From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Tue, 18 Jul 2017 10:01:18 +0000 (+0100)
Subject: JAL-2599 modified state transition probability storage
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5c0ff498481786fc5fd2ecf359d6b65f82adaa3a;p=jalview.git

JAL-2599 modified state transition probability storage
---

diff --git a/src/jalview/datamodel/HMMNode.java b/src/jalview/datamodel/HMMNode.java
index 30a6a8d..cf95a1b 100644
--- a/src/jalview/datamodel/HMMNode.java
+++ b/src/jalview/datamodel/HMMNode.java
@@ -42,14 +42,15 @@ public class HMMNode
   {
     this.insertEmissions = insertEmissionsL;
   }
+
   public List<Double> getStateTransitions()
   {
     return stateTransitions;
   }
 
-  public void setStateTransitions(List<Double> stateTransitionsL)
+  public void setStateTransitions(List<Double> stateTransitionsM)
   {
-    this.stateTransitions = stateTransitionsL;
+    this.stateTransitions = stateTransitionsM;
   }
 
   public Integer getAlignmentColumn()
diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 4514a41..8df98e3 100644
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -102,13 +102,19 @@ public class HiddenMarkovModel
 
   private final String MASKED_VALUE = "MM";
   
-  final static String[] TRANSITION_TYPES = new String[] { "m->m", "m->i",
-      "m->d", "i->m", "i->i", "d->m", "d->d" };
+  public static final int MATCHTOMATCH = 0;
 
-  public String getTransitionType(int index)
-  {
-    return TRANSITION_TYPES[index];
-  }
+  public static final int MATCHTOINSERT = 1;
+
+  public static final int MATCHTODELETE = 2;
+
+  public static final int INSERTTOMATCH = 3;
+
+  public static final int INSERTTOINSERT = 4;
+
+  public static final int DELETETOMATCH = 5;
+
+  public static final int DELETETODELETE = 6;
 
   public Map<Integer, Integer> getNodeLookup()
   {
@@ -120,11 +126,6 @@ public class HiddenMarkovModel
     this.nodeLookup = nodeLookup;
   }
 
-  public String[] getTransitionTypes()
-  {
-    return TRANSITION_TYPES;
-  }
-
   public List<Character> getSymbols()
   {
     return symbols;
@@ -357,17 +358,16 @@ public class HiddenMarkovModel
    * @return
    */
   public Double getStateTransitionProbability(int alignColumn,
-          String transition)
+          int transition)
   {
     int transitionIndex;
     int nodeIndex;
     Double probability;
-    transitionIndex = getTransitionType(transition);
     if (nodeLookup.containsKey(alignColumn + 1))
     {
       nodeIndex = nodeLookup.get(alignColumn + 1);
       probability = getNode(nodeIndex).getStateTransitions()
-            .get(transitionIndex);
+              .get(transition);
       return probability;
     }
     else
@@ -703,44 +703,6 @@ public class HiddenMarkovModel
   }
 
   /**
-   * 
-   * @param transition
-   *          type of transition occuring
-   * @return index value representing position along stateTransition array.
-   */
-  public Integer getTransitionType(String transition)
-  {
-    Integer index;
-    switch (transition)
-    {
-    case "mm":
-      index = 0;
-      break;
-    case "mi":
-      index = 1;
-      break;
-    case "md":
-      index = 2;
-      break;
-    case "im":
-      index = 3;
-      break;
-    case "ii":
-      index = 4;
-      break;
-    case "dm":
-      index = 5;
-      break;
-    case "dd":
-      index = 6;
-      break;
-    default:
-      index = null;
-    }
-    return index;
-  }
-
-  /**
    * find the index of the node in a hidden Markov model based on the column in
    * the alignment
    * 
@@ -767,8 +729,6 @@ public class HiddenMarkovModel
   }
 
   /**
-   * creates the HMM annotation
-   * 
    * @return
    */
   public AlignmentAnnotation createAnnotation(int length)
diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index 6945ea6..16a1222 100644
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -47,6 +47,8 @@ public class HMMFile extends AlignFile
 
   private final String EMPTY = "";
 
+  private static final String TRANSITIONTYPELINE = "m->m     m->i     m->d     i->m     i->i     d->m     d->d";
+
   public HMMFile(FileParse source) throws IOException
   {
     super(false, source);
@@ -364,12 +366,7 @@ public class HMMFile extends AlignFile
     strSymbols = charListToStringList(charSymbols);
     symbolLine += addData(11, 9, strSymbols);
     file.append(symbolLine + NEW_LINE);
-
-    String transitionTypeLine = "";
-    List<String> transitionTypes;
-    transitionTypes = stringArrayToStringList(hmm.getTransitionTypes());
-    transitionTypeLine += addData(16, 9, transitionTypes);
-    file.append(transitionTypeLine + NEW_LINE);
+    file.append(TRANSITIONTYPELINE + NEW_LINE);
 
     int length = hmm.getLength();
 
diff --git a/test/jalview/io/HMMFileTest.java b/test/jalview/io/HMMFileTest.java
index 36a2491..70bfc27 100644
--- a/test/jalview/io/HMMFileTest.java
+++ b/test/jalview/io/HMMFileTest.java
@@ -202,21 +202,6 @@ public class HMMFileTest {
   }
   
   @Test
-  public void testGetTransitionType()
-  {
-    HiddenMarkovModel hmm = fn3.getHMM();
-    assertEquals(hmm.getTransitionType("mm").intValue(), 0);
-    assertEquals(hmm.getTransitionType("mi").intValue(), 1);
-    assertEquals(hmm.getTransitionType("md").intValue(), 2);
-    assertEquals(hmm.getTransitionType("im").intValue(), 3);
-    assertEquals(hmm.getTransitionType("ii").intValue(), 4);
-    assertEquals(hmm.getTransitionType("dm").intValue(), 5);
-    assertEquals(hmm.getTransitionType("dd").intValue(), 6);
-    assertNull(hmm.getTransitionType("df"));
-  
-  }
-  
-  @Test
   public void testFillList()
   {
     Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");