Added wordbag serialization to Clusterer

src/main/java/edu/usc/softarch/arcade/clustering/Architecture.java

@@ -42,8 +42,8 @@ public class Architecture extends TreeMap<String, Cluster> {
 	/**
 	 * The path to where this data structure should be serialized.
 	 */
-	private final String projectPath;
-	private final SimMeasure.SimMeasureType simMeasure;
+	public final String projectPath;
+	public final SimMeasure.SimMeasureType simMeasure;
 	/**
 	 * The total number of features that can exist in any clusters of this
 	 * architecture. For architectures constructed from structural data such as
@@ -330,8 +330,7 @@ public void writeToRsf(String path) throws FileNotFoundException {
 
 		Map<Integer, String> architectureIndex = computeArchitectureIndex();
 
-		try (PrintWriter out = new PrintWriter(
-			new OutputStreamWriter(
+		try (PrintWriter out = new PrintWriter(new OutputStreamWriter(
 				new FileOutputStream(rsfFile), StandardCharsets.UTF_8))) {
 			for (Map.Entry<Integer, String> cluster : architectureIndex.entrySet()) {
 				Integer clusterIndex = cluster.getKey();
@@ -351,7 +350,7 @@ public void writeToRsf(String path) throws FileNotFoundException {
 	 * a unique identifier. The names of the entities are broken down into
 	 * separate entries by the serialization method.
 	 */
-	private Map<Integer, String> computeArchitectureIndex() {
+	protected Map<Integer, String> computeArchitectureIndex() {
 		List<String> orderedClusterNames = this.values().stream()
 			.map(Cluster::getName).sorted().collect(Collectors.toList());
 

src/main/java/edu/usc/softarch/arcade/clustering/Cluster.java

@@ -4,10 +4,12 @@
 import java.util.BitSet;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
 
+import edu.usc.softarch.arcade.topics.Concern;
 import edu.usc.softarch.arcade.topics.DocTopicItem;
 import edu.usc.softarch.arcade.topics.UnmatchingDocTopicItemsException;
 
@@ -211,6 +213,9 @@ public double computeStructuralCentroid(int numFeatures) {
 
 		return centroidAvg / getNumEntities();
 	}
+
+	public Concern computeConcern(Map<Integer, List<String>> wordBags) {
+		return this.dti.computeConcern(wordBags); }
 	//endregion
 
 	//region OBJECT METHODS

src/main/java/edu/usc/softarch/arcade/clustering/Clusterer.java

@@ -63,8 +63,10 @@ public static Architecture run(ClusteringAlgorithmType algorithm,
 		// Compute the clustering algorithm and return the resulting architecture
 		runner.computeArchitecture(stopCrit, stoppingCriterionName,	simMeasure);
 		// Compute DTI word bags if concern-based technique is used
-		if (runner.architecture instanceof ConcernArchitecture)
+		if (runner.architecture instanceof ConcernArchitecture) {
 			((ConcernArchitecture) runner.architecture).computeConcernWordBags();
+			((ConcernArchitecture) runner.architecture).serializeBagOfWords();
+		}
 
 		return runner.architecture;
 	}

src/main/java/edu/usc/softarch/arcade/clustering/ConcernArchitecture.java

@@ -3,11 +3,18 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import edu.usc.softarch.arcade.clustering.simmeasures.SimMeasure;
 import edu.usc.softarch.arcade.topics.Concern;
+import edu.usc.softarch.arcade.topics.DocTopicItem;
 import edu.usc.softarch.arcade.topics.DocTopics;
 import edu.usc.softarch.arcade.topics.UnmatchingDocTopicItemsException;
 
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -127,10 +134,40 @@ private void removeClassesWithoutDTI(Map<Cluster, Cluster> parentClassMap) {
 		super.removeAll(excessClusters);
 		super.removeAll(excessInners);
 	}
-	//endregion
 
-	//region PROCESSING
 	public List<Concern> computeConcernWordBags() {
-		return this.docTopics.getConcerns(); }
+		List<Concern> concernList = new ArrayList<>();
+		for (Cluster cluster : this.values())
+			concernList.add(cluster.computeConcern(this.docTopics.getTopicWordLists()));
+
+		return concernList;
+	}
+	//endregion
+
+	//region SERIALIZATION
+	public void serializeBagOfWords() throws FileNotFoundException {
+		String fs = File.separator;
+		String path = this.projectPath + fs + this.projectName + "_"
+			+ this.simMeasure + "_concerns.txt";
+		File outputFile = new File(path);
+		outputFile.getParentFile().mkdirs();
+
+		Map<Integer, String> architectureIndex = computeArchitectureIndex();
+
+		try (PrintWriter out = new PrintWriter(new OutputStreamWriter(
+				new FileOutputStream(outputFile), StandardCharsets.UTF_8))) {
+			StringBuilder output = new StringBuilder();
+
+			for (Map.Entry<Integer, String> cluster : architectureIndex.entrySet()) {
+				DocTopicItem dti = this.get(cluster.getValue()).getDocTopicItem();
+				Concern concernWords = dti.getConcern();
+				output.append(cluster.getKey());
+				output.append(concernWords);
+				output.append(System.lineSeparator());
+			}
+
+			out.print(output);
+		}
+	}
 	//endregion
 }

src/main/java/edu/usc/softarch/arcade/topics/DocTopicItem.java

@@ -198,6 +198,14 @@ public double getJsDivergence(DocTopicItem toCompare)
 
 		return Maths.jensenShannonDivergence(sortedP, sortedQ);
 	}
+
+	//TODO make this less horrible
+	public Concern getConcern() {
+		if (this.concern == null)
+			throw new IllegalStateException("Attempted to get concern before " +
+				"it was computed");
+		return new Concern(this.concern);
+	}
 	//endregion
 
 	//region PROCESSING

src/main/java/edu/usc/softarch/arcade/topics/DocTopics.java

@@ -153,13 +153,8 @@ else if (dti.source.endsWith(".S")) {
 		return null;
 	}
 
-	public List<Concern> getConcerns() {
-		List<Concern> concernList = new ArrayList<>();
-		for (DocTopicItem dti : dtItemList)
-			concernList.add(dti.computeConcern(this.topicWordLists));
-
-		return concernList;
-	}
+	public Map<Integer, List<String>> getTopicWordLists() {
+		return topicWordLists; }
 	// #endregion ACCESSORS ------------------------------------------------------
 
 	// #region PROCESSING --------------------------------------------------------