Merge branch 'web' of https://gitlab.cas.mcmaster.ca/schankuc/2XB3 into

web

# Conflicts:
#	src/search/Histogram.java
#	src/sort/Bound.java

.gitignore

@@ -7,6 +7,8 @@
 *.blg
 *DS_Store*
 *.csv
+*/bin
 *.ser
 .idea/
 *.class
+logs/
\ No newline at end of file

makefile

 server:
+	mkdir -p tomcat/webapps/Trawl/WEB-INF/classes
+	chmod u+x tomcat/bin/startup.sh
+	chmod u+x tomcat/bin/shutdown.sh
+	chmod u+x tomcat/bin/catalina.sh
 	cp -rf bin/* tomcat/webapps/Trawl/WEB-INF/classes
 
 start: server

makefile2

-TOMCAT_DIR = tomcat/webapps/Trawl
-BIN_DIR = tomcat/webapps/Trawl/bin
-
-server: $(BIN_DIR)/TrawlExpert.class $(BIN_DIR)/../WEB-INF/classes/com/example/web/Director.class
-	javac -d $(TOMCAT_DIR)/WEB-INF/classes/ -classpath tomcat/lib/servlet-api.jar $(TOMCAT_DIR)/src/com/example/listener/StartUpContext.java
-
-
-start:
-	tomcat/bin/startup.sh
-
-stop:
-	tomcat/bin/shutdown.sh
-
-$(BIN_DIR)/TrawlExpert.class: $(BIN_DIR)/data/BioTree.class $(BIN_DIR)/data/DataStore.class $(BIN_DIR)/data/Date.class $(BIN_DIR)/data/FileProcessor.class $(BIN_DIR)/data/Record.class $(BIN_DIR)/data/TaxonNode.class $(BIN_DIR)/data/TaxonType.class $(BIN_DIR)/data/WormsAPI.class $(BIN_DIR)/search/BasicSearch.class $(BIN_DIR)/search/BST.class $(BIN_DIR)/search/Histogram.class $(BIN_DIR)/sort/Bound.class $(BIN_DIR)/sort/GeneralCompare.class $(BIN_DIR)/sort/GeneralRange.class $(BIN_DIR)/sort/KDT.class $(BIN_DIR)/sort/MergeSort.class $(BIN_DIR)/sort/RangeHelper.class
-	javac -d $(TOMCAT_DIR)/WEB-INF/classes/ -classpath $(TOMCAT_DIR)/lib/servlet-api.jar:$(BIN_DIR):bin:json-simple-1.1.1.jar $(TOMCAT_DIR)/src/com/example/model/TrawlExpert.java
-
-$(BIN_DIR)/data/BioTree.class: src/data/BioTree.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/BioTree.java
-
-$(BIN_DIR)/data/DataStore.class: src/data/DataStore.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/DataStore.java
-
-$(BIN_DIR)/data/Date.class: src/Data/date.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/Date.java
-
-$(BIN_DIR)/data/FileProcessor.class: src/data/FileProcessor.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/FileProcessor.java
-
-$(BIN_DIR)/data/Record.class: src/data/Record.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/Record.java
-
-$(BIN_DIR)/data/TaxonNode.class: src/data/TaxonNode.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/TaxonNode.java
-
-$(BIN_DIR)/data/TaxonType.class: src/data/TaxonType.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/TaxonType.java
-
-$(BIN_DIR)/data/WormsAPI.class: src/data/WormsAPI.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/WormsAPI.java
-
-$(BIN_DIR)/search/BasicSearch.class: src/search/BasicSearch.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/BasicSearch.java
-
-$(BIN_DIR)/search/BST.class: src/search/BST.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/BST.java
-
-$(BIN_DIR)/search/Histogram.class: src/search/Histogram.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/Histogram.java
-
-$(BIN_DIR)/sort/Bound.class: src/sort/Bound.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/Bound.java
-
-$(BIN_DIR)/sort/GeneralCompare.class: src/sort/GeneralCompare.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/GeneralCompare.java
-
-$(BIN_DIR)/sort/GeneralRange.class: src/sort/GeneralRange.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/GeneralRange.java
-
-$(BIN_DIR)/sort/KDT.class: src/sort/KDT.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/KDT.java
-
-$(BIN_DIR)/sort/MergeSort.class: src/sort/MergeSort.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/MergeSort.java
-
-$(BIN_DIR)/sort/RangeHelper.class: src/sort/RangeHelper.java
-	javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/RangeHelper.java
-
-$(BIN_DIR)/../WEB-INF/classes/com/example/web/Director.class: $(BIN_DIR)/com/example/web/Director.java
-	javac -d $(TOMCAT_DIR)/WEB-INF/classes -classpath src/tomcat/lib/servlet-api.jar:$(BIN_DIR) $(BIN_DIR)/com/example/web/Director.java
\ No newline at end of file

