Upgraded Settings class to allow for covariates to be built from

provided values.

src/main/java/ca/joeltherrien/randomforest/Settings.java

@@ -1,10 +1,10 @@
 package ca.joeltherrien.randomforest;
 
+import ca.joeltherrien.randomforest.covariates.Covariate;
+import ca.joeltherrien.randomforest.covariates.CovariateSettings;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
-import lombok.AllArgsConstructor;
+import lombok.*;
-import lombok.Builder;
-import lombok.Data;
 
 import java.io.File;
 import java.io.IOException;
@@ -17,6 +17,7 @@ import java.util.List;
 @Data
 @Builder
 @AllArgsConstructor
+@EqualsAndHashCode
 public class Settings {
 
     private int numberOfSplits = 5;
@@ -27,7 +28,7 @@ public class Settings {
     private String groupDifferentiator;
     private String treeResponseCombiner;
 
-    private List<String> covariates = new ArrayList<>();
+    private List<CovariateSettings> covariates = new ArrayList<>();
 
     // number of covariates to randomly try
     private int mtry = 0;
@@ -45,6 +46,7 @@ public class Settings {
 
     public static Settings load(File file) throws IOException {
         final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+        //mapper.enableDefaultTyping();
 
         final Settings settings = mapper.readValue(file, Settings.class);
 
@@ -54,6 +56,10 @@ public class Settings {
 
     public void save(File file) throws IOException {
         final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+        //mapper.enableDefaultTyping();
+
+        // Jackson can struggle with some types of Lists, such as that returned by the useful List.of(...)
+        this.covariates = new ArrayList<>(this.covariates);
 
         mapper.writeValue(file, this);
     }

src/main/java/ca/joeltherrien/randomforest/covariates/BooleanCovariate.java

@@ -3,10 +3,12 @@ package ca.joeltherrien.randomforest.covariates;
 import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
 
 @RequiredArgsConstructor
-public class BooleanCovariate implements Covariate<Boolean>{
+public final class BooleanCovariate implements Covariate<Boolean>{
 
     @Getter
     private final String name;

src/main/java/ca/joeltherrien/randomforest/covariates/BooleanCovariateSettings.java

@@ -0,0 +1,18 @@
+package ca.joeltherrien.randomforest.covariates;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@NoArgsConstructor // required by Jackson
+@Data
+public final class BooleanCovariateSettings extends CovariateSettings<Boolean> {
+
+    public BooleanCovariateSettings(String name){
+        super(name);
+    }
+
+    @Override
+    BooleanCovariate build() {
+        return new BooleanCovariate(name);
+    }
+}

src/main/java/ca/joeltherrien/randomforest/covariates/CovariateSettings.java

@@ -0,0 +1,33 @@
+package ca.joeltherrien.randomforest.covariates;
+
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+
+/**
+ * Nuisance class to work with Jackson for persisting settings.
+ *
+ * @param <V>
+ */
+@NoArgsConstructor // required for Jackson
+@Getter
+@JsonTypeInfo(
+        use = JsonTypeInfo.Id.NAME,
+        include = JsonTypeInfo.As.PROPERTY,
+        property = "type")
+@JsonSubTypes({
+        @JsonSubTypes.Type(value = BooleanCovariateSettings.class, name = "boolean"),
+        @JsonSubTypes.Type(value = NumericCovariateSettings.class, name = "numeric"),
+        @JsonSubTypes.Type(value = FactorCovariateSettings.class, name = "factor")
+})
+public abstract class CovariateSettings<V> {
+
+    String name;
+
+    CovariateSettings(String name){
+        this.name = name;
+    }
+
+    abstract Covariate<V> build();
+}

src/main/java/ca/joeltherrien/randomforest/covariates/FactorCovariateSettings.java

@@ -0,0 +1,24 @@
+package ca.joeltherrien.randomforest.covariates;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@NoArgsConstructor // required by Jackson
+@Data
+public final class FactorCovariateSettings extends CovariateSettings<String> {
+
+    private List<String> levels;
+
+    public FactorCovariateSettings(String name, List<String> levels){
+        super(name);
+        this.levels = new ArrayList<>(levels); // Jackson struggles with List.of(...)
+    }
+
+    @Override
+    FactorCovariate build() {
+        return new FactorCovariate(name, levels);
+    }
+}

src/main/java/ca/joeltherrien/randomforest/covariates/NumericCovariate.java

@@ -8,7 +8,7 @@ import java.util.concurrent.ThreadLocalRandom;
 import java.util.stream.Collectors;
 
 @RequiredArgsConstructor
-public class NumericCovariate implements Covariate<Double>{
+public final class NumericCovariate implements Covariate<Double>{
 
     @Getter
     private final String name;

src/main/java/ca/joeltherrien/randomforest/covariates/NumericCovariateSettings.java

@@ -0,0 +1,18 @@
+package ca.joeltherrien.randomforest.covariates;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@NoArgsConstructor // required by Jackson
+@Data
+public final class NumericCovariateSettings extends CovariateSettings<Double> {
+
+    public NumericCovariateSettings(String name){
+        super(name);
+    }
+
+    @Override
+    NumericCovariate build() {
+        return new NumericCovariate(name);
+    }
+}

src/test/java/ca/joeltherrien/randomforest/settings/TestPersistence.java

@@ -2,10 +2,13 @@ package ca.joeltherrien.randomforest.settings;
 
 import ca.joeltherrien.randomforest.Settings;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import ca.joeltherrien.randomforest.covariates.*;
 import org.junit.jupiter.api.Test;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.List;
 
 public class TestPersistence {
@@ -13,7 +16,12 @@ public class TestPersistence {
     @Test
     public void testSaving() throws IOException {
         final Settings settingsOriginal = Settings.builder()
-                .covariates(List.of("x1", "x2", "x3"))
+                .covariates(List.of(
+                        new NumericCovariateSettings("x1"),
+                        new BooleanCovariateSettings("x2"),
+                        new FactorCovariateSettings("x3", List.of("cat", "mouse", "dog"))
+                        )
+                )
                 .dataFileLocation("data.csv")
                 .groupDifferentiator("WeightedVarianceGroupDifferentiator")
                 .responseCombiner("MeanResponseCombiner")