JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

[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 8b84829..cd6d7f5 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -21,6 +21,7 @@
 package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
@@ -29,6 +30,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.math.MatrixI;
 
 import java.util.Arrays;
 
@@ -98,7 +100,7 @@ public class FeatureDistanceModelTest
     alf.getFeatureRenderer().findAllFeatures(true);
     Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
             .size(), 3, "Number of feature types");
-    Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+    assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     return alf;
   }
 
@@ -107,15 +109,16 @@ public class FeatureDistanceModelTest
   {
     AlignFrame alf = getTestAlignmentFrame();
     FeatureDistanceModel fsm = new FeatureDistanceModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+    MatrixI dm = fsm
+            .findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue(dm[0][2] == 0f,
+    assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
-    Assert.assertTrue(dm[0][1] > dm[0][2],
+    assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
   }
 
@@ -126,14 +129,15 @@ public class FeatureDistanceModelTest
     // hiding first two columns shouldn't affect the tree
     alf.getViewport().hideColumns(0, 1);
     FeatureDistanceModel fsm = new FeatureDistanceModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+    MatrixI dm = fsm
+            .findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue(dm[0][2] == 0f,
+    assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
-    Assert.assertTrue(dm[0][1] > dm[0][2],
+    assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
   }
 
@@ -145,20 +149,23 @@ public class FeatureDistanceModelTest
     alf.getViewport().hideColumns(3, 4);
     alf.getViewport().hideColumns(0, 1);
     FeatureDistanceModel fsm = new FeatureDistanceModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+    MatrixI dm = fsm
+            .findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue(
-            dm[0][2] == 0f,
+    assertEquals(
+            dm.getValue(0, 2),
+            0d,
             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
-    Assert.assertTrue(
-            dm[0][1] == 0f,
+    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++)
     {
-      Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns "
+      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)");
     }
@@ -179,7 +186,7 @@ public class FeatureDistanceModelTest
     SequenceFeature sf = null;
     sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
     aseq.addSequenceFeature(sf);
-    Assert.assertTrue(sf.isContactFeature());
+    assertTrue(sf.isContactFeature());
     af.refreshFeatureUI(true);
     af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
     Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
@@ -241,19 +248,20 @@ public class FeatureDistanceModelTest
     alf.getFeatureRenderer().findAllFeatures(true);
 
     FeatureDistanceModel fsm = new FeatureDistanceModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    float[][] distances = fsm.findDistances(alf.getViewport()
+    MatrixI distances = fsm.findDistances(alf.getViewport()
             .getAlignmentView(true));
-    assertEquals(distances.length, 2);
-    assertEquals(distances[0][0], 0f);
-    assertEquals(distances[1][1], 0f);
+    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[0][1], 1f);
-    assertEquals(distances[1][0], 1f);
+    assertEquals(distances.getValue(0, 1), 1f);
+    assertEquals(distances.getValue(1, 0), 1f);
   }
 
 }