makefile~

-server: /TrawlExpert.java
-	javac -classpath 

src/Main.java

 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Scanner;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.json.simple.parser.ParseException;
 
 import data.BioTree;
 import data.DataStore;
+import data.Date;
 import data.FileProcessor;
 import data.Record;
+import data.WormsAPI;
+import search.BST;
 import search.BasicSearch;
+import search.BasicSearchResult;
+import search.Histogram;
+import sort.Bound;
+import sort.GeneralRange;
 import sort.KDT;
+import sort.RangeHelper;
+import utils.Stopwatch;
 
 public class Main {
 	public static void main(String[] args) {
@@ -27,7 +42,7 @@ public class Main {
 			BioTree.write("data/biotree/");
 			DataStore.records.writeToFile("data/kdt.ser");
 		};
-		BasicSearch.init();
+		init();
 	}
 	
 	private static void printLogo() {
@@ -53,4 +68,135 @@ public class Main {
 				"                      `-'             `````````");
 		System.out.println("Loading.......");
 	}
+	
+	public static void init() {
+		System.out.println("Welcome!");
+		while(true) {
+			System.out.println("Main Menu");
+			System.out.println("Available commands:");
+			System.out.println("\ttree [taxonId / scientific name]");
+			System.out.println("\trecords (taxonId / scientific name) [-t start end]");
+			System.out.print("> ");
+			Pattern pat = Pattern.compile("([a-zA-Z]+)[ ]?([0-9a-zA-Z ]+[0-9a-zA-Z])?[ ]?[-]?([a-zA-Z])?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?");
+			Scanner s = new Scanner(System.in);
+			String line = s.nextLine();
+			Matcher matcher = pat.matcher(line);
+			if (!matcher.find()) continue;
+			
+			//tree
+			//tree taxonId
+			//tree scientific name
+			//records taxonId
+			//records scientific name
+			String command = matcher.group(1);
+			
+			if (command.equals("records"))
+				rangeSearch(matcher);
+			else if (command.equals("tree"))
+				printTree(matcher);
+		}
+	}
+	
+	private static void rangeSearch(Matcher matcher) {
+		Integer start = null;
+		Integer end = null;
+		if (matcher.group(3) != null)
+			if (matcher.group(3).equals("t")) {
+				if (matcher.group(4) != null)
+					start = Integer.parseInt(matcher.group(4));
+				if (matcher.group(5) != null)
+					end = Integer.parseInt(matcher.group(5));
+			}
+		
+		Integer taxonId = null;
+		try {
+			taxonId = Integer.parseInt(matcher.group(2));
+		} catch (NumberFormatException e) {
+			if (taxonId == null) {
+				try {
+					taxonId = WormsAPI.nameToRecordID(matcher.group(2));
+				} catch (IOException e1) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				} catch (ParseException e1) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		}
+		
+		BasicSearchResult result = BasicSearch.range(taxonId, start, end);
+		
+		System.out.println("Found " + result.n() + " records in " + result.time() + " seconds.");
+		
+		while(true) {
+			System.out.println("Available commands: list, histogram, sum, exit");
+			System.out.print("> ");
+			
+			Scanner s = new Scanner(System.in);
+			String command = s.nextLine();
+			
+			if (command.equals("list"))
