Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/test/jalview/schemes/HmmerLocalBackgroundTest.java b/test/jalview/schemes/HmmerLocalBackgroundTest.java
new file mode 100644 (file)
index 0000000..5f2bb8f
--- /dev/null
+++ b/test/jalview/schemes/HmmerLocalBackgroundTest.java
@@ -0,0 +1,77 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Sequence;
+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 HmmerLocalBackgroundTest {
+
+  @Test(groups = "Functional")
+  public void testFindColour() throws MalformedURLException, IOException
+  {
+    HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+            DataSourceType.FILE);
+
+    /*
+     * alignment with 20 residues and background frequencies:
+     * A/a, S 3/20 = 0.15
+     * M, K 4/20 = 0.2
+     * V 2/20 = 0.1
+     * Q, R, L 1/20 = 0.05
+     * log(totalCount) = log(20) = 2.996
+     */
+    SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
+    SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AnnotatedCollectionI ac = new Alignment(
+            new SequenceI[]
+            { hmmSeq, seq1, seq2 });
+    ColourSchemeI scheme = new HmmerLocalBackground(ac);
+
+    /*
+     * 'A' in column 1, node 2, match emission 2.77204
+     * e-2.77204 = 0.0625 
+     * background frequency is 0.15
+     * ratio is < 1, 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);
+
+    /*
+     * 'L' in column 3, node 4, match emission 1.98342
+     * e-1.98342 = 0.1376 
+     * background frequency is 0.05
+     * ratio is 2.752, log is 1.012
+     * colour is graduated 1.012/2.996 or 86/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('L', 3, null, null, 0);
+    assertEquals(actual, new Color(169, 169, 255));
+
+    /*
+     * invalid symbol is White
+     */
+    actual = scheme.findColour('X', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+  }
+
+}