JAL-3215 remove redundant min/max constants, refactor ctr, add tests

diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index e6672fc..938417d 100755 (executable)
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -38,8 +38,7 @@ public class BuriedColourScheme extends ScoreColourScheme
    */
   public BuriedColourScheme()
   {
-    super(ResidueProperties.aaIndex, ResidueProperties.buried,
-            ResidueProperties.buriedmin, ResidueProperties.buriedmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.buried);
   }
 
   /**

diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 2724f77..10a7ce5 100755 (executable)
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -29,8 +29,7 @@ public class HelixColourScheme extends ScoreColourScheme
 {
   public HelixColourScheme()
   {
-    super(ResidueProperties.aaIndex, ResidueProperties.helix,
-            ResidueProperties.helixmin, ResidueProperties.helixmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.helix);
   }
 
   @Override

diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index d886bdf..c8cf4c7 100755 (executable)
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -38,8 +38,7 @@ public class HydrophobicColourScheme extends ScoreColourScheme
    */
   public HydrophobicColourScheme()
   {
-    super(ResidueProperties.aaIndex, ResidueProperties.hyd,
-            ResidueProperties.hydmin, ResidueProperties.hydmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.hyd);
   }
 
   /**

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index d435065..fb5d5a8 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -433,35 +433,19 @@ public class ResidueProperties
 
   public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
       1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
-      1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
-
-  public static final double helixmin = 0.57;
-
-  public static final double helixmax = 1.51;
+      1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.57 };
 
   public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
       1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
-      1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
-
-  public static final double strandmin = 0.37;
-
-  public static final double strandmax = 1.7;
+      1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.37 };
 
   public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
       0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
-      0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
-
-  public static final double turnmin = 0.47;
-
-  public static final double turnmax = 1.56;
+      0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0.47, 0.47 };
 
   public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
       1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4,
-      0.3, 1.358, 0.00 };
-
-  public static final double buriedmin = 0.05;
-
-  public static final double buriedmax = 4.6;
+      0.3, 1.358, 0.05 };
 
   // This is hydropathy index
   // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
@@ -470,13 +454,6 @@ public class ResidueProperties
       -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
       -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
 
-  public static final double hydmax = 4.5;
-
-  public static final double hydmin = -3.9;
-
-  // public static final double hydmax = 1.38;
-  // public static final double hydmin = -2.53;
-
   // not currently used
   // public static final Map<String, Color> ssHash = new Hashtable<String,
   // Color>();
@@ -874,21 +851,6 @@ public class ResidueProperties
   {
   }
 
-  public static double getHydmax()
-  {
-    return hydmax;
-  }
-
-  public static double getHydmin()
-  {
-    return hydmin;
-  }
-
-  public static double[] getHyd()
-  {
-    return hyd;
-  }
-
   public static Map<String, Integer> getAA3Hash()
   {
     return aa3Hash;

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index eae76e1..442306d 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -28,10 +28,13 @@ import jalview.util.Comparison;
 import java.awt.Color;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A base class for colour schemes which define a graduated colour range based
+ * on
+ * <ul>
+ * <li>a minimum colour</li>
+ * <li>a maximum colour</li>
+ * <li>a score assigned to each residue</li>
+ * </ul>
  */
 public class ScoreColourScheme extends ResidueColourScheme
 {
@@ -42,23 +45,19 @@ public class ScoreColourScheme extends ResidueColourScheme
   public double[] scores;
 
   /**
-   * Creates a new ScoreColourScheme object.
+   * Constructor
    * 
+   * @param symbolIndex
+   *          a lookup where the index is a character e.g. 'R' or 'r', and the
+   *          value is its position in the colour table lookup
    * @param scores
-   *          DOCUMENT ME!
-   * @param min
-   *          DOCUMENT ME!
-   * @param max
-   *          DOCUMENT ME!
+   *          per residue, indices matching colors lookup
    */
-  public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
-          double max)
+  public ScoreColourScheme(int symbolIndex[], double[] scores)
   {
     super(symbolIndex);
-
+    setMinMax(scores);
     this.scores = scores;
-    this.min = min;
-    this.max = max;
 