+				printRecords(result.results());
+			else if (command.equals("histogram")) {
+				printHistogram(result.histogram());
+			} else if (command.equals("exit"))
+				return;
+			else if (command.equals("sum")) {
+				System.out.println(result.sum());
+			}
+		}
+	}
+	
+	private static void printRecords(Iterable<Record> results) {
+		String format = "|%1$-45s|%2$-15s|%3$-15s|%4$-15s|%5$-15s|%6$-15s\n";
+		System.out.format(format, "Scientific Name", "IndividualCount", "Latitude", "Longitude","Year","Month","Day");
+		for (Record r: results) {
+			System.out.println(r);
+		}
+	}
+	
+	private static void printTree(Matcher matcher) {
+		Integer taxonId;
+		String name;
+		if (matcher.group(2) == null)
+			BioTree.printTree();
+		else {
+			name = matcher.group(2);
+			try {
+				taxonId = Integer.parseInt(name);
+				BioTree.printTree(taxonId);
+			} catch (Exception e) {
+				BioTree.printTree(name);
+			}
+		}
+		System.out.println();
+	}
+	
+	/**
+	 * Prints a histogram based on a BST of records
+	 * 
+	 * @param record -An BST of records
+	 */
+	public static void printHistogram(BST<Integer,Integer> record) {
+		int max = 0;
+		int scale = 100;
+		Iterable<Integer> results = record.keys();
+		for (Integer year: results) {
+			if (max < record.get(year)) max =record.get(year);
+
+		}
+		System.out.println("     |" + (new String(new char[scale]).replace('\0', '-')) + "|");
+		String format = "%1$-5d|%2$-" + (scale + 1) + "s";
+		for (Integer year: results) {
+			String s = "=";
+			int loopc = (int) ((float)(record.get(year)/ (float) max) * scale);
+			for (int j=0; j< loopc; j++) {
+				s+="=";
+			}
+			System.out.format(format, year, s);
+			System.out.println("| " + record.get(year));
+		}
+		System.out.format("Scale: one = is %d individuals.\n", max / scale);
+	}
 }

src/data/BioTree.java

@@ -2,6 +2,7 @@ package data;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.ObjectInputStream;
@@ -169,33 +170,10 @@ public class BioTree implements Serializable {
 	 */
 	public static Integer processRecord(String scientificName) throws IOException, ParseException {
 		//reverse lookup based on name, try adding the found taxonId.
-		System.out.println("Processing " + scientificName);
-		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 the taxonId was not found in the local database
-		if (res == null) {
-			try {
-				taxonId = WormsAPI.nameToID(scientificName);
-			} catch (Exception e) {
-				taxonId = WormsAPI.nameToRecordID(scientificName);
-				if (taxonId != null)
-					incorrectNames.put(scientificName, taxonId);
-				else {
-					incorrectNames.put(scientificName, -1);
-				}
-			}
-		}
-		else
-			taxonId = res.getTaxonId();
+		Integer taxonId = nameToTaxonId(scientificName);
+		System.out.println(scientificName + ": " + taxonId);
 		if (taxonId == null) return null;
-		if (taxonId == -999)
-			taxonId = WormsAPI.nameToRecordID(scientificName);
+		if (taxonId == -1)   return null;
 		if (processTaxonId(taxonId)) return null;
 		return taxonId;
 	}
@@ -259,6 +237,58 @@ public class BioTree implements Serializable {
 		return idNodes.get(taxonId);
 	}
 	
