Merge

Author: Delfil

src/main/java/tudelft/ti2806/pl3/data/Gender.java

@@ -4,5 +4,19 @@
  * Created by tombrouws on 15/06/15.
  */
 public enum Gender {
-	MALE, FEMALE
+	MALE, FEMALE;
+	
+	/**
+	 * Parses a string to {@code Gender}.
+	 * 
+	 * @param string
+	 *            the string to parse
+	 * @return the gender parsed
+	 */
+	public static Gender parse(String string) {
+		if (string.equalsIgnoreCase("Male")) {
+			return MALE;
+		}
+		return FEMALE;
+	}
 }

src/main/java/tudelft/ti2806/pl3/data/meta/MetaParser.java

@@ -16,49 +16,68 @@
  * Created by tombrouws on 15/06/15.
  */
 public class MetaParser {
-
+	
 	/**
 	 * Parses a metadata file and puts the information in genomes if they exist.
 	 *
 	 * @param metadata
-	 * 		the file to parse
+	 *            the file to parse
 	 * @param genomeMap
-	 * 		the map of genomes to put the data in
+	 *            the map of genomes to put the data in
 	 * @throws FileNotFoundException
-	 * 		when the file cannot be found
+	 *             when the file cannot be found
 	 */
 	public static void parseMeta(File metadata, Map<String, Genome> genomeMap) throws FileNotFoundException {
-		BufferedReader br = new BufferedReader(new InputStreamReader(
-				new BufferedInputStream(new FileInputStream(metadata))));
+		BufferedReader br = new BufferedReader(new InputStreamReader(new BufferedInputStream(new FileInputStream(
+				metadata))));
+		parseMeta(br, genomeMap);
+		try {
+			br.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	/**
+	 * Parses a metadata file and puts the information in genomes if they exist.
+	 * 
+	 * @param br
+	 *            the {@link BufferedReader} to read from
+	 * @param genomeMap
+	 *            the map of genomes to put the data in
+	 */
+	private static void parseMeta(BufferedReader br, Map<String, Genome> genomeMap) {
 		try {
 			if (br.ready()) {
 				br.readLine();
 			}
 			while (br.ready()) {
 				String[] data = br.readLine().split("\t");
 				data[0] = data[0].replaceAll("-", "_");
-				if (genomeMap.containsKey(data[0])) {
-					Genome g = genomeMap.get(data[0]);
-
-					if (data[1].equals("Negative")) {
-						g.setHivStatus(false);
-					} else {
-						g.setHivStatus(true);
-					}
-					g.setAge(Integer.parseInt(data[2]));
-
-					if (data[3].equals("Male")) {
-						g.setGender(Gender.MALE);
-					} else {
-						g.setGender(Gender.FEMALE);
-					}
-
-					g.setLocation(data[4]);
-					g.setIsolationDate(data[5]);
-				}
+				readData(data, genomeMap);
 			}
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
 	}
+	
+	/**
+	 * Parses a piece of meta data for a single {@link Genome}.
+	 * 
+	 * @param data
+	 *            the string array to parse
+	 * @param genomeMap
+	 *            the map of genomes to put the data in
+	 */
+	private static void readData(String[] data, Map<String, Genome> genomeMap) {
+		if (!genomeMap.containsKey(data[0])) {
+			return;
+		}
+		Genome g = genomeMap.get(data[0]);
+		g.setHivStatus(!data[1].equals("Negative"));
+		g.setAge(Integer.parseInt(data[2]));
+		g.setGender(Gender.parse(data[3]));
+		g.setLocation(data[4]);
+		g.setIsolationDate(data[5]);
+	}
 }