X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureColourFinderTest.java;h=c0095fe55de459cc5c64b4ef6e2973202e34c12a;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=a7f228972b19800a39f3a032f42cc6cb2ccdd393;hpb=5adae4008da23589cee57f638dfe02095e1840fd;p=jalview.git

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index a7f2289..c0095fe 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -2,22 +2,26 @@ 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.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.BeforeClass;
 import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 /**
@@ -39,7 +43,7 @@ import org.testng.annotations.Test;
  */
 public class FeatureColourFinderTest
 {
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private SequenceI seq;
 
@@ -49,7 +53,7 @@ public class FeatureColourFinderTest
 
   private FeatureRenderer fr;
 
-  @BeforeClass(alwaysRun = true)
+  @BeforeTest(alwaysRun = true)
   public void setUp()
   {
     // aligned column 8 is sequence position 6
@@ -63,18 +67,16 @@ public class FeatureColourFinderTest
   }
 
   /**
-   * 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);
 
@@ -85,6 +87,9 @@ public class FeatureColourFinderTest
     {
       fr.setGroupVisibility(group, true);
     }
+
+    fr.clearRenderOrder();
+    av.setShowSequenceFeatures(true);
   }
 
   @Test(groups = "Functional")
@@ -122,6 +127,10 @@ public class FeatureColourFinderTest
     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()
   {
@@ -131,7 +140,7 @@ public class FeatureColourFinderTest
     fr.featuresAdded();
     av.setShowSequenceFeatures(true);
     Color c = finder.findFeatureColour(null, seq, 6);
-    assertEquals(c, Color.white);
+    assertNull(c);
   }
 
   @Test(groups = "Functional")
@@ -164,9 +173,9 @@ 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);
@@ -174,7 +183,7 @@ 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);
@@ -208,8 +217,8 @@ 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);
@@ -217,7 +226,7 @@ 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);
@@ -278,6 +287,28 @@ 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,
@@ -292,7 +323,7 @@ public class FeatureColourFinderTest
      */
     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);
@@ -369,9 +400,9 @@ 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));
@@ -381,7 +412,7 @@ public class FeatureColourFinderTest
      * 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));
@@ -397,9 +428,10 @@ public class FeatureColourFinderTest
 
     /*
      * 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);
@@ -416,8 +448,8 @@ 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());
 
@@ -433,5 +465,93 @@ public class FeatureColourFinderTest
      */
     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);
   }
 }