+	/**
+	 * Get the species at a given index (taxonId). This assumes that the
+	 * node already exists or else it will return null. As such, it is best
+	 * to use this function once all the data has been parsed and the BioTree
+	 * has been built. 
+	 * 
+	 * @param i
+	 *            The speciesid (index) of the species.
+	 * @return The Species object.
+	 * @throws ParseException 
+	 * @throws IOException 
+	 */
+	public static TaxonNode getTaxonRecord(String scientificName) throws IOException, ParseException {
+		return idNodes.get(nameToTaxonId(scientificName));
+	}
+	
+	/**
+	 * Get the TaxonNode containing information about the given scientific name. 
+	 * This assumes that thenode already exists locally or else it will return null. 
+	 * As such, it is best to use this function once all the data has been parsed 
+	 * and the BioTree has been built. 
+	 * 
+	 * @param scientificName
+	 *            The scientific name of the taxon.
+	 * @return The Species object.
+	 * @throws ParseException 
+	 * @throws IOException 
+	 */
+	public static Integer nameToTaxonId(String scientificName) throws IOException, ParseException {
+		Integer taxonId;
+		//look up based on string literal, return if found
+		TaxonNode tx = strNodes.get(scientificName);
+		if (tx != null) return tx.getTaxonId();
+		else System.out.println(scientificName + " not in local db");
+		//look up in local incorrect names database, return if it exists
+		taxonId = incorrectNames.get(scientificName);
+		if (taxonId != null) {
+			tx = idNodes.get(taxonId);
+			if (tx != null) return tx.getTaxonId();
+		} else {		//otherwise use Worms to look it up
+			System.out.println(scientificName + " not in incor db");
+			taxonId = WormsAPI.nameToRecordID(scientificName);
+			if (taxonId == null) //if nothing is found, mark this species as not existing.
+				incorrectNames.put(scientificName, -1);
+			else {
+				System.out.println(scientificName + " found in Worms: " + taxonId);
+				incorrectNames.put(scientificName, taxonId);
+			}
+		}
+		return taxonId;
+	}
+	
 	public static Iterable<Integer> getNonEmptyChildren(int taxonId){
 		ArrayList<Integer> result = new ArrayList<Integer>();
 		

src/data/FileProcessor.java

@@ -153,7 +153,9 @@ public class FileProcessor {
 		int errorCount=0;	// TESTING ONLY
 		if (!matchEventId.group(10).equals("NA")) {
 			try{
-				al.add(createRecord(Integer.parseInt(matchEventId.group(3)), matchEventId.group(1), BioTree.processRecord(matchEventId.group(10)), Integer.parseInt(matchEventId.group(2)), Float.parseFloat(matchEventId.group(7)), Float.parseFloat(matchEventId.group(8)), Integer.parseInt(matchEventId.group(4)), Integer.parseInt(matchEventId.group(5)), Integer.parseInt(matchEventId.group(6))));
+				Integer taxonId = BioTree.processRecord(matchEventId.group(10));
+				if (taxonId != null)
+					al.add(createRecord(Integer.parseInt(matchEventId.group(3)), matchEventId.group(1), taxonId, Integer.parseInt(matchEventId.group(2)), Float.parseFloat(matchEventId.group(7)), Float.parseFloat(matchEventId.group(8)), Integer.parseInt(matchEventId.group(4)), Integer.parseInt(matchEventId.group(5)), Integer.parseInt(matchEventId.group(6))));
 			} catch(IOException e) {
 				System.out.println("Input Error:" + e);
 			} catch(NullPointerException e) {

src/data/WormsAPI.java

@@ -31,7 +31,7 @@ public class WormsAPI {
 		 * System.out.println(taxnodes[i].getTaxonType());
 		 * System.out.println(taxnodes[i].getName()); }
 		 */
-
+		System.out.println(nameToRecordID("Hello"));
 	}
 
 	/**
@@ -107,8 +107,6 @@ public class WormsAPI {
 		int id =  (int) (long) ((JSONObject)json.get(0)).get("AphiaID");
 		
 		return id;
-		
-		
 	}
 
 	/**

src/model/TrawlExpert.java

 package model;
 
