JAL-1632 'includeGaps' applied to FeatureDistanceModel (needs review)

[jalview.git] / test / jalview / analysis / scoremodels / FeatureDistanceModelTest.java

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 1ebef8e..2411b55 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,10 +23,15 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -258,10 +263,91 @@ public class FeatureDistanceModelTest
     assertEquals(distances.height(), 2);
     assertEquals(distances.getValue(0, 0), 0d);
     assertEquals(distances.getValue(1, 1), 0d);
+
     // these left to fail pending resolution of
-    // JAL-2424 (dividing score by 6, not 5)
+    // JAL-2424 (computing score as 5/6, should be 5/5)
     assertEquals(distances.getValue(0, 1), 1f);
     assertEquals(distances.getValue(1, 0), 1f);
   }
 
+  /**
+   * Verify computed distances with varying parameter options
+   */
+  @Test(groups = "Functional")
+  public void testFindDistances_withParams()
+  {
+    AlignFrame af = setupAlignmentView();
+    AlignViewport viewport = af.getViewport();
+    AlignmentView view = viewport.getAlignmentView(false);
+
+    FeatureDistanceModel sm = new FeatureDistanceModel();
+    sm.configureFromAlignmentView(af.alignPanel);
+  
+    /*
+     * feature distance model always normalises by region width
+     * gap-gap is always included (but scores zero)
+     * the only variable parameter is 'includeGaps'
+     */
+
+    /*
+     * include gaps
+     * score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
+    // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
+     */
+    SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+    MatrixI distances = sm.findDistances(view, params);
+    assertEquals(distances.getValue(0, 0), 0d);
+    assertEquals(distances.getValue(1, 1), 0d);
+    assertEquals(distances.getValue(0, 1), 13d / 7); // should be 13d/6
+    assertEquals(distances.getValue(1, 0), 13d / 7);
+  
+    /*
+     * exclude gaps
+     * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
+    // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
+     */
+    params = new SimilarityParams(true, true, false, true);
+    distances = sm.findDistances(view, params);
+    assertEquals(distances.getValue(0, 1), 6d / 7);// should be 6d/6
+  }
+
+  /**
+   * <pre>
+   * Set up
+   *   column      1 2 3 4 5 6
+   *        seq s1 F R - K - S
+   *        seq s2 F S - - L
+   *   s1 chain    c c   c   c
+   *   s1 domain   d d   d   d
+   *   s2 chain    c c     c
+   *   s2 metal    m m     m
+   *   s2 Pfam     P P     P
+   *      scores:  3 3 0 2 3 2
+   * </pre>
+   * 
+   * @return
+   */
+  protected AlignFrame setupAlignmentView()
+  {
+    /*
+     * for now, using space for gap to match callers of
+     * AlignmentView.getSequenceStrings()
+     * may change this to '-' (with corresponding change to matrices)
+     */
+    SequenceI s1 = new Sequence("s1", "FR K S");
+    SequenceI s2 = new Sequence("s2", "FS  L");
+
+    s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null));
+    s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f,
+            null));
+    s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null));
+    s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null));
+    s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null));
+    AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
+    AlignFrame af = new AlignFrame(al, 300, 300);
+    af.setShowSeqFeatures(true);
+    af.getFeatureRenderer().findAllFeatures(true);
+    return af;
+  }
+
 }