Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / test / jalview / schemes / Blosum62ColourSchemeTest.java

diff --git a/test/jalview/schemes/Blosum62ColourSchemeTest.java b/test/jalview/schemes/Blosum62ColourSchemeTest.java
new file mode 100644 (file)
index 0000000..0b5b6bd
--- /dev/null
+++ b/test/jalview/schemes/Blosum62ColourSchemeTest.java
@@ -0,0 +1,56 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class Blosum62ColourSchemeTest
+{
+  /**
+   * Test the method that determines colour as:
+   * <ul>
+   * <li>white if there is no consensus</li>
+   * <li>white if 'residue' is a gap</li>
+   * <li>dark blue if residue matches consensus (or joint consensus)</li>
+   * <li>else, total the residue's Blosum score with the consensus residue(s)</li>
+   * <ul>
+   * <li>if positive, light blue, else white</li>
+   * </ul>
+   * <ul>
+   */
+  @Test
+  public void testFindColour()
+  {
+    ColourSchemeI blosum = new Blosum62ColourScheme();
+    Color lightBlue = new Color(204, 204, 255);
+    Color darkBlue = new Color(154, 154, 255);
+
+    /*
+     * findColour does not use column, sequence or pid score
+     * we assume consensus residue is computed as upper case
+     */
+    assertEquals(blosum.findColour('A', 0, null, "A", 0f), darkBlue);
+    assertEquals(blosum.findColour('a', 0, null, "A", 0f), darkBlue);
+
+    /*
+     * L has a Blosum score of 
+     * -1 with A
+     * -4 with B
+     * 0 with F
+     * 2 with I
+     * -1 with T
+     * 1 with V
+     * etc
+     */
+    assertEquals(blosum.findColour('L', 0, null, "A", 0f), Color.white); // -1
+    assertEquals(blosum.findColour('L', 0, null, "B", 0f), Color.white); // -4
+    assertEquals(blosum.findColour('L', 0, null, "F", 0f), Color.white); // 0
+    assertEquals(blosum.findColour('L', 0, null, "I", 0f), lightBlue); // 2
+    assertEquals(blosum.findColour('L', 0, null, "TV", 0f), Color.white); // 0
+    assertEquals(blosum.findColour('L', 0, null, "IV", 0f), lightBlue); // 3
+    assertEquals(blosum.findColour('L', 0, null, "IT", 0f), lightBlue); // 1
+    assertEquals(blosum.findColour('L', 0, null, "IAT", 0f), Color.white); // 0
+  }
+}