Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_21...

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

diff --git a/test/jalview/schemes/HmmerGlobalBackgroundTest.java b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
new file mode 100644 (file)
index 0000000..1cdee91
--- /dev/null
+++ b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
@@ -0,0 +1,90 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HmmerGlobalBackgroundTest {
+
+  @Test(groups = "Functional")
+  public void testFindColour() throws MalformedURLException, IOException
+  {
+    HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+            DataSourceType.FILE);
+
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
+    ColourSchemeI scheme = new HmmerGlobalBackground(al);
+
+    /*
+     * 'A' in column 1, node 2, match emission 2.77204
+     * e-2.77204 = 0.0625 
+     * background frequency is 0.0826
+     * ratio is 0.757, log is negative, colour is Orange
+     */
+    Color actual = scheme.findColour('A', 1, null, null, 0);
+    assertEquals(actual, Color.ORANGE);
+
+    // gap is white
+    actual = scheme.findColour('-', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour(' ', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour('.', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+
+    /*
+     * 'Y' in column 4, node 5, match emission 4.41426
+     * e-4.41426 = 0.0121 
+     * background frequency is 0.0292
+     * ratio is 0.414, log is negative, colour is Orange
+     */
+    actual = scheme.findColour('Y', 4, null, null, 0);
+    assertEquals(actual, Color.ORANGE);
+
+    /*
+     * 'M' in column 109, no matching node, colour is reddish
+     */
+    actual = scheme.findColour('M', 109, null, null, 0);
+    assertEquals(actual, new Color(230, 0, 0));
+
+    /*
+     * 'I' in column 6, node 7, match emission 1.33015
+     * e-1.33015 = 0.2644
+     * background frequency is 0.0593
+     * ratio is 4.459, log is 1.495
+     * colour is graduated 1.495/4.52 or 84/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('I', 6, null, null, 0);
+    assertEquals(actual, new Color(171, 171, 255));
+
+    /*
+     * 'V' in column 14, node 15, match emission 0.44769
+     * e-0.44769 = 0.6391
+     * background frequency is 0.0686
+     * ratio is 9.316, log is 2.232
+     * colour is graduated 2.232/4.52 or 126/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('V', 14, null, null, 0);
+    assertEquals(actual, new Color(129, 129, 255));
+
+    /*
+     * invalid symbol is White
+     */
+    actual = scheme.findColour('X', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+  }
+
+}