Formatted file using eclipse

src/biotree/WormsAPI.java

@@ -6,124 +6,129 @@ import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
 import java.net.URL;
 
-
 //Need to add library
 
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 import org.json.simple.JSONObject;
 
-
-
-
-
-
 public class WormsAPI {
-	
+
 	public static void main(String[] args) throws IOException, ParseException {
-		//small test
+		// small test
 		System.out.println(nameToID("Neogobius melanostomus"));
 		/*
-		TaxonNode[] taxnodes = idToClassification(126916);
+		 * TaxonNode[] taxnodes = idToClassification(126916);
+		 * 
+		 * for (int i =0; i < taxnodes.length;i++) {
+		 * System.out.println(taxnodes[i].getTaxonId());
+		 * System.out.println(taxnodes[i].getTaxonType());
+		 * System.out.println(taxnodes[i].getName()); }
+		 */
 
-		for (int i =0; i < taxnodes.length;i++) {
-			System.out.println(taxnodes[i].getTaxonId());
-			System.out.println(taxnodes[i].getTaxonType());
-			System.out.println(taxnodes[i].getName());
-		}
-		*/
-		
 	}
-	
+
 	/**
-	 * Search the WORMS database by scientific name to return Aphia (taxon) ID.
-	 * This must be an exact name or it will fail. Use fuzzyNameToID if the name 
-	 * is not exact.
-	 * @param scientificName Scientific name of taxon (family, genus, species, etc)
+	 * Search the WORMS database by scientific name to return Aphia (taxon) ID. This
+	 * must be an exact name or it will fail. Use fuzzyNameToID if the name is not
+	 * exact.
+	 * 
+	 * @param scientificName
+	 *            Scientific name of taxon (family, genus, species, etc)
 	 * @return Aphia (taxon) ID of given scientific name.
 	 * @throws IOException
 	 */
-	public static int nameToID(String scientificName) throws IOException{
+	public static int nameToID(String scientificName) throws IOException {
 		scientificName = repSpaces(scientificName);
-		String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaIDByName/%s?marine_only=false", scientificName));
-		
+		String resp = makeRequest(
+				String.format("http://marinespecies.org/rest/AphiaIDByName/%s?marine_only=false", scientificName));
+
 		return Integer.parseInt(resp);
 	}
-	
+
 	/**
-	 * Search the WORMS database by fuzzy scientific name (a slightly misspelled name).
-	 * This has the advantage of being more flexible but it can be less accurate and it
-	 * is slower. If you have the actual scientific name, use nameToID() instead.
-	 * @param fuzzyName Fuzzy scientific name of taxon (family, genus, species, etc)
+	 * Search the WORMS database by fuzzy scientific name (a slightly misspelled
+	 * name). This has the advantage of being more flexible but it can be less
+	 * accurate and it is slower. If you have the actual scientific name, use
+	 * nameToID() instead.
+	 * 
+	 * @param fuzzyName
+	 *            Fuzzy scientific name of taxon (family, genus, species, etc)
 	 * @return Aphia (taxon) ID of given scientific name.
 	 * @throws IOException
 	 */
-	public static int fuzzyNameToID(String fuzzyName) throws IOException{
+	public static int fuzzyNameToID(String fuzzyName) throws IOException {
 		fuzzyName = repSpaces(fuzzyName);
-		String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D=%s&marine_only=true", fuzzyName));
-		
-		//TODO: finish this function.
+		String resp = makeRequest(String.format(
+				"http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D=%s&marine_only=true",
+				fuzzyName));
+
+		// TODO: finish this function.
 		return 123123;
 	}
-	
+
 	/**
 	 * Search by taxonId (AphiaID) and return bioclassification of that and above.
-	 * 	
+	 * 
 	 * /AphiaClassificationByAphiaID/{ID}
-	 * @throws IOException 
-	 * @throws ParseException 
+	 * 
+	 * @throws IOException
+	 * @throws ParseException
 	 */
 
 	public static TaxonNode[] idToClassification(int taxonId) throws IOException, ParseException {
-		String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaClassificationByAphiaID/%d", taxonId));
+		String resp = makeRequest(
+				String.format("http://marinespecies.org/rest/AphiaClassificationByAphiaID/%d", taxonId));
 		JSONParser parser = new JSONParser();
 		JSONObject json = (JSONObject) parser.parse(resp);
-		
-		//Assume length of 8 based on number of taxontypes
+
+		// Assume length of 8 based on number of taxontypes
 		TaxonNode[] taxnodes = new TaxonNode[8];
-		int arraysize = parseIdCall(taxnodes,json,0); 
+		int arraysize = parseIdCall(taxnodes, json, 0);
 		TaxonNode[] copiedArray = new TaxonNode[arraysize];
 
