
+ 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);
}
@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"));
+ 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(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fr.setColour("kd", fc);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
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
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)
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
* 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));
-
+
/*
* ..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][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));
/*
* add a feature
- * it will be automatically set visible but the viewport
- * is still configured not to show features
+ * 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);
/*
* 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());
*/
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