setParam should throw Exception #493

LinguaPhylo · Jun 10, 2024 · 05253d7 · 05253d7
1 parent 4903cb9
commit 05253d7
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Showing 6 changed files with 50 additions and 37 deletions.
diff --git a/examples/birth-death/birthDeathRhoSampling.lphy b/examples/birth-death/birthDeathRhoSampling.lphy
@@ -5,4 +5,4 @@ T ~ BirthDeathSampling(diversification=diversification, turnover=turnover, rho=0
 sf ~ Dirichlet(conc=[2.0, 2.0, 2.0, 2.0]);
 er ~ Dirichlet(conc=[2.0, 4.0, 2.0, 2.0, 4.0, 2.0]);
 Q = gtr(freq=sf, rates=er); // construct the GTR instantaneous rate matrix
-D ~ PhyloCTMC(tree=T, Q=Q, mu=0.5, L=1000);
+D ~ PhyloCTMC(tree=T, Q=Q, mu=0.5, L=100);
diff --git a/lphy-base/src/main/java/lphy/base/distribution/ExpMarkovChain.java b/lphy-base/src/main/java/lphy/base/distribution/ExpMarkovChain.java
@@ -109,27 +109,20 @@ public Map<String, Value> getParams() {
         }
     }
 
-    public void setInitialMean(Value<Double> initialMean) {
-        this.initialMean = initialMean;
-    }
-
-    public void setFirstValue(Value<Double> firstValue) {
-        this.firstValue = firstValue;
-    }
-
-    public void setN(Value<Integer> n) {
-        this.n = n;
+    //TODO cannot work with Number. Perhaps change to setParam
+    public void setInitialMean(double initialMean) {
+        this.initialMean.setValue(initialMean);
+        constructDistribution(random);
     }
 
-    public Value<Double> getInitialMean() {
-        return initialMean;
+    public void setFirstValue(double firstValue) {
+        this.firstValue.setValue(firstValue);
+        constructDistribution(random);
     }
 
-    public Value<Double> getFirstValue() {
-        return firstValue;
+    public void setN(int n) {
+        this.n.setValue(n);
+        constructDistribution(random);
     }
 
-    public Value<Integer> getN() {
-        return n;
-    }
 }
diff --git a/lphy-base/src/main/java/lphy/base/distribution/RandomBooleanArray.java b/lphy-base/src/main/java/lphy/base/distribution/RandomBooleanArray.java
@@ -61,11 +61,12 @@ public Map<String, Value> getParams() {
         }};
     }
 
-    public void setLength(Value<Integer> length) {
-        this.length = length;
+    //TODO cannot work with Number. Perhaps change to setParam
+    public void setLength(int length) {
+        this.length.setValue(length);
     }
 
-    public void setHammingWeight(Value<Integer> hammingWeight) {
-        this.hammingWeight = hammingWeight;
+    public void setHammingWeight(int hammingWeight) {
+        this.hammingWeight.setValue(hammingWeight);
     }
 }
diff --git a/lphy-base/src/main/java/lphy/base/distribution/RandomComposition.java b/lphy-base/src/main/java/lphy/base/distribution/RandomComposition.java
@@ -59,11 +59,14 @@ public Map<String, Value> getParams() {
         }};
     }
 
-    public void setN(Value<Integer> n) {
-        this.n = n;
+    //TODO cannot work with Number. Perhaps change to setParam
+    public void setN(int n) {
+        this.n.setValue(n);
+        constructDistribution(random);
     }
 
-    public void setK(Value<Integer> k) {
-        this.k = k;
+    public void setK(int k) {
+        this.k.setValue(k);
+        constructDistribution(random);
     }
 }
diff --git a/lphy-base/src/main/java/lphy/base/distribution/UniformDiscrete.java b/lphy-base/src/main/java/lphy/base/distribution/UniformDiscrete.java
@@ -60,12 +60,15 @@ public Map<String, Value> getParams() {
         }};
     }
 
-    public void setLower(Value<Integer> lower) {
-        this.lower = lower;
+    //TODO change to setParam ?
+    public void setLower(int lower) {
+        this.lower.setValue(lower);
+        constructDistribution(random);
     }
 
-    public void setUpper(Value<Integer> upper) {
-        this.upper = upper;
+    public void setUpper(int upper) {
+        this.upper.setValue(upper);
+        constructDistribution(random);
     }
 
     public Value<Integer> getLower() {

diff --git a/lphy/src/main/java/lphy/core/model/Generator.java b/lphy/src/main/java/lphy/core/model/Generator.java
@@ -64,34 +64,47 @@ default String getTypeName() {
      * This default code is to find whether any setter methods exist,
      * then it would not need to be overwritten,
      * otherwise this method must be overwritten to set the values by argument names.
+     * The setter sets the primary type inside the Value, such as,
+     * <code>public void setLambda(double p) {</code>
+     * <code>    this.lambda.setValue(p);    </code>
+     * <code>}</code>
      * @param paramName   parameter (argument) name
      * @param value       {@link Value}
      */
     default void setParam(String paramName, Value<?> value) {
+        // TODO this does not work for Number
         // such as, public void setLambda(double p) {
         //        this.lambda.setValue(p);
         //        constructDistribution(random); }
         String methodName = "set" + Character.toUpperCase(paramName.charAt(0)) + paramName.substring(1);
 
         try {
+            // just one setter
             Method method = getClass().getMethod(methodName, value.value().getClass());
 
             method.invoke(this, value.value());
         } catch (NoSuchMethodException e) {
-
+            // multiple setters due to multiple parameters
             Method[] methods = getClass().getMethods();
             for (Method method : methods) {
                 if (method.getName().equals(methodName)) {
                     try {
                         method.invoke(this, value.value());
                         break;
                     } catch (IllegalArgumentException mismatch) {
-                        //TODO Cannot handle inheritance, such as Number, but value.getType() is Double
-                        LoggerUtils.log.severe(mismatch.getMessage() + ", where " + methodName +
-                                "(" + method.getGenericParameterTypes()[0] + ") does not match the value type " +
-                                value.getType() + "!\nPlease overwrite setParam() instead of using setters !");
-                    } catch (InvocationTargetException | IllegalAccessException ignored) {
-                        LoggerUtils.log.severe(methodName + " err : " + ignored.getMessage());
+                        //TODO Cannot handle inheritance, such as Number,
+                        // it must specify to primary type, such as double
+                        String msg = mismatch.getMessage() + " in " + this.getClass().getSimpleName() +
+                                ", where " + methodName + "(" + method.getGenericParameterTypes()[0] +
+                                ") does not match the value type " + value.getType() +
+                                "!\nPlease either overwrite setParam(), or change setter value type to " +
+                                value.getType() + " !";
+                        LoggerUtils.log.severe(msg); // log to studio as well
+                        throw new RuntimeException(msg, e);
+                    } catch (InvocationTargetException | IllegalAccessException err) {
+                        String msg = methodName + " err : " + err.getMessage();
+                        LoggerUtils.log.severe(msg); // log to studio as well
+                        throw new RuntimeException(msg, e);
                     }
                 }
             }