Add basic Settings class with persistence.

pom.xml

@@ -12,6 +12,7 @@
         <java.version>1.10</java.version>
         <maven.compiler.target>1.10</maven.compiler.target>
         <maven.compiler.source>1.10</maven.compiler.source>
+        <jackson.version>2.9.6</jackson.version>
     </properties>
 
 
@@ -23,6 +24,23 @@
             <scope>provided</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.5</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-yaml</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
 
         <dependency>
             <groupId>org.junit.jupiter</groupId>

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

@@ -0,0 +1,62 @@
+package ca.joeltherrien.randomforest;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This class is saved & loaded using a saved configuration file. It contains all relevant settings when training a forest.
+ */
+@Data
+@Builder
+@AllArgsConstructor
+public class Settings {
+
+    private int numberOfSplits = 5;
+    private int nodeSize = 5;
+    private int maxNodeDepth = 1000000; // basically no maxNodeDepth
+
+    private String responseCombiner;
+    private String groupDifferentiator;
+    private String treeResponseCombiner;
+
+    private List<String> covariates = new ArrayList<>();
+
+    // number of covariates to randomly try
+    private int mtry = 0;
+
+    // number of trees to try
+    private int ntree = 500;
+
+    private String dataFileLocation = "data.csv";
+    private String saveTreeLocation = "trees/";
+
+    private int numberOfThreads = 1;
+    private boolean saveProgress = false;
+
+    public Settings(){} // required for Jackson
+
+    public static Settings load(File file) throws IOException {
+        final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+
+        final Settings settings = mapper.readValue(file, Settings.class);
+
+        return settings;
+
+    }
+
+    public void save(File file) throws IOException {
+        final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+
+        mapper.writeValue(file, this);
+    }
+
+
+}

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

@@ -0,0 +1,42 @@
+package ca.joeltherrien.randomforest.settings;
+
+import ca.joeltherrien.randomforest.Settings;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+public class TestPersistence {
+
+    @Test
+    public void testSaving() throws IOException {
+        final Settings settingsOriginal = Settings.builder()
+                .covariates(List.of("x1", "x2", "x3"))
+                .dataFileLocation("data.csv")
+                .groupDifferentiator("WeightedVarianceGroupDifferentiator")
+                .responseCombiner("MeanResponseCombiner")
+                .treeResponseCombiner("MeanResponseCombiner")
+                .maxNodeDepth(100000)
+                .mtry(2)
+                .nodeSize(5)
+                .ntree(500)
+                .numberOfSplits(5)
+                .numberOfThreads(1)
+                .saveProgress(true)
+                .saveTreeLocation("trees/")
+                .build();
+
+        final File templateFile = new File("template.yaml");
+        settingsOriginal.save(templateFile);
+
+        final Settings reloadedSettings = Settings.load(templateFile);
+
+        assertEquals(settingsOriginal, reloadedSettings);
+
+        templateFile.delete();
+
+
+    }
+}