     // Make colours in constructor
     // Why wasn't this done earlier?
@@ -84,6 +83,26 @@ public class ScoreColourScheme extends ResidueColourScheme
     }
   }
 
+  /**
+   * Inspects score values and saves the minimum and maximum
+   * 
+   * @param vals
+   */
+  void setMinMax(double[] vals)
+  {
+    double dMin = Double.MAX_VALUE;
+    double dMax = -Double.MAX_VALUE;
+
+    for (int i = 0; i < vals.length - 1; i++)
+    {
+      dMin = Math.min(dMin, vals[i]);
+      dMax = Math.max(dMax, vals[i]);
+    }
+
+    this.min = vals.length == 0 ? 0d : dMin;
+    this.max = vals.length == 0 ? 0d : dMax;
+  }
+
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
@@ -121,6 +140,6 @@ public class ScoreColourScheme extends ResidueColourScheme
   public ColourSchemeI getInstance(AlignViewportI view,
           AnnotatedCollectionI coll)
   {
-    return new ScoreColourScheme(symbolIndex, scores, min, max);
+    return new ScoreColourScheme(symbolIndex, scores);
   }
 }

diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index ef55d69..c1b15e4 100755 (executable)
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -38,8 +38,7 @@ public class StrandColourScheme extends ScoreColourScheme
    */
   public StrandColourScheme()
   {
-    super(ResidueProperties.aaIndex, ResidueProperties.strand,
-            ResidueProperties.strandmin, ResidueProperties.strandmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.strand);
   }
 
   /**

diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 7d8035a..b8b2d90 100755 (executable)
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -38,8 +38,7 @@ public class TurnColourScheme extends ScoreColourScheme
    */
   public TurnColourScheme()
   {
-    super(ResidueProperties.aaIndex, ResidueProperties.turn,
-            ResidueProperties.turnmin, ResidueProperties.turnmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.turn);
   }
 
   /**

diff --git a/test/jalview/schemes/BuriedColourSchemeTest.java b/test/jalview/schemes/BuriedColourSchemeTest.java
index cdb0e80..034fd5d 100644 (file)
--- a/test/jalview/schemes/BuriedColourSchemeTest.java
+++ b/test/jalview/schemes/BuriedColourSchemeTest.java
@@ -9,8 +9,8 @@ import org.testng.annotations.Test;
 public class BuriedColourSchemeTest
 {
   /**
-   * Turn colours are based on the scores in ResidueProperties.buried A = 1.7, R
-   * = 0.1, N = 0.4, D = 0.4... min = 0.05 max = 4.6
+   * Buried colours are derived from the scores in ResidueProperties.buried A =
+   * 1.7, R = 0.1, N = 0.4, D = 0.4... min = 0.05 max = 4.6
    * <p>
    * scores are scaled to c 0-1 between min and max and colour is (0, 1-c, c)
    */
@@ -21,13 +21,43 @@ public class BuriedColourSchemeTest
 
     float min = 0.05f;
     float max = 4.6f;
+    assertEquals((float) scheme.min, min);
+    assertEquals((float) scheme.max, max);
+
     float a = (1.7f - min) / (max - min);
-    assertEquals(scheme.findColour('A', 0, null), new Color(0, 1 - a, a));
+    Color expected = new Color(0, 1 - a, a);
+    assertEquals(scheme.findColour('A', 0, null), expected);
 
     float d = (0.4f - min) / (max - min);
-    assertEquals(scheme.findColour('D', 0, null), new Color(0, 1 - d, d));
+    expected = new Color(0, 1 - d, d);
+    assertEquals(scheme.findColour('D', 0, null), expected);
 
     assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+    assertEquals(scheme.findColour('A', 0, null), new Color(0, 163, 92));
+    assertEquals(scheme.findColour('r', 0, null), new Color(0, 252, 3));
+    assertEquals(scheme.findColour('n', 0, null), new Color(0, 235, 20));
+    assertEquals(scheme.findColour('d', 0, null), new Color(0, 235, 20));
+    assertEquals(scheme.findColour('c', 0, null), new Color(0, 0, 255));
+    assertEquals(scheme.findColour('q', 0, null), new Color(0, 241, 14));
+    assertEquals(scheme.findColour('e', 0, null), new Color(0, 241, 14));
+    assertEquals(scheme.findColour('g', 0, null), new Color(0, 157, 98));
+    assertEquals(scheme.findColour('h', 0, null), new Color(0, 213, 42));
+    assertEquals(scheme.findColour('I', 0, null), new Color(0, 84, 171));
+    assertEquals(scheme.findColour('L', 0, null), new Color(0, 123, 132));
+    assertEquals(scheme.findColour('K', 0, null), new Color(0, 255, 0));
+    assertEquals(scheme.findColour('M', 0, null), new Color(0, 151, 104));
+    assertEquals(scheme.findColour('F', 0, null), new Color(0, 135, 120));
+    assertEquals(scheme.findColour('P', 0, null), new Color(0, 224, 31));
+    assertEquals(scheme.findColour('S', 0, null), new Color(0, 213, 42));
+    assertEquals(scheme.findColour('T', 0, null), new Color(0, 219, 36));
+    assertEquals(scheme.findColour('W', 0, null), new Color(0, 168, 87));
+    assertEquals(scheme.findColour('Y', 0, null), new Color(0, 230, 25));
+    assertEquals(scheme.findColour('v', 0, null), new Color(0, 95, 160));
+    assertEquals(scheme.findColour('b', 0, null), new Color(0, 235, 20));
+    assertEquals(scheme.findColour('z', 0, null), new Color(0, 241, 14));
+    assertEquals(scheme.findColour('x', 0, null), new Color(0, 182, 73));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 0));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 0));
   }
 
 }

diff --git a/test/jalview/schemes/HelixColourSchemeTest.java b/test/jalview/schemes/HelixColourSchemeTest.java
index ed46419..ddca303 100644 (file)
--- a/test/jalview/schemes/HelixColourSchemeTest.java
+++ b/test/jalview/schemes/HelixColourSchemeTest.java
@@ -21,6 +21,9 @@ public class HelixColourSchemeTest
 
     float min = 0.57f;
     float max = 1.51f;
+    assertEquals((float) scheme.min, min);
+    assertEquals((float) scheme.max, max);
+
     float a = (1.42f - min) / (max - min);
     assertEquals(scheme.findColour('A', 0, null), new Color(a, 1 - a, a));
 
@@ -28,6 +31,32 @@ public class HelixColourSchemeTest
     assertEquals(scheme.findColour('D', 0, null), new Color(d, 1 - d, d));
 
     assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+
+    assertEquals(scheme.findColour('A', 0, null), new Color(231, 24, 231));
+    assertEquals(scheme.findColour('r', 0, null), new Color(111, 144, 111));
+    assertEquals(scheme.findColour('n', 0, null), new Color(27, 228, 27));
+    assertEquals(scheme.findColour('d', 0, null), new Color(119, 136, 119));
+    assertEquals(scheme.findColour('c', 0, null), new Color(35, 220, 35));
+    assertEquals(scheme.findColour('q', 0, null), new Color(146, 109, 146));
+    assertEquals(scheme.findColour('e', 0, null), new Color(255, 0, 255));
+    assertEquals(scheme.findColour('g', 0, null), new Color(0, 255, 0));
+    assertEquals(scheme.findColour('h', 0, null), new Color(117, 138, 117));
+    assertEquals(scheme.findColour('I', 0, null), new Color(138, 117, 138));
+    assertEquals(scheme.findColour('L', 0, null), new Color(174, 81, 174));
+    assertEquals(scheme.findColour('K', 0, null), new Color(160, 95, 160));
+    assertEquals(scheme.findColour('M', 0, null), new Color(239, 16, 239));
+    assertEquals(scheme.findColour('F', 0, null), new Color(152, 103, 152));
+    assertEquals(scheme.findColour('P', 0, null), new Color(0, 255, 0));
+    assertEquals(scheme.findColour('S', 0, null), new Color(54, 201, 54));
+    assertEquals(scheme.findColour('T', 0, null), new Color(71, 184, 71));
+    assertEquals(scheme.findColour('W', 0, null), new Color(138, 117, 138));
+    assertEquals(scheme.findColour('Y', 0, null), new Color(33, 222, 33));
+    assertEquals(scheme.findColour('v', 0, null), new Color(133, 122, 133));
+    assertEquals(scheme.findColour('b', 0, null), new Color(73, 182, 73));
+    assertEquals(scheme.findColour('z', 0, null), new Color(201, 54, 201));
+    assertEquals(scheme.findColour('x', 0, null), new Color(117, 138, 117));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 0));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 0));
   }
 
 }

diff --git a/test/jalview/schemes/HydrophobicColourSchemeTest.java b/test/jalview/schemes/HydrophobicColourSchemeTest.java
index f3b93a9..a0a2281 100644 (file)
--- a/test/jalview/schemes/HydrophobicColourSchemeTest.java
+++ b/test/jalview/schemes/HydrophobicColourSchemeTest.java
@@ -19,17 +19,43 @@ public class HydrophobicColourSchemeTest
   {
     ScoreColourScheme scheme = new HydrophobicColourScheme();
 
-    float min = -3.9f;
+    float min = -4.5f;
     float max = 4.5f;
+    assertEquals((float) scheme.min, min);
+    assertEquals((float) scheme.max, max);
+
     float a = (1.8f - min) / (max - min);
-    assertEquals(scheme.findColour('A', 0, null),
- new Color(a, 0, 1 - a));
+    assertEquals(scheme.findColour('A', 0, null), new Color(a, 0, 1 - a));
 
     float d = (-3.5f - min) / (max - min);
-    assertEquals(scheme.findColour('D', 0, null),
- new Color(d, 0, 1 - d));
+    assertEquals(scheme.findColour('D', 0, null), new Color(d, 0, 1 - d));
 
     assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+    assertEquals(scheme.findColour('A', 0, null), new Color(179, 0, 76));
+    assertEquals(scheme.findColour('r', 0, null), new Color(0, 0, 255));
+    assertEquals(scheme.findColour('n', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('d', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('c', 0, null), new Color(198, 0, 57));
+    assertEquals(scheme.findColour('q', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('e', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('g', 0, null), new Color(116, 0, 139));
+    assertEquals(scheme.findColour('h', 0, null), new Color(37, 0, 218));
+    assertEquals(scheme.findColour('I', 0, null), new Color(255, 0, 0));
+    assertEquals(scheme.findColour('L', 0, null), new Color(235, 0, 20));
+    assertEquals(scheme.findColour('K', 0, null), new Color(17, 0, 238));
+    assertEquals(scheme.findColour('M', 0, null), new Color(181, 0, 74));
+    assertEquals(scheme.findColour('F', 0, null), new Color(207, 0, 48));
+    assertEquals(scheme.findColour('P', 0, null), new Color(82, 0, 173));
+    assertEquals(scheme.findColour('S', 0, null), new Color(105, 0, 150));
+    assertEquals(scheme.findColour('T', 0, null), new Color(108, 0, 147));
+    assertEquals(scheme.findColour('W', 0, null), new Color(102, 0, 153));
+    assertEquals(scheme.findColour('Y', 0, null), new Color(91, 0, 164));
+    assertEquals(scheme.findColour('v', 0, null), new Color(247, 0, 9));
+    assertEquals(scheme.findColour('b', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('z', 0, null), new Color(28, 0, 227));
+    assertEquals(scheme.findColour('x', 0, null), new Color(114, 0, 141));
+    assertEquals(scheme.findColour('?', 0, null), new Color(128, 0, 128));
+    assertEquals(scheme.findColour('?', 0, null), new Color(128, 0, 128));
   }
 
