Add HiddenMarkovModel class

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
new file mode 100644 (file)
index 0000000..b422ef1
--- /dev/null
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -0,0 +1,143 @@
+package jalview.datamodel;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Data structure to hold a HMM file
+ */
+/**
+ * @author TZVanaalten
+ * 
+ */
+public class HiddenMarkovModel
+{
+
+  // Stores file properties
+  private Map<String, String> fileProperties = new HashMap<>();
+
+  public String getAccessionNumber()
+  {
+    return fileProperties.get("ACC");
+  }
+
+  public String getDescription()
+  {
+    return fileProperties.get("DESC");
+  }
+
+  public int getModelLength()
+  {
+    return Integer.parseInt(fileProperties.get("LENG"));
+  }
+
+  public int getMaxInstanceLength()
+  {
+    return Integer.parseInt(fileProperties.get("MAXL"));
+  }
+
+  // gets type of symbol alphabet - "amino", "DNA", "RNA"
+  public String getAlphabetType()
+  {
+    return fileProperties.get("ALPH");
+  }
+
+  // returns boolean indicating whether the reference annotation character field
+  // for each match state is valid or ignored
+  public boolean getReferenceAnnotationFlag()
+  {
+    if (fileProperties.get("RF") == "yes")
+    {
+      return true;
+    }
+    return false;
+  }
+
+  // returns boolean indicating whether the model mask annotation character
+  // field
+  // for each match state is valid or ignored
+  public boolean getModelMaskedFlag()
+  {
+    if (fileProperties.get("MM") == "yes")
+    {
+      return true;
+    }
+    return false;
+  }
+
+  // returns boolean indicating whether the consensus residue field
+  // for each match state is valid or ignored
+  public boolean getConsensusResidueAnnotationFlag()
+  {
+    if (fileProperties.get("CONS") == "yes")
+    {
+      return true;
+    }
+    return false;
+  }
+
+  // returns boolean indicating whether the consensus structure character field
+  // for each match state is valid or ignored
+  public boolean getConsensusStructureAnnotationFlag()
+  {
+    if (fileProperties.get("CS") == "yes")
+    {
+      return true;
+    }
+    return false;
+  }
+
+  // returns boolean indicating whether the model mask annotation character
+  // field
+  // for each match state is valid or ignored
+  public boolean getMapAnnotationFlag()
+  {
+    if (fileProperties.get("MAP") == "yes")
+    {
+      return true;
+    }
+    return false;
+  }
+
+  // not sure whether to implement this
+  // public Date getDate()
+  // {
+
+  // }
+
+  // not sure whether to implement this
+  // public String getCommandLineLog()
+  // {
+
+  // }
+
+  // gets the number of sequences that the HMM was trained on
+  public int getSequenceNumber()
+  {
+    return Integer.parseInt(fileProperties.get("NSEQ"));
+  }
+
+  // gets the effective number determined during sequence weighting
+  public int getEffectiveSequenceNumber()
+  {
+    return Integer.parseInt(fileProperties.get("EFFN"));
+  }
+
+  public int getCheckSum()
+  {
+    return Integer.parseInt(fileProperties.get("CKSUM"));
+  }
+
+  // need to ask if BigDecimal is best decimal type for this purpose
+  // and how to limit number of decimals
+  public double getGatheringThresholdGA1()
+  {
+    return Double.parseDouble((fileProperties.get("GA1")));
+  }
+
+  public void put(String key, String value)
+  {
+    fileProperties.put(key, value);
+  }
+
+}