From 2c0e6c2187f27dd7c6860818516daf1419effa76 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Thu, 15 Jun 2017 12:38:03 +0100
Subject: [PATCH] Update HiddenMarkovModel class

---
 src/jalview/datamodel/EValueStatistic.java        |   40 +++++++++++++++++++++
 test/jalview/datamodel/HiddenMarkovModelTest.java |   16 +++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 src/jalview/datamodel/EValueStatistic.java
 create mode 100644 test/jalview/datamodel/HiddenMarkovModelTest.java

diff --git a/src/jalview/datamodel/EValueStatistic.java b/src/jalview/datamodel/EValueStatistic.java
new file mode 100644
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
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);
+  }
+
+}
\ No newline at end of file
-- 
1.7.10.2