X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Futil%2FHMMProbabilityDistributionAnalyserTest.java;h=ec59c1465097d23c0977c1e4005fe2790f75cef5;hb=614e136583b401b4273d92723fec158d84d4cb52;hp=a6b93f55ccd57f50b90a1d50c2220d1b78f01a9f;hpb=dad3f91c2f9a38ce8c64a688b6f1ba4f539af9fc;p=jalview.git

diff --git a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
index a6b93f5..ec59c14 100644
--- a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
+++ b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
@@ -1,13 +1,13 @@
 package jalview.util;
 
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNull;
-
 import jalview.datamodel.HMMNode;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
@@ -18,6 +18,8 @@ import java.util.Vector;
 
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class HMMProbabilityDistributionAnalyserTest {
 
   HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
@@ -51,11 +53,11 @@ public class HMMProbabilityDistributionAnalyserTest {
     for (int i = 1; i < 9; i++)
     {
       HMMNode node = new HMMNode();
-      node.setAlignmentColumn(i - 1);
+      node.setResidueNumber(i - 1);
       nodes.add(node);
 
     }
-    analyser.hmm.setNodes(nodes);
+    PA.setValue(analyser.hmm, "nodes", nodes);
 
     SequenceI[] sequence = new Sequence[] {
         new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
@@ -73,10 +75,10 @@ public class HMMProbabilityDistributionAnalyserTest {
   {
     analyser.readBinned("test/jalview/util/");
     Map<String, Double> map = analyser.binned;
-    assertEquals(map.get("1.8"), 4.53);
-    assertEquals(map.get("3.4"), 2.65);
-    assertEquals(map.get("6.4"), 10.8);
-    assertEquals(map.get("0"), 5.4);
+    assertEquals((double) map.get("1.8"), 4.53);
+    assertEquals((double) map.get("3.4"), 2.65);
+    assertEquals((double) map.get("6.4"), 10.8);
+    assertEquals((double) map.get("0"), 5.4);
   }
 
   @Test
@@ -85,11 +87,11 @@ public class HMMProbabilityDistributionAnalyserTest {
     analyser.readRaw("test/jalview/util/");
     List<ArrayList<Double>> list = analyser.raw;
 
-    assertEquals(list.get(0).get(0), 1.43);
+    assertEquals((double) list.get(0).get(0), 1.43);
     assertNull(list.get(0).get(2));
-    assertEquals(list.get(1).get(1), 1.2);
-    assertEquals(list.get(2).get(0), 5.6);
-    assertEquals(list.get(2).get(2), 6.8);
+    assertEquals((double) list.get(1).get(1), 1.2);
+    assertEquals((double) list.get(2).get(0), 5.6);
+    assertEquals((double) list.get(2).get(2), 6.8);
 
   }
 
@@ -106,12 +108,12 @@ public class HMMProbabilityDistributionAnalyserTest {
     analyser.processData(6);
     Map<String, Double> map = analyser.binned;
     List<ArrayList<Double>> list = analyser.raw;
-    assertEquals(map.get("1.8"), 4.863, 0.001d);
-    assertEquals(map.get("3.4"), 2.65);
-    assertEquals(map.get("0"), 5.4);
-    assertEquals(map.get("6.4"), 10.8);
-    assertEquals(map.get("1.4"), 0.166667, 0.00001d);
-    assertEquals(map.get("4.4"), 0.5);
+    assertEquals((double) map.get("1.8"), 4.863d, 0.001d);
+    assertEquals((double) map.get("3.4"), 2.65);
+    assertEquals((double) map.get("0"), 5.4);
+    assertEquals((double) map.get("6.4"), 10.8);
+    assertEquals((double) map.get("1.4"), 0.166667, 0.00001d);
+    assertEquals((double) map.get("4.4"), 0.5);
 
   }
 }