X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModelTest.java;h=a1623f62b7ea4a080ca6cae82a64bd60e5064a50;hb=49db0dff1da16c3355b43a41498c1fc93ef47e91;hp=4bcf5ab4b2cf95935f33729ff5dbd4a6a89e4807;hpb=917622345899487d12d4e12bc1e0272d6ca86a87;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 4bcf5ab..a1623f6 100644
--- 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.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
@@ -32,7 +33,6 @@ 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;
@@ -85,18 +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);
@@ -199,22 +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);
   }
 
@@ -280,7 +280,7 @@ public class FeatureDistanceModelTest
   public void testFindDistances_withParams()
   {
     AlignFrame af = setupAlignmentView();
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     AlignmentView view = viewport.getAlignmentView(false);
 
     ScoreModelI sm = new FeatureDistanceModel();