Merge branch 'develop' into releases/Release_2_11_2_Branch

[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 6b1fbd2..6b87dd4 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
@@ -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);
@@ -265,8 +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);
@@ -311,12 +330,12 @@ 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 +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
@@ -382,7 +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)
@@ -391,7 +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
@@ -406,7 +425,7 @@ 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 +497,15 @@ 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 +529,7 @@ public class FeatureColourFinderTest
     fr.setFeaturePriority(data);
 
     av.setShowSequenceFeatures(true);
-  
+
     /*
      * position 2, column 1, score 0 - below threshold - default colour
      */
@@ -523,7 +542,7 @@ public class FeatureColourFinderTest
      */
     c = finder.findFeatureColour(Color.blue, seq, 3);
     assertEquals(c, Color.green);
-  
+
     /*
      * position 7, column 9, score 10 - maximum colour in range
      */