 }

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
index b45e0d3..decd9dd 100644 (file)
--- a/test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -102,9 +102,9 @@ public class ResidueColourSchemeTest
      */
     assertTrue(new UserColourScheme().isApplicableTo(peptide));
     assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
-    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {})
             .isApplicableTo(peptide));
-    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+    assertTrue(new ScoreColourScheme(new int[] {}, new double[] {})
             .isApplicableTo(nucleotide));
     ResidueColourScheme rcs = new PIDColourScheme();
     assertTrue(rcs.isApplicableTo(peptide));
@@ -190,7 +190,7 @@ public class ResidueColourSchemeTest
             new RNAInteractionColourScheme().getSchemeName());
     assertEquals("User Defined", new UserColourScheme().getSchemeName());
     assertEquals("Score", new ScoreColourScheme(new int[] {},
-            new double[] {}, 0, 0d).getSchemeName());
+            new double[] {}).getSchemeName());
     assertEquals("% Identity", new PIDColourScheme().getSchemeName());
     assertEquals("Follower", new FollowerColourScheme().getSchemeName());
     assertEquals("T-Coffee Scores",

diff --git a/test/jalview/schemes/StrandColourSchemeTest.java b/test/jalview/schemes/StrandColourSchemeTest.java
index 4a8d0e9..db3f7a2 100644 (file)
--- a/test/jalview/schemes/StrandColourSchemeTest.java
+++ b/test/jalview/schemes/StrandColourSchemeTest.java
@@ -21,15 +21,41 @@ public class StrandColourSchemeTest
 
     float min = 0.37f;
     float max = 1.7f;
+    assertEquals((float) scheme.min, min);
+    assertEquals((float) scheme.max, max);
+
     float a = (0.83f - min) / (max - min);
-    assertEquals(scheme.findColour('A', 0, null),
- new Color(a, a, 1 - a));
+    assertEquals(scheme.findColour('A', 0, null), new Color(a, a, 1 - a));
 
     float d = (0.54f - min) / (max - min);
-    assertEquals(scheme.findColour('D', 0, null),
- new Color(d, d, 1 - d));
+    assertEquals(scheme.findColour('D', 0, null), new Color(d, d, 1 - d));
 
     assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+    assertEquals(scheme.findColour('A', 0, null), new Color(88, 88, 167));
+    assertEquals(scheme.findColour('r', 0, null), new Color(107, 107, 148));
+    assertEquals(scheme.findColour('n', 0, null), new Color(100, 100, 155));
+    assertEquals(scheme.findColour('d', 0, null), new Color(33, 33, 222));
+    assertEquals(scheme.findColour('c', 0, null), new Color(157, 157, 98));
+    assertEquals(scheme.findColour('q', 0, null), new Color(140, 140, 115));
+    assertEquals(scheme.findColour('e', 0, null), new Color(0, 0, 255));
+    assertEquals(scheme.findColour('g', 0, null), new Color(73, 73, 182));
+    assertEquals(scheme.findColour('h', 0, null), new Color(96, 96, 159));
+    assertEquals(scheme.findColour('I', 0, null), new Color(236, 236, 19));
+    assertEquals(scheme.findColour('L', 0, null), new Color(178, 178, 77));
+    assertEquals(scheme.findColour('K', 0, null), new Color(71, 71, 184));
+    assertEquals(scheme.findColour('M', 0, null), new Color(130, 130, 125));
+    assertEquals(scheme.findColour('F', 0, null), new Color(194, 194, 61));
+    assertEquals(scheme.findColour('P', 0, null), new Color(35, 35, 220));
+    assertEquals(scheme.findColour('S', 0, null), new Color(73, 73, 182));
+    assertEquals(scheme.findColour('T', 0, null), new Color(157, 157, 98));
+    assertEquals(scheme.findColour('W', 0, null), new Color(192, 192, 63));
+    assertEquals(scheme.findColour('Y', 0, null), new Color(211, 211, 44));
+    assertEquals(scheme.findColour('v', 0, null), new Color(255, 255, 0));
+    assertEquals(scheme.findColour('b', 0, null), new Color(67, 67, 188));
+    assertEquals(scheme.findColour('z', 0, null), new Color(71, 71, 184));
+    assertEquals(scheme.findColour('x', 0, null), new Color(121, 121, 134));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 0, 255));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 0, 255));
   }
 
