Merge branch 'develop' into releases/Release_2_11_2_Branch

[jalview.git] / test / jalview / renderer / ResidueShaderTest.java

diff --git a/test/jalview/renderer/ResidueShaderTest.java b/test/jalview/renderer/ResidueShaderTest.java
index eba5f59..78f00c8 100644 (file)
--- a/test/jalview/renderer/ResidueShaderTest.java
+++ b/test/jalview/renderer/ResidueShaderTest.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;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -161,9 +181,12 @@ public class ResidueShaderTest
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
-    assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
-    assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
-    assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
+    assertEquals(new Color(235, 225, 215),
+            ccs.applyConservation(colour, 7));
+    assertEquals(new Color(215, 195, 175),
+            ccs.applyConservation(colour, 8));
+    assertEquals(new Color(195, 165, 135),
+            ccs.applyConservation(colour, 9));
     assertEquals(colour, ccs.applyConservation(colour, 10));
     assertEquals(colour, ccs.applyConservation(colour, 11));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
@@ -186,10 +209,10 @@ public class ResidueShaderTest
     colours[23] = Color.red; // gap colour
     ColourSchemeI cs = new UserColourScheme(colours);
     rs = new ResidueShader(cs);
-  
+
     assertEquals(Color.red, rs.findColour(' ', 7, null));
     assertEquals(Color.blue, rs.findColour('Q', 7, null));
-  
+
     /*
      * stub Conservation to return a given consensus string
      */
@@ -204,14 +227,14 @@ public class ResidueShaderTest
       }
     };
     rs.setConservation(cons);
-  
+
     /*
      * with 0% threshold, there should be no fading
      */
     rs.setConservationInc(0);
     assertEquals(Color.red, rs.findColour(' ', 7, null));
     assertEquals(Color.blue, rs.findColour('Q', 7, null));
-  
+
     /*
      * with 40% threshold, 'fade factor' is 
      * (11-score)/10 * 40/20 = (11-score)/5
@@ -261,12 +284,14 @@ public class ResidueShaderTest
   protected ProfilesI getStubConsensus(final String modalResidue,
           final float pid)
   {
-    ProfilesI consensus = new ProfilesI() {
+    ProfilesI consensus = new ProfilesI()
+    {
 
       @Override
       public ProfileI get(int i)
       {
-        return new ProfileI() {
+        return new ProfileI()
+        {
           @Override
           public void setCounts(ResidueCount residueCounts)
           {
@@ -312,7 +337,8 @@ public class ResidueShaderTest
           public int getNonGapped()
           {
             return 0;
-         }};
+          }
+        };
       }
 
       @Override
@@ -326,7 +352,7 @@ public class ResidueShaderTest
       {
         return 0;
       }
-      
+
     };
     return consensus;
   }