JAL-2994 disable tests for FileUtils path search methods on bamboo

[jalview.git] / test / jalview / util / HMMProbabilityDistributionAnalyserTest.java

diff --git a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
index 815ea66..4dbf05e 100644 (file)
--- a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
+++ b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
@@ -7,8 +7,6 @@ import jalview.datamodel.HMMNode;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -20,6 +18,8 @@ import java.util.Vector;
 
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class HMMProbabilityDistributionAnalyserTest {
 
   HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
@@ -46,18 +46,18 @@ public class HMMProbabilityDistributionAnalyserTest {
   {
     analyser.sequences = new Vector<>();
     analyser.hmm = new HiddenMarkovModel();
-    analyser.hmm.addFileProperty("LENG", "8");
+    analyser.hmm.setProperty("LENG", "8");
 
     List<HMMNode> nodes = new ArrayList<>();
     nodes.add(new HMMNode());
     for (int i = 1; i < 9; i++)
     {
       HMMNode node = new HMMNode();
-      node.setAlignmentColumn(i);
+      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"),
@@ -103,10 +103,8 @@ public class HMMProbabilityDistributionAnalyserTest {
             "test/jalview/util/test_Fams_for_probability_analysis"));
     BufferedReader brHMM = new BufferedReader(new FileReader(
             "test/jalview/util/test_HMMs_for_probability_analysis"));
-    FileParse parserFam = new FileParse(brFam, "", DataSourceType.FILE);
-    FileParse parserHMM = new FileParse(brHMM, "", DataSourceType.FILE);
-    analyser.readStockholm(parserFam);
-    analyser.readHMM(parserHMM);
+    analyser.readStockholm(brFam);
+    analyser.readHMM(brHMM);
     analyser.processData(6);
     Map<String, Double> map = analyser.binned;
     List<ArrayList<Double>> list = analyser.raw;