Update HiddenMarkovModel class

diff --git a/src/jalview/datamodel/EValueStatistic.java b/src/jalview/datamodel/EValueStatistic.java
new file mode 100644 (file)
index 0000000..4641d2e
--- /dev/null
+++ b/src/jalview/datamodel/EValueStatistic.java
@@ -0,0 +1,40 @@
+package jalview.datamodel;
+
+/**
+ * bean which stores e-Value Statistics
+ * 
+ * @author TZVanaalten
+ *
+ */
+public class EValueStatistic
+{
+  final String alignmentModeConfiguration;
+
+  final double locationOfDistribution;
+
+  final double slopeOfDistribution;
+
+  public EValueStatistic(String configuration, double slope,
+          double location)
+  {
+    alignmentModeConfiguration = configuration;
+    locationOfDistribution = location;
+    slopeOfDistribution = slope;
+  }
+
+  public String getAlignmentModeConfiguration()
+  {
+    return alignmentModeConfiguration;
+  }
+
+  public double getLocationOfDistribution()
+  {
+    return locationOfDistribution;
+  }
+
+  public double getSlopeOfDistribution()
+  {
+    return slopeOfDistribution;
+  }
+
+}

diff --git a/test/jalview/datamodel/HiddenMarkovModelTest.java b/test/jalview/datamodel/HiddenMarkovModelTest.java
new file mode 100644 (file)
index 0000000..ae1bf55
--- /dev/null
+++ b/test/jalview/datamodel/HiddenMarkovModelTest.java
@@ -0,0 +1,16 @@
+package jalview.datamodel;
+
+import org.testng.annotations.Test;
+
+public class HiddenMarkovModelTest
+{
+  HiddenMarkovModel hmm = new HiddenMarkovModel();
+
+  @Test
+  public void testGetGatheringThresholdGA1()
+  {
+    hmm.put("GA1", "10.1");
+    // assertEquals(hmm.getGatheringThresholdGA1(), 10.1);
+  }
+
+}
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