Updated with latest from mchmmer branch

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

diff --git a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
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+++ b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
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+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 java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMProbabilityDistributionAnalyserTest {
+
+  HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+  @Test
+  public void testMoveToFile() throws IOException
+  {
+
+    BufferedReader br = new BufferedReader(new FileReader(
+            "test/jalview/util/test_Fams_for_probability_analysis"));
+    analyser.moveLocationBy(1, br);
+
+    String line = br.readLine();
+    assertEquals(line, "# STOCKHOLM 1.0");
+    line = br.readLine();
+    assertEquals(line, "seq1 ATW");
+    line = br.readLine();
+    assertEquals(line, "seq2 ATI");
+
+  }
+
+  @Test
+  public void testCountValidResidues()
+  {
+    analyser.sequences = new Vector<>();
+    analyser.hmm = new HiddenMarkovModel();
+    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.setResidueNumber(i - 1);
+      nodes.add(node);
+
+    }
+    PA.setValue(analyser.hmm, "nodes", nodes);
+
+    SequenceI[] sequence = new Sequence[] {
+        new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
+        new Sequence("seq3", "--.ATccGc") };
+    analyser.sequences.add(sequence[0]);
+    analyser.sequences.add(sequence[1]);
+    analyser.sequences.add(sequence[2]);
+
+    int count = analyser.countValidResidues();
+    assertEquals(count, 16);
+  }
+
+  @Test(priority = 0)
+  public void testReadBinned() throws IOException
+  {
+    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);
+  }
+
+  @Test
+  public void testReadRaw() throws IOException
+  {
+    analyser.readRaw("test/jalview/util/");
+    List<ArrayList<Double>> list = analyser.raw;
+
+    assertEquals(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);
+
+  }
+
+  @Test(priority = 1)
+  public void testProcessData() throws IOException
+  {
+    analyser.keepRaw = true;
+    BufferedReader brFam = new BufferedReader(new FileReader(
+            "test/jalview/util/test_Fams_for_probability_analysis"));
+    BufferedReader brHMM = new BufferedReader(new FileReader(
+            "test/jalview/util/test_HMMs_for_probability_analysis"));
+    analyser.readStockholm(brFam);
+    analyser.readHMM(brHMM);
+    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);
+
+  }
+}