X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureColourFinderTest.java;h=6b87dd4c1a2325a43f9d174ea2067bf10e9ce4cb;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=ecabfca55be5ea90a5d59a7c4918ee57756db9c3;hpb=fb2d7072a283815141262d70d5f11a5e966d500b;p=jalview.git diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java index ecabfca..6b87dd4 100644 --- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java @@ -1,7 +1,28 @@ +/* + * 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 . + * 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; @@ -10,10 +31,11 @@ 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; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import java.awt.Color; import java.util.List; @@ -49,15 +71,14 @@ public class FeatureColourFinderTest private AlignFrame af; - private FeatureRenderer fr; + private FeatureRendererModel fr; @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(); @@ -132,8 +153,8 @@ public class FeatureColourFinderTest @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); @@ -171,9 +192,9 @@ public class FeatureColourFinderTest * - 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); @@ -181,7 +202,7 @@ public class FeatureColourFinderTest /* * ..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); @@ -215,8 +236,8 @@ public class FeatureColourFinderTest /* * 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); @@ -224,7 +245,7 @@ public class FeatureColourFinderTest /* * 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); @@ -263,8 +284,8 @@ public class FeatureColourFinderTest /* * 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); @@ -285,21 +306,43 @@ public class FeatureColourFinderTest } @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); @@ -332,7 +375,7 @@ public class FeatureColourFinderTest 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 @@ -358,7 +401,7 @@ public class FeatureColourFinderTest 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) @@ -367,7 +410,7 @@ public class FeatureColourFinderTest 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 @@ -376,19 +419,19 @@ public class FeatureColourFinderTest * 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)); @@ -424,8 +467,8 @@ public class FeatureColourFinderTest /* * 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()); @@ -452,26 +495,41 @@ public class FeatureColourFinderTest @Test(groups = "Functional") public void testFindFeatureColour_graduatedWithThreshold() { - 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 + 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(min, max, 0, 10); + FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10); fc.setAboveThreshold(true); fc.setThreshold(5f); - fr.setColour("kd", fc); + 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 */ @@ -479,11 +537,12 @@ public class FeatureColourFinderTest assertEquals(c, Color.blue); /* - * position 4, column 3, score 5 - at threshold - default colour + * 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.blue); - + assertEquals(c, Color.green); + /* * position 7, column 9, score 10 - maximum colour in range */ @@ -502,10 +561,11 @@ public class FeatureColourFinderTest assertEquals(c, min); /* - * position 4, column 3, score 5 - at threshold - default colour + * 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.blue); + assertEquals(c, Color.green); /* * position 7, column 9, score 10 - above threshold - default colour