 		System.arraycopy(taxnodes, 0, copiedArray, 0, arraysize);
-		
+
 		return copiedArray;
-		
+
 	}
-	
-	
-	
+
 	/**
-	 * Perform a GET request to the given URL and return the content of the response.
-	 * @param url The URL to which to make a request.
+	 * Perform a GET request to the given URL and return the content of the
+	 * response.
+	 * 
+	 * @param url
+	 *            The URL to which to make a request.
 	 * @return The content returned by the server (if successful).
 	 * @throws IOException
 	 */
 	private static String makeRequest(String url) throws IOException {
-		//Request method adapted from http://www.baeldung.com/java-http-request
-		//create new URL instance
+		// Request method adapted from http://www.baeldung.com/java-http-request
+		// create new URL instance
 		URL urll = new URL(url);
-		//create and set up connection
+		// create and set up connection
 		HttpURLConnection con = (HttpURLConnection) urll.openConnection();
 		con.setRequestMethod("GET");
-		
+
 		int status = con.getResponseCode();
-		
-		BufferedReader in = new BufferedReader(
-				  new InputStreamReader(con.getInputStream()));
+
+		BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
 		String inputLine;
 		StringBuffer content = new StringBuffer();
 		while ((inputLine = in.readLine()) != null) {
-		    content.append(inputLine);
+			content.append(inputLine);
 		}
 		in.close();
 		con.disconnect();
-		
+
 		return content.toString();
 	}
-	
+
 	/**
 	 * Helper to replace a space with the correct one for URLs.
-	 * @param in Input string
+	 * 
+	 * @param in
+	 *            Input string
 	 * @return String with spaces replaced by "%20" for spaces in URLs.
 	 */
 	private static String repSpaces(String in) {
@@ -131,37 +136,43 @@ public class WormsAPI {
 	}
 
 	/**
-	 * Parses the json request recursively and also keeping track of the array length
-	 * @param nodes the TaxonNode array
-	 * @param current current rank level of JSON file
-	 * @param n index of where the TaxonNode is being stored at 
+	 * Parses the json request recursively and also keeping track of the array
+	 * length
+	 * 
+	 * @param nodes
+	 *            the TaxonNode array
+	 * @param current
+	 *            current rank level of JSON file
+	 * @param n
+	 *            index of where the TaxonNode is being stored at
 	 * @return arraysize number of elements added within array
 	 */
-	private static int parseIdCall(TaxonNode[] nodes,JSONObject current,int n) {
+	private static int parseIdCall(TaxonNode[] nodes, JSONObject current, int n) {
 		boolean checktype = false;
 		TaxonNode curNode = null;
 		int arraysize = n;
-		//Checks if rank matches the TaxonType Enum
+		// Checks if rank matches the TaxonType Enum
 		for (TaxonType c : TaxonType.values()) {
-			
-	        if (c.name().equals((String)current.get("rank"))) {
-	            checktype= true;
-	            break;
-	        }
-	        else checktype = false;
-	    }
+
+			if (c.name().equals((String) current.get("rank"))) {
+				checktype = true;
+				break;
+			} else
+				checktype = false;
+		}
 		JSONObject child = (JSONObject) current.get("child");
-		
+
 		if (checktype == true) {
-			curNode = new TaxonNode((long) current.get("AphiaID"),TaxonType.valueOf((String) current.get("rank")) ,(String) current.get("scientificname"));
-			nodes[n]= curNode;
+			curNode = new TaxonNode((long) current.get("AphiaID"), TaxonType.valueOf((String) current.get("rank")),
+					(String) current.get("scientificname"));
+			nodes[n] = curNode;
 			n++;
 		}
-		//If child is null, return 
-		if ((JSONObject) current.get("child") == null ) 
+		// If child is null, return
+		if ((JSONObject) current.get("child") == null)
 			return n;
 		arraysize = parseIdCall(nodes, child, n);
 		return arraysize;
 	}
-	
+
 }