lots of bugfixing, storage of incorrect names, etc

src/biotree/BioTree.java

@@ -10,8 +10,9 @@ public class BioTree {
 	//FIXME: replace with a single kd-tree
 	private static BST<Integer, TaxonNode> idNodes = new BST<Integer, TaxonNode>();
 	private static BST<String, TaxonNode> strNodes = new BST<String, TaxonNode>();
+	private static BST<String, Integer> incorrectNames = new BST<String, Integer>();
 	
-	public static void main(String[] args) throws IOException {
+	public static void main(String[] args) throws IOException, ParseException {
 		BioTree.processRecord("Catostomus commersoni");
 	}
 	
@@ -64,16 +65,27 @@ public class BioTree {
 	 * @param scientificName The scientific name of the possible new entry
 	 * @return taxonId of new / existing entry
 	 * @throws IOException 
+	 * @throws ParseException 
 	 */
-	public static Integer processRecord(String scientificName) throws IOException {
+	public static Integer processRecord(String scientificName) throws IOException, ParseException {
 		//reverse lookup based on name, try adding the found taxonId.
 		TaxonNode res = strNodes.get(scientificName);
+		if (res == null) {
+			System.out.println("Not already found.");
+			Integer incorrectNameId = incorrectNames.get(scientificName);
+			if (incorrectNameId != null) if (incorrectNameId == -1) return null;
+			res = idNodes.get(incorrectNameId);
+		}
 		Integer taxonId = null;
 		if (res == null) {
 			try {
 				taxonId = WormsAPI.nameToID(scientificName);
 			} catch (Exception e) {
 				taxonId = WormsAPI.fuzzyNameToID(scientificName);
+				if (taxonId != null)
+					incorrectNames.put(scientificName, taxonId);
+				else
+					incorrectNames.put(scientificName, -1);
 			}
 			if (taxonId == -999)
 				taxonId = WormsAPI.fuzzyNameToID(scientificName);

src/biotree/FileProcessor.java

@@ -8,6 +8,8 @@ import java.util.Scanner; // Testing ONLY
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.json.simple.parser.ParseException;
+
 /**
  * This class reads and parses files in the format of occurences.csv
  * It provides methods to get chunks of data. 
@@ -41,8 +43,10 @@ public class FileProcessor {
 	 * Initialize Processing.
 	 *  Reads file at path. 
 	 *  Calls parse() for each line
+	 * @throws ParseException 
+	 * @throws NumberFormatException 
 	 */
-	private static void initProcessing() {
+	private static void initProcessing() throws NumberFormatException, ParseException {
 		FileReader fr;
 		BufferedReader br;
 
@@ -65,6 +69,7 @@ public class FileProcessor {
 			
 			//initialize the storage of records
 			DataStore.init(al.toArray(new Record[al.size()]));
+			al = null;
 			
 			s.close();//Testing ONLY
 			br.close();
@@ -81,8 +86,10 @@ public class FileProcessor {
 	 * 
 	 * @param currentLine, a line/row of data
 	 * @throws IOException
+	 * @throws ParseException 
+	 * @throws NumberFormatException 
 	 */
-	private static void parse(String currentLine) throws IOException {
+	private static void parse(String currentLine) throws IOException, NumberFormatException, ParseException {
 		/* Regex Pattern Grouping Guide
 		 * 	Retrieve String Groups with: matchEventId.group(x):
 		 *  group 0: full matched string
@@ -125,8 +132,10 @@ public class FileProcessor {
 	 * Calls BioTree's processRecord and another method to create a Record
 	 * 
 	 * @param matchEventId
+	 * @throws ParseException 
+	 * @throws NumberFormatException 
 	 */
-	public static void createObjects(Matcher matchEventId) {
+	public static void createObjects(Matcher matchEventId) throws NumberFormatException, ParseException {
 		// Call BioTree
 		Record rec = null;
 //		if(matchEventId.group(9) != null) {
@@ -170,7 +179,7 @@ public class FileProcessor {
 		return new Record(eventId, occurId, taxonId, individualCount, latitude, longitude, year, month, day);
 	}
 	
-	public static void main(String[] args) {
+	public static void main(String[] args) throws NumberFormatException, ParseException {
 		initProcessing();
 	}
 }

src/biotree/WormsAPI.java

@@ -64,13 +64,14 @@ public class WormsAPI {
 	 * @throws IOException
 	 * @throws ParseException 
 	 */
-	public static int fuzzyNameToID(String fuzzyName) throws IOException, ParseException {
-		//System.out.println("Fuzzy name: " + fuzzyName);
+	public static Integer fuzzyNameToID(String fuzzyName) throws IOException, ParseException {
+		System.out.println("Fuzzy name: " + fuzzyName);
 		fuzzyName = repSpaces(fuzzyName);
 		String resp = makeRequest(String.format(
-				"http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%%5B%%5D=%s&marine_only=true",
+				"http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%%5B%%5D=%s&marine_only=false",
 				fuzzyName));
 
+		if (resp.length() == 0) return null;
 		JSONParser parser = new JSONParser();
 		
 		JSONArray json = (JSONArray) parser.parse(resp);

src/search/BST.java

@@ -28,7 +28,7 @@ public class BST<Key extends Comparable<Key>, Value> {
 		else return x.N;
 	}
 	
-	public Value get(Key key) { return get(root, key); }
+	public Value get(Key key) { if (key == null) return null; return get(root, key); }
 	
 	private Value get(Node x, Key key) {
 		if (x == null) return null;