Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / test / jalview / renderer / seqfeatures / FeatureColourFinderTest.java

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 637bbf4..c22ce7d 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -25,10 +25,10 @@ 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 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;
@@ -37,13 +37,14 @@ import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
+import jalview.api.AlignViewportI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
+
 /**
  * Unit tests for feature colour determination, including but not limited to
  * <ul>
@@ -63,7 +64,7 @@ import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  */
 public class FeatureColourFinderTest
 {
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private SequenceI seq;
 
@@ -73,12 +74,13 @@ public class FeatureColourFinderTest
 
   private FeatureRendererModel fr;
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(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();
@@ -153,8 +155,8 @@ 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);
@@ -182,7 +184,6 @@ public class FeatureColourFinderTest
     Color c = finder.findFeatureColour(null, seq, 15);
     assertEquals(c, fr.getColor(sf2, fc));
   }
-
   @Test(groups = "Functional")
   public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
   {
@@ -305,8 +306,8 @@ 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);
@@ -351,12 +352,12 @@ 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
@@ -396,7 +397,7 @@ 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
@@ -422,7 +423,7 @@ 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)
@@ -431,7 +432,7 @@ 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
@@ -446,7 +447,7 @@ 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)
@@ -518,15 +519,15 @@ 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
@@ -550,7 +551,7 @@ public class FeatureColourFinderTest
     fr.setFeaturePriority(data);
 
     av.setShowSequenceFeatures(true);
-
+  
     /*
      * position 2, column 1, score 0 - below threshold - default colour
      */
@@ -563,7 +564,7 @@ public class FeatureColourFinderTest
      */
     c = finder.findFeatureColour(Color.blue, seq, 3);
     assertEquals(c, Color.green);
-
+  
     /*
      * position 7, column 9, score 10 - maximum colour in range
      */