X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureColourFinderTest.java;h=fe77dd26802bcd5f02b3a57a7c05c3daf752f639;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f6dfed61c2aad8161b7c007bb365cfa59977dba2;hpb=cff4383502a703f29d0d632d05656e95ebb2db8b;p=jalview.git diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java index f6dfed6..fe77dd2 100644 --- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java @@ -11,10 +11,11 @@ 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; @@ -50,15 +51,14 @@ 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(); @@ -133,8 +133,8 @@ 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); @@ -172,9 +172,9 @@ 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); @@ -182,7 +182,7 @@ 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); @@ -216,8 +216,8 @@ 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); @@ -225,7 +225,7 @@ 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); @@ -264,8 +264,8 @@ 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); @@ -310,19 +310,19 @@ public class FeatureColourFinderTest @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); @@ -355,7 +355,7 @@ 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 @@ -381,7 +381,7 @@ 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) @@ -390,7 +390,7 @@ 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 @@ -399,19 +399,19 @@ 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)); @@ -447,8 +447,8 @@ 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()); @@ -477,22 +477,22 @@ public class FeatureColourFinderTest { 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")); - + 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(kdFeature, fc); @@ -503,13 +503,13 @@ public class FeatureColourFinderTest /* * render order is kd above Metal */ - Object[][] data = new Object[2][]; - data[0] = new Object[] { kdFeature, fc, true }; - data[1] = new Object[] { metalFeature, green, true }; + 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 */ @@ -522,7 +522,7 @@ public class FeatureColourFinderTest */ c = finder.findFeatureColour(Color.blue, seq, 3); assertEquals(c, Color.green); - + /* * position 7, column 9, score 10 - maximum colour in range */