From b5e91918d2443923adb989782372df090206a73c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 25 Mar 2019 16:10:52 +0000
Subject: [PATCH] JAL-3215 extract method, unit test, bug fix

---
 src/jalview/schemes/ScoreColourScheme.java      |   31 ++++++++++----
 test/jalview/schemes/ScoreColourSchemeTest.java |   49 +++++++++++++++++++++++
 2 files changed, 72 insertions(+), 8 deletions(-)
 create mode 100644 test/jalview/schemes/ScoreColourSchemeTest.java

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 66bb5b4..aef5f22 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -53,13 +53,18 @@ public class ScoreColourScheme extends ResidueColourScheme
   /**
    * Constructor
    * 
+   * @param name
    * @param symbolIndex
    *          a lookup where the index is a char e.g. 'R' or 'r', and the value
    *          is its position in the colour table lookup
-   * @param scores
+   * @param theScores
    *          per residue, with indices corresponding to those for colour lookup
+   * @param minColour
+   *          graduated colour at minimum score value
+   * @param maxColour
+   *          graduated colour at maximum score value
    */
-  public ScoreColourScheme(String name, int[] symbolIndex, double[] scores,
+  public ScoreColourScheme(String name, int[] symbolIndex, double[] theScores,
           Color minColour, Color maxColour)
   {
     super(symbolIndex);
@@ -67,14 +72,24 @@ public class ScoreColourScheme extends ResidueColourScheme
     this.minColour = minColour;
     this.maxColour = maxColour;
 
-    setMinMax(scores);
-    this.scores = scores;
+    setMinMax(theScores);
+    computeColours(theScores);
+  }
+
+  /**
+   * Calculates and saves a graduated score based colour for each residue
+   * 
+   * @param theScores
+   */
+  protected void computeColours(double[] theScores)
+  {
+    this.scores = theScores;
 
-    int iSize = scores.length;
-    colors = new Color[scores.length];
+    int iSize = theScores.length;
+    colors = new Color[theScores.length];
     for (int i = 0; i < iSize; i++)
     {
-      colors[i] = getScoreColour(scores[i]);
+      colors[i] = getScoreColour(theScores[i]);
     }
   }
 
@@ -117,7 +132,7 @@ public class ScoreColourScheme extends ResidueColourScheme
     double dMin = Double.MAX_VALUE;
     double dMax = -Double.MAX_VALUE;
 
-    for (int i = 0; i < vals.length - 1; i++)
+    for (int i = 0; i < vals.length; i++)
     {
       dMin = Math.min(dMin, vals[i]);
       dMax = Math.max(dMax, vals[i]);
diff --git a/test/jalview/schemes/ScoreColourSchemeTest.java b/test/jalview/schemes/ScoreColourSchemeTest.java
new file mode 100644
index 0000000..1cba878
--- /dev/null
+++ b/test/jalview/schemes/ScoreColourSchemeTest.java
@@ -0,0 +1,49 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ScoreColourSchemeTest
+{
+  @Test
+  public void testGetScoreColour()
+  {
+    Color minColour = new Color(100, 150, 50);
+    Color maxColour = new Color(20, 220, 90);
+
+    double[] scores = new double[] { 6.2d /* A */, -2.4d /* R */,
+        7.9d /* N */ };
+    ScoreColourScheme cs = new ScoreColourScheme("test",
+            ResidueProperties.aaIndex, scores, minColour, maxColour);
+
+    /*
+     * basic sanity checks
+     */
+    assertEquals(cs.min, -2.4d);
+    assertEquals(cs.max, 7.9d);
+    assertEquals(cs.minColour, minColour);
+    assertEquals(cs.maxColour, maxColour);
+    assertEquals(cs.findColour('R'), minColour);
+    assertEquals(cs.findColour('n'), maxColour);
+    
+    /*
+     * a score of 3 gets a graduated colour between (100, 150, 50) (-2.4) and 
+     * (20, 220, 90) (7.9)
+     */
+    double score = 3d;
+    float f = (float) ((score - cs.min)/ (cs.max - cs.min)); // 5.4 / 10.3
+    assertEquals(f, 0.52427, 0.0001d);
+    int expectR = Math.round(100 + f * (20 - 100)); // 100 - 41.94 = 58.06 = 58
+    assertEquals(expectR, 58);
+    int expectG = Math.round(150 + f * (220 - 150)); // 150 + 36.699 = 187
+    assertEquals(expectG, 187);
+    int expectB = Math.round(50 + f * (90 - 50)); // 50 + 20.97 = 71
+    assertEquals(expectB, 71);
+
+    assertEquals(cs.getScoreColour(score),
+            new Color(expectR, expectG, expectB));
+  }
+}
-- 
1.7.10.2