 }

diff --git a/test/jalview/schemes/TurnColourSchemeTest.java b/test/jalview/schemes/TurnColourSchemeTest.java
index 5e6baf0..29b555a 100644 (file)
--- a/test/jalview/schemes/TurnColourSchemeTest.java
+++ b/test/jalview/schemes/TurnColourSchemeTest.java
@@ -21,6 +21,9 @@ public class TurnColourSchemeTest
 
     float min = 0.47f;
     float max = 1.56f;
+    assertEquals((float) scheme.min, min);
+    assertEquals((float) scheme.max, max);
+
     float a = (0.66f - min) / (max - min);
     assertEquals(scheme.findColour('A', 0, null),
             new Color(a, 1 - a, 1 - a));
@@ -30,6 +33,31 @@ public class TurnColourSchemeTest
             new Color(d, 1 - d, 1 - d));
 
     assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+    assertEquals(scheme.findColour('A', 0, null), new Color(44, 211, 211));
+    assertEquals(scheme.findColour('r', 0, null), new Color(112, 143, 143));
+    assertEquals(scheme.findColour('n', 0, null), new Color(255, 0, 0));
+    assertEquals(scheme.findColour('d', 0, null), new Color(232, 23, 23));
+    assertEquals(scheme.findColour('c', 0, null), new Color(168, 87, 87));
+    assertEquals(scheme.findColour('q', 0, null), new Color(119, 136, 136));
+    assertEquals(scheme.findColour('e', 0, null), new Color(63, 192, 192));
+    assertEquals(scheme.findColour('g', 0, null), new Color(255, 0, 0));
+    assertEquals(scheme.findColour('h', 0, null), new Color(112, 143, 143));
+    assertEquals(scheme.findColour('I', 0, null), new Color(0, 255, 255));
+    assertEquals(scheme.findColour('L', 0, null), new Color(28, 227, 227));
+    assertEquals(scheme.findColour('K', 0, null), new Color(126, 129, 129));
+    assertEquals(scheme.findColour('M', 0, null), new Color(30, 225, 225));
+    assertEquals(scheme.findColour('F', 0, null), new Color(30, 225, 225));
+    assertEquals(scheme.findColour('P', 0, null), new Color(246, 9, 9));
+    assertEquals(scheme.findColour('S', 0, null), new Color(225, 30, 30));
+    assertEquals(scheme.findColour('T', 0, null), new Color(115, 140, 140));
+    assertEquals(scheme.findColour('W', 0, null), new Color(115, 140, 140));
+    assertEquals(scheme.findColour('Y', 0, null), new Color(157, 98, 98));
+    assertEquals(scheme.findColour('v', 0, null), new Color(7, 248, 248));
+    assertEquals(scheme.findColour('b', 0, null), new Color(243, 12, 12));
+    assertEquals(scheme.findColour('z', 0, null), new Color(91, 164, 164));
+    assertEquals(scheme.findColour('x', 0, null), new Color(124, 131, 131));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 255));
+    assertEquals(scheme.findColour('?', 0, null), new Color(0, 255, 255));
   }
 
 }