+import java.io.IOException;
+
 import org.json.simple.parser.ParseException;
 
 import data.BioTree;
 import data.DataStore;
 import data.FileProcessor;
 import data.Record;
+import data.TaxonNode;
 import search.BasicSearch;
+import search.BasicSearchResult;
 import sort.KDT;
 
 public class TrawlExpert {
@@ -32,4 +36,22 @@ public class TrawlExpert {
 	public Iterable<Integer> listAllSpecies(){
 		return BioTree.getNonEmptyChildren(2);
 	}
+	
+	public BasicSearchResult rangeSearch(Integer taxonId, Integer yearLo, Integer yearHi) {
+		return BasicSearch.range(taxonId, yearLo, yearHi);
+	}
+	
+	public TaxonNode getTaxonRecord(Integer taxonId) {
+		return BioTree.getTaxonRecord(taxonId);
+	}
+	
+	public TaxonNode getTaxonRecord(String scientificName) {
+		try {
+			return BioTree.getTaxonRecord(scientificName);
+		} catch (IOException | ParseException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
 }

src/model/TrawlExpert2.java

-package com.example.model;
-import java.util.*;
-public class TrawlExpert {
-
-public List getBrands(String phylum) {
-    List brands = new ArrayList();
-    if (phylum.equals("Arthropoda")) {
-        brands.add("Some arthropoda data");
-        brands.add("Some more Arthropoda data");
-    }
-    else {
-        brands.add("This aint arthropoda");
-        brands.add("Under construction");
-    }
-    return brands;
-    }
-}
-
-// For Testing on Java's Console
-// public static void main(String[]args){
-//     String color = "amber";
-//     System.out.println(brand.get(0));
-// }
\ No newline at end of file

src/sandbox/.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

src/sandbox/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>sandbox</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

src/sandbox/GeneralCompare.java

+package sandbox;
+
+public interface GeneralCompare {
+	public int eval(Comparable a1, Comparable a2);
+
+}

src/sandbox/Point.java

@@ -7,19 +7,19 @@ public class Point implements Comparable<Point>, Serializable {
 	 * 
 	 */
 	private static final long serialVersionUID = 5361956730616676054L;
-	private final int x;
-	private final int y;
+	private final double x;
+	private final double y;
 	
-	public Point(int x, int y) {
+	public Point(double x, double y) {
 		this.x = x;
 		this.y = y;
 	}
 	
-	public int getX() {
+	public double getX() {
 		return this.x;
 	}
 	
-	public int getY() {
+	public double getY() {
 		return this.y;
 	}
 	

src/sandbox/TestLambdas.java

@@ -7,9 +7,9 @@ package sandbox;
 public class TestLambdas {
 	public static void main(String[] args) {
 		//declare the instances of BinaryIntExpression
-		BinaryIntExpression b0;
-		BinaryIntExpression b1;
-		BinaryIntExpression b2;
+		GeneralCompare<Integer> b0;
+		GeneralCompare<Integer> b1;
+		GeneralCompare<Integer> b2;
 		BinaryIntExpression b3;
 		BinaryIntExpression b4;
 		BinaryIntExpression b5;
@@ -34,13 +34,13 @@ public class TestLambdas {
 		};
 			
 		//call the main function using the instances as a parameter.
-		result = binaryOperation(1,2,b0);
+		result = binaryIntegerOperation(1,2,b0);
 		System.out.println(result);
 		
-		result = binaryOperation(1,2,b1);
+		result = binaryIntegerOperation(1,2,b1);
 		System.out.println(result);
 		
-		result = binaryOperation(1,2,b2);
+		result = binaryIntegerOperation(1,2,b2);
 		System.out.println(result);
 		
 		result = binaryOperation(1,2,b3);
@@ -61,4 +61,9 @@ public class TestLambdas {
 		return exp.eval(a1, a2);
 	}
 	
