X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureColourFinderTest.java;h=637bbf4be45a828f47995c514f01d9e72f00dae5;hb=f83b6877ab7ff3fc5db5c946e16c74e016437311;hp=6b1fbd2f1b6fc3f16c78bdad47997f33d7f04821;hpb=74393b51f368cb9f58589472d432a433d9c4386d;p=jalview.git
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 6b1fbd2..637bbf4 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -6,6 +26,13 @@ import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
+import java.awt.Color;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@@ -17,13 +44,6 @@ 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.BeforeMethod;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
/**
* Unit tests for feature colour determination, including but not limited to
*
@@ -58,8 +78,7 @@ public class FeatureColourFinderTest
{
// 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();
@@ -134,8 +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);
@@ -143,6 +162,27 @@ public class FeatureColourFinderTest
assertNull(c);
}
+ /**
+ * Nested features coloured by label - expect the colour of the enclosed
+ * feature
+ */
+ @Test(groups = "Functional")
+ public void testFindFeatureColour_nestedFeatures()
+ {
+ SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null);
+ seq.addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
+ 0f, null);
+ seq.addSequenceFeature(sf2);
+ FeatureColourI fc = new FeatureColour(Color.red);
+ fc.setColourByLabel(true);
+ fr.setColour("domain", fc);
+ fr.featuresAdded();
+ av.setShowSequenceFeatures(true);
+ Color c = finder.findFeatureColour(null, seq, 15);
+ assertEquals(c, fr.getColor(sf2, fc));
+ }
+
@Test(groups = "Functional")
public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
{
@@ -265,8 +305,8 @@ 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);
@@ -311,12 +351,12 @@ 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
@@ -356,7 +396,7 @@ 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
@@ -382,7 +422,7 @@ 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)
@@ -391,7 +431,7 @@ 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
@@ -406,7 +446,7 @@ public class FeatureColourFinderTest
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)
@@ -478,15 +518,15 @@ 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
@@ -510,7 +550,7 @@ public class FeatureColourFinderTest
fr.setFeaturePriority(data);
av.setShowSequenceFeatures(true);
-
+
/*
* position 2, column 1, score 0 - below threshold - default colour
*/
@@ -523,7 +563,7 @@ public class FeatureColourFinderTest
*/
c = finder.findFeatureColour(Color.blue, seq, 3);
assertEquals(c, Color.green);
-
+
/*
* position 7, column 9, score 10 - maximum colour in range
*/