X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModelTest.java;h=92f15429a87778b1fb22cd891e4561bed9021693;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=cd6d7f510089b68d8aff8b75a6dcc153e75ce4ab;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index cd6d7f5..92f1542 100644
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,10 +23,16 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.analysis.ScoreModelI;
+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;
@@ -69,8 +75,8 @@ public class FeatureDistanceModelTest
    */
   public AlignFrame getTestAlignmentFrame()
   {
-    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
-            alntestFile, DataSourceType.PASTE);
+    AlignFrame alf = new FileLoader(false)
+            .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE);
     AlignmentI al = alf.getViewport().getAlignment();
     Assert.assertEquals(al.getHeight(), 4);
     Assert.assertEquals(al.getWidth(), 5);
@@ -79,18 +85,18 @@ public class FeatureDistanceModelTest
       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
       if (sf1[i * 2] > 0)
       {
-        ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
-                sf1[i * 2], sf1[i * 2 + 1], "sf1"));
+        ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
+                sf1[i * 2 + 1], "sf1"));
       }
       if (sf2[i * 2] > 0)
       {
-        ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
-                sf2[i * 2], sf2[i * 2 + 1], "sf2"));
+        ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
+                sf2[i * 2 + 1], "sf2"));
       }
       if (sf3[i * 2] > 0)
       {
-        ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
-                sf3[i * 2], sf3[i * 2 + 1], "sf3"));
+        ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
+                sf3[i * 2 + 1], "sf3"));
       }
     }
     alf.setShowSeqFeatures(true);
@@ -98,8 +104,9 @@ public class FeatureDistanceModelTest
     alf.getFeatureRenderer().setVisible("sf2");
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
-    Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
-            .size(), 3, "Number of feature types");
+    Assert.assertEquals(
+            alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3,
+            "Number of feature types");
     assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     return alf;
   }
@@ -108,14 +115,13 @@ public class FeatureDistanceModelTest
   public void testFeatureScoreModel() throws Exception
   {
     AlignFrame alf = getTestAlignmentFrame();
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
@@ -128,13 +134,12 @@ public class FeatureDistanceModelTest
     AlignFrame alf = getTestAlignmentFrame();
     // hiding first two columns shouldn't affect the tree
     alf.getViewport().hideColumns(0, 1);
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
@@ -148,26 +153,25 @@ public class FeatureDistanceModelTest
     // hide columns and check tree changes
     alf.getViewport().hideColumns(3, 4);
     alf.getViewport().hideColumns(0, 1);
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    // getName() can become static in Java 8
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
-    assertEquals(
-            dm.getValue(0, 2),
-            0d,
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
+    assertEquals(dm.getValue(0, 2), 0d,
             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
-    assertEquals(
-            dm.getValue(0, 1),
-            0d,
+    assertEquals(dm.getValue(0, 1), 0d,
             "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
     for (int s = 0; s < 3; s++)
     {
-      assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
-              + alf.getViewport().getAlignment().getSequenceAt(s).getName()
-              + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
+      assertTrue(dm.getValue(s, 3) > 0d,
+              "After hiding last two columns "
+                      + alf.getViewport().getAlignment().getSequenceAt(s)
+                              .getName()
+                      + "(" + s
+                      + ") should still be distinct from FER1_MAIZE (3)");
     }
   }
 
@@ -189,26 +193,33 @@ public class FeatureDistanceModelTest
     assertTrue(sf.isContactFeature());
     af.refreshFeatureUI(true);
     af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
-    Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
-            .size(), 1, "Should be just one feature type displayed");
+    Assert.assertEquals(
+            af.getFeatureRenderer().getDisplayedFeatureTypes().size(), 1,
+            "Should be just one feature type displayed");
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
-            .size(), 1);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(),
+            1);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
-            .size(), 1);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(),
+            1);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(),
+            0);
   }
 
   @Test(groups = { "Functional" })
@@ -232,36 +243,120 @@ public class FeatureDistanceModelTest
      *     20120 (two features of the same type doesn't affect score)
      *  giving an average (pairwise distance) of 5/5 or 1.0 
      */
-    s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
-            null));
-    s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
-            null));
-    s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
-            null));
+    s1.addSequenceFeature(
+            new SequenceFeature("domain", null, 1, 3, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("variant", null, 2, 4, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("variant", null, 3, 5, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("domain", null, 2, 4, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("variant", null, 1, 2, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("variant", null, 5, 5, 0f, null));
     alf.setShowSeqFeatures(true);
     alf.getFeatureRenderer().findAllFeatures(true);
 
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI distances = fsm.findDistances(alf.getViewport()
-            .getAlignmentView(true));
+    AlignmentView alignmentView = alf.getViewport().getAlignmentView(true);
+    MatrixI distances = sm.findDistances(alignmentView,
+            SimilarityParams.Jalview);
     assertEquals(distances.width(), 2);
     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)
-    assertEquals(distances.getValue(0, 1), 1f);
-    assertEquals(distances.getValue(1, 0), 1f);
+
+    assertEquals(distances.getValue(0, 1), 1d,
+            "expected identical pairs. (check normalisation for similarity score)");
+    assertEquals(distances.getValue(1, 0), 1d);
+  }
+
+  /**
+   * 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);
+
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            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
+     */
+    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 / 6); // should be 13d/6
+    assertEquals(distances.getValue(1, 0), 13d / 6);
+
+    /*
+     * exclude gaps
+     * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
+     */
+    params = new SimilarityParams(true, true, false, true);
+    distances = sm.findDistances(view, params);
+    assertEquals(distances.getValue(0, 1), 6d / 6);// 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;
   }
 
 }