+	public static int binaryIntegerOperation(int a1, int a2, GeneralCompare<Integer> exp) {
+		//call the eval() function in the given BinaryIntExpression.
+		return exp.eval(a1, a2);
+	}
+	
 }

src/search/BasicSearch.java

 package search;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Scanner;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.json.simple.parser.ParseException;
-
 import utils.Stopwatch;
 import data.BioTree;
 import data.DataStore;
 import data.Date;
 import data.Record;
-import data.WormsAPI;
 import sort.Bound;
 import sort.GeneralRange;
 import sort.RangeHelper;
 
+/**
+ * Provides functionality for range searching the Record database.
+ * @author Christopher W. Schankula
+ *
+ */
 public class BasicSearch {
-	public static void init() {
-		System.out.println("Welcome!");
-		while(true) {
-			System.out.println("Main Menu");
-			System.out.println("Available commands:");
-			System.out.println("\ttree [taxonId / scientific name]");
-			System.out.println("\trecords (taxonId / scientific name) [-t start end]");
-			System.out.print("> ");
-			Pattern pat = Pattern.compile("([a-zA-Z]+)[ ]?([0-9a-zA-Z ]+[0-9a-zA-Z])?[ ]?[-]?([a-zA-Z])?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?([A-Za-z0-9]+)?[ ]?");
-			Scanner s = new Scanner(System.in);
-			String line = s.nextLine();
-			Matcher matcher = pat.matcher(line);
-			if (!matcher.find()) continue;
-			
-			//tree
-			//tree taxonId
-			//tree scientific name
-			//records taxonId
-			//records scientific name
-			String command = matcher.group(1);
-			
-			if (command.equals("records"))
-				rangeSearch(matcher);
-			else if (command.equals("tree"))
-				printTree(matcher);
-		}
-	}
-	
-	private static void rangeSearch(Matcher matcher) {
-		Integer start = null;
-		Integer end = null;
+	/**
+	 * Returns all records matching any of the children of the given TaxonID and in the 
+	 * date range given
+	 * @param taxonId The TaxonID for which to search
+	 * @param yearLo The lower bound on the year range
+	 * @param yearHi The upper bound on the year range
+	 * @return
+	 */
+	public static BasicSearchResult range(Integer taxonId, Integer yearLo, Integer yearHi){
 		GeneralRange<Record> a0 = RangeHelper.date(Bound.ANY);
-		if (matcher.group(3) != null)
-			if (matcher.group(3).equals("t")) {
-				if (matcher.group(4) != null)
-					start = Integer.parseInt(matcher.group(4));
-				if (matcher.group(5) != null)
-					end = Integer.parseInt(matcher.group(5));
-				Date lower = new Date(start,01,01);
-				Date upper = new Date(end+1,01,01);
-				
-				a0 = RangeHelper.date(Bound.LOWHIGH, lower, upper);
-			}
 		
-		Integer taxonId = null;
-		try {
-			taxonId = Integer.parseInt(matcher.group(2));
-		} catch (NumberFormatException e) {
-			if (taxonId == null) {
-				try {
-					taxonId = WormsAPI.nameToRecordID(matcher.group(2));
-				} catch (IOException e1) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
-				} catch (ParseException e1) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
-				}
-			}
+		if ((yearLo != null) && (yearHi != null)) {
+			Date lower = new Date(yearLo,01,01);
+			Date upper = new Date(yearHi+1,01,01);
+			a0 = RangeHelper.date(Bound.LOWHIGH, lower, upper);
 		}
 		
 		GeneralRange<Record> a2 = r -> 0;
@@ -86,9 +39,9 @@ public class BasicSearch {
 		
 		GeneralRange<Record> a1;
 		
-		Stopwatch sw = new Stopwatch();
 		Iterable<Integer> searches = BioTree.getNonEmptyChildren(taxonId);
 		
+		Stopwatch sw = new Stopwatch();
 		ArrayList<Record> results = new ArrayList<Record>();
 		for (Integer txId: searches) {
 			a1 = RangeHelper.taxonID(Bound.EQUALS, txId);
@@ -98,53 +51,8 @@ public class BasicSearch {
 			
 			results.addAll((Collection<? extends Record>) DataStore.records.rangeSearch(axes));
 		}
+		double time = sw.elapsedTime();
 		
