Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[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 6df8a66..16ca70d 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,6 +23,7 @@ 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;
@@ -84,18 +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);
@@ -113,12 +114,12 @@ 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(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
@@ -133,11 +134,11 @@ 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(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
@@ -153,11 +154,12 @@ 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(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(
@@ -197,22 +199,22 @@ public class FeatureDistanceModelTest
     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)
+    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)
+    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)
+    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)
+    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)
+    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)
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
             .size(), 0);
   }
 
@@ -252,21 +254,20 @@ public class FeatureDistanceModelTest
     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), SimilarityParams.Jalview);
+    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 (computing score as 5/6, should be 5/5)
-    // see also PCATest.testComputeSimilarity_featureDistances()
     assertEquals(distances.getValue(0, 1), 1d,
             "expected identical pairs. (check normalisation for similarity score)");
     assertEquals(distances.getValue(1, 0), 1d);
@@ -282,9 +283,10 @@ public class FeatureDistanceModelTest
     AlignViewport viewport = af.getViewport();
     AlignmentView view = viewport.getAlignmentView(false);
 
-    FeatureDistanceModel sm = new FeatureDistanceModel();
-    sm.configureFromAlignmentView(af.alignPanel);
-  
+    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)
@@ -305,7 +307,6 @@ public class FeatureDistanceModelTest
     /*
      * 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);