correct implementation of Sequence #511 #502

LinguaPhylo · Jul 29, 2024 · b882f6d · b882f6d
1 parent 79ec66b
commit b882f6d
Showing 1 changed file with 30 additions and 11 deletions.
diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/Sequence.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/Sequence.java
@@ -26,17 +26,17 @@ public class Sequence extends ParametricDistribution<SimpleAlignment> {
 
     Value<Integer> nchar;
 
-    public Sequence(@ParameterInfo(name = DistributionConstants.pParamName, narrativeName = "probability distribution", description = "the probability distribution over integer states 1 to K.") Value<Double[]> probs,
-                    @ParameterInfo(name = LParamName, narrativeName="length", description = "length of the alignment") Value<Integer> nchar) {
-        super();
-        this.probs = probs; // check probs is same dimension as nucleotide datatype
-        this.nchar = nchar;
-        this.sequenceType =  new Value<>(null, SequenceType.NUCLEOTIDE); // default data type is nucleotide
-    }
+//    public Sequence(@ParameterInfo(name = DistributionConstants.pParamName, narrativeName = "probability distribution", description = "the probability distribution over integer states 1 to K.") Value<Double[]> probs,
+//                    @ParameterInfo(name = LParamName, narrativeName="length", description = "length of the alignment") Value<Integer> nchar) {
+//        super();
+//        this.probs = probs; // check probs is same dimension as nucleotide datatype
+//        this.nchar = nchar;
+//        this.sequenceType =  new Value<>(null, SequenceType.NUCLEOTIDE); // default data type is nucleotide
+//    }
 
     public Sequence(@ParameterInfo(name = DistributionConstants.pParamName, description = "the probability distribution over integer states 1 to K.") Value<Double[]> probs,
                     @ParameterInfo(name = LParamName, narrativeName="length", description = "length of the alignment") Value<Integer> nchar,
-                    @ParameterInfo(name = dataTypeParamName, narrativeName="data type", description = "the sequence type of the alignment") Value<SequenceType> sequenceType) {
+                    @ParameterInfo(name = dataTypeParamName, optional = true, narrativeName="data type", description = "the sequence type of the alignment") Value<SequenceType> sequenceType) {
         super();
         this.probs = probs; // check probs is same dimension as datatype
         this.nchar = nchar;
@@ -52,7 +52,9 @@ protected void constructDistribution(RandomGenerator random) {
             description="Create one sequence given the length and the probability distribution over each state.")
     public RandomVariable<SimpleAlignment> sample() {
         Taxa t = Taxa.createTaxa(1);
-        SimpleAlignment alignment = new SimpleAlignment(t, nchar.value(), sequenceType.value());
+        SequenceType sequenceType = getSequenceType();
+
+        SimpleAlignment alignment = new SimpleAlignment(t, nchar.value(), sequenceType);
 
         for (int i = 0; i < nchar.value(); i++) {
             int value = sample(probs.value(), random);
@@ -62,7 +64,8 @@ public RandomVariable<SimpleAlignment> sample() {
     }
 
     private State translate(int i) {
-        return sequenceType.value().getState(i);
+        SequenceType sequenceType = getSequenceType();
+        return sequenceType.getState(i);
     }
 
     private int sample(Double[] p, RandomGenerator random) {
@@ -81,8 +84,24 @@ public Map<String,Value> getParams() {
         return new TreeMap<>() {{
             put(DistributionConstants.pParamName, probs);
             put(LParamName, nchar);
-            put(dataTypeParamName, sequenceType);
+            if (sequenceType != null) put(dataTypeParamName, sequenceType);
         }};
     }
 
+    @Override
+    public void setParam(String paramName, Value value) {
+        if (paramName.equals(DistributionConstants.pParamName)) probs = value;
+        else if (paramName.equals(LParamName)) nchar = value;
+        else if (paramName.equals(dataTypeParamName)) sequenceType = value;
+        else throw new RuntimeException("Unrecognised parameter name: " + paramName);
+
+        super.setParam(paramName, value); // constructDistribution
+    }
+
+    public SequenceType getSequenceType() {
+        if (sequenceType == null || sequenceType.value() == null)
+            return SequenceType.NUCLEOTIDE; // default data type is nucleotide
+        else
+            return sequenceType.value();
+    }
 }