-		double elapsed = sw.elapsedTime();
-		
-		System.out.println("Found " + ((ArrayList<Record>) results).size() + " records in " + elapsed + " seconds.");
-		
-		while(true) {
-			System.out.println("Available commands: list, histogram, sum, exit");
-			System.out.print("> ");
-			
-			Scanner s = new Scanner(System.in);
-			String command = s.nextLine();
-			
-			if (command.equals("list"))
-				printRecords(results);
-			else if (command.equals("histogram")) {
-				Histogram.printHistogram(Histogram.histogram(results));
-			} else if (command.equals("exit"))
-				return;
-			else if (command.equals("sum")) {
-				int sum = Histogram.sum(results);
-				System.out.println(sum);
-			}
-		}
-	}
-	
-	private static void printRecords(Iterable<Record> results) {
-		String format = "|%1$-45s|%2$-15s|%3$-15s|%4$-15s|%5$-15s|%6$-15s\n";
-		System.out.format(format, "Scientific Name", "IndividualCount", "Latitude", "Longitude","Year","Month","Day");
-		for (Record r: results) {
-			System.out.println(r);
-		}
-	}
-	
-	private static void printTree(Matcher matcher) {
-		Integer taxonId;
-		String name;
-		if (matcher.group(2) == null)
-			BioTree.printTree();
-		else {
-			name = matcher.group(2);
-			try {
-				taxonId = Integer.parseInt(name);
-				BioTree.printTree(taxonId);
-			} catch (Exception e) {
-				BioTree.printTree(name);
-			}
-		}
-		System.out.println();
+		return new BasicSearchResult(results, time);
 	}
 }

src/search/BasicSearchResult.java

+package search;
+
+import java.util.ArrayList;
+
+import data.Record;
+
+public class BasicSearchResult {
+	private ArrayList<Record> results;
+	private final double time;
+	private BST<Integer, Integer> histogram;
+	private Integer sum;
+	
+	public BasicSearchResult(ArrayList<Record> results, double time) {
+		this.results = results;
+		this.time = time;
+	}
+
+	public Iterable<Record> results() {
+		return (Iterable<Record>) results;
+	}
+	
+	public int n() {
+		return results.size();
+	}
+	
+	public double time() {
+		return time;
+	}
+	
+	public BST<Integer, Integer> histogram() {
+		if (this.histogram == null)
+			this.histogram = Histogram.histogram(results());
+		return histogram;
+	}
+	
+	public int sum() {
+		if (sum == null) {
+			sum = 0;
+			for (Record r: results())
+				sum += r.getCount();
+		}
+		return this.sum;
+	}
+}

src/search/CC.java

+package search;
+
+public class CC {
+
+	private boolean[] marked;
+	private int[] id;
+	private int count;
+	
+	public static void main(String[] args) {
+		Graph g = new Graph(5);
+		g.addEdge(4, 3);
+		g.addEdge(2, 3);
+		g.addEdge(1, 2);
+		g.addEdge(0, 2);
+		CC component = new CC(g);
+		System.out.println(component.connected(0, 2));
+	}
+	
+	public CC(Graph G){
+		marked = new boolean[G.V()];
+		id = new int[G.V()];
+		for(int s = 0; s < G.V(); s++){
+			if(!marked[s]){
+				dfs(G,s);
+				count++;
+			}
+		}
+	}
+	
+	private void dfs(Graph G, int v){
+		marked[v] = true;
+		id[v] = count;
+		for(int w : G.adj(v)){
+			if(!marked[w])
+				dfs(G, w);
+		}
+	}
+	
+	public boolean connected(int v, int w){
+		return id[v] == id[w];
+	}
+	
+	public int id(int v){
+		return id[v];
+	}
+	
+	public int count(){
+		return count;
+	}
+}