redo structure of website directory

.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="lib" path="json-simple-1.1.1.jar"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<classpathentry kind="lib" path="json-simple-1.1.1.jar"/>
+	<classpathentry kind="lib" path="tomcat/lib/servlet-api.jar"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.gitignore

@@ -9,4 +9,4 @@
 *.csv
 *.ser
 .idea/
-
+*.class

makefile

+server:
+	cp -rf bin/* tomcat/webapps/Trawl/WEB-INF/classes
+
+start:
+	tomcat/bin/startup.sh
+
+stop:
+	tomcat/bin/shutdown.sh
\ No newline at end of file

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/TrawlExpert.java

+import org.json.simple.parser.ParseException;
+
+import data.BioTree;
+import data.DataStore;
+import data.FileProcessor;
+import data.Record;
+import search.BasicSearch;
+import sort.KDT;
+
+public class TrawlExpert {
+	public TrawlExpert() {
+		//load data
+		try {
+			BioTree.init("data/biotree/");
+			DataStore.records = new KDT<Record>("data/kdt.ser");
+		} catch (Exception e0) {
+			try {
+				BioTree.init();
+				FileProcessor.initProcessing();
+			} catch (NumberFormatException | ParseException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			BioTree.write("data/biotree/");
+			DataStore.records.writeToFile("data/kdt.ser");
+		};
+		BasicSearch.init();
+	}
+}

src/model/TrawlExpert.java

+package model;
+
+import org.json.simple.parser.ParseException;
+
+import data.BioTree;
+import data.DataStore;
+import data.FileProcessor;
+import data.Record;
+import search.BasicSearch;
+import sort.KDT;
+
+public class TrawlExpert {
+	public TrawlExpert() {
+		
+	}
+	
+	public String sayHello() {
+		return "Hello";
+	}
+}

src/tomcat/webapps/Trawl/bin/com/example/model/TrawlExpert.java → 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));
+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