JAL-838 added 'SeqSpace' PID mode, added parameters to findDistances and

[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 cd6d7f5..1ebef8e 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -113,9 +113,9 @@ public class FeatureDistanceModelTest
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.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),
@@ -132,9 +132,9 @@ public class FeatureDistanceModelTest
     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.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),
@@ -152,9 +152,9 @@ public class FeatureDistanceModelTest
     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.findDistances(
+            alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(
             dm.getValue(0, 2),
             0d,
@@ -253,7 +253,7 @@ public class FeatureDistanceModelTest
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
     MatrixI distances = fsm.findDistances(alf.getViewport()
-            .getAlignmentView(true));
+            .getAlignmentView(true), SimilarityParams.Jalview);
     assertEquals(distances.width(), 2);
     assertEquals(distances.height(), 2);
     assertEquals(distances.getValue(0, 0), 0d);