serialization for BioTree!

.gitignore

@@ -7,3 +7,4 @@
 *.blg
 *DS_Store*
 *.csv
+*.ser

src/data/BioTree.java

 package data;
 
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
 
 import org.json.simple.parser.ParseException;
 
 import search.BST;
+import sort.KDT;
 
-public class BioTree {
+public class BioTree implements Serializable {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4291273291916906661L;
 	//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, ParseException {
-		BioTree.processRecord("Micropterus dolomieui");
+		BioTree.processRecord(123123);
+		//BioTree.write("biotree");
+		BioTree.init("biotree");
+		System.out.println(idNodes.get(2));
 	}
 	
 	/**
@@ -29,9 +42,53 @@ public class BioTree {
 	 * 
 	 * @param fn
 	 *            Filename to read from
+	 * @return 
 	 */
 	public static void init(String fn) {
-
+		BST<Integer, TaxonNode> idNodes = null;
+		try {
+	         FileInputStream fileIn = new FileInputStream(fn+"/idnodes.ser");
+	         ObjectInputStream in = new ObjectInputStream(fileIn);
+	         idNodes = (BST<Integer, TaxonNode>) in.readObject();
+	         in.close();
+	         fileIn.close();
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      } catch (ClassNotFoundException c) {
+	         System.out.println("Employee class not found");
+	         c.printStackTrace();
+	      }
+		BioTree.idNodes = idNodes;
+		
+		BST<String, TaxonNode> strNodes = null;
+		try {
+	         FileInputStream fileIn = new FileInputStream(fn+"/strNodes.ser");
+	         ObjectInputStream in = new ObjectInputStream(fileIn);
+	         strNodes = (BST<String, TaxonNode>) in.readObject();
+	         in.close();
+	         fileIn.close();
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      } catch (ClassNotFoundException c) {
+	         System.out.println("Employee class not found");
+	         c.printStackTrace();
+	      }
+		BioTree.strNodes = strNodes;
+		
+		BST<String, Integer> incorrectNames = null;
+		try {
+	         FileInputStream fileIn = new FileInputStream(fn+"/incorNames.ser");
+	         ObjectInputStream in = new ObjectInputStream(fileIn);
+	         incorrectNames = (BST<String, Integer>) in.readObject();
+	         in.close();
+	         fileIn.close();
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      } catch (ClassNotFoundException c) {
+	         System.out.println("Employee class not found");
+	         c.printStackTrace();
+	      }
+		BioTree.incorrectNames = incorrectNames;
 	}
 
 	/**
@@ -42,7 +99,41 @@ public class BioTree {
 	 *            Filename to write to
 	 */
 	public static void write(String fn) {
-
+		try {
+	         FileOutputStream fileOut =
+	        		 new FileOutputStream(fn+"/idNodes.ser");
+	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
+	         out.writeObject(BioTree.idNodes);
+	         out.close();
+	         fileOut.close();
+	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      }
+		
+		try {
+	         FileOutputStream fileOut =
+	        		 new FileOutputStream(fn+"/strNodes.ser");
+	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
+	         out.writeObject(BioTree.strNodes);
+	         out.close();
+	         fileOut.close();
+	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      }
+		
+		try {
+	         FileOutputStream fileOut =
+	        		 new FileOutputStream(fn+"/incorNames.ser");
+	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
+	         out.writeObject(BioTree.incorrectNames);
+	         out.close();
+	         fileOut.close();
+	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      }
 	}
 
 	/**

src/data/TaxonNode.java

 package data;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 
 /**
@@ -11,7 +12,11 @@ import java.util.ArrayList;
  * https://stackoverflow.com/questions/2697182/how-to-use-an-array-list
  */
 	
-public class TaxonNode {
+public class TaxonNode implements Serializable {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -317741592166253773L;
 	private final int taxonId;
 	private final TaxonType taxonType;
 	private final String name;

src/search/BST.java

 package search;
 
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.NoSuchElementException;
 
-public class BST<Key extends Comparable<Key>, Value> {
+import sort.KDT;
+
+public class BST<Key extends Comparable<Key>, Value> implements Serializable {
+	/**
+	 * 
+	 */
+	public static void main(String[] args) {
+		//BST<Integer,Integer> bst = new BST<Integer, Integer>();
+		//bst.put(75, 9);
+		//bst.writeToFile("bst.ser");
+		BST<Integer, Integer> bst = new BST<Integer, Integer>("bst.ser");
+		
+		System.out.println(bst.get(75));
+	}
+	
+	private static final long serialVersionUID = 8775155124761510511L;
 	private Node root;
 	
-	private class Node{
+	public BST(String fn) {
+		BST<Key,Value> bst = null;
+		try {
+	         FileInputStream fileIn = new FileInputStream(fn);
+	         ObjectInputStream in = new ObjectInputStream(fileIn);
+	         bst = (BST<Key,Value>) in.readObject();
+	         in.close();
+	         fileIn.close();
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      } catch (ClassNotFoundException c) {
+	         System.out.println("Employee class not found");
+	         c.printStackTrace();
+	      }
+		this.root = bst.root;
+	}
+	
+	public BST() {
+		root = null;
+	}
+	
+	private class Node implements Serializable {
+		/**
+		 * 
+		 */
+		private static final long serialVersionUID = -8145778479611668151L;
 		private Key key;
 		private Value val;
 		private Node left, right;
@@ -183,4 +229,18 @@ public class BST<Key extends Comparable<Key>, Value> {
 		if (x == null) return 0;
 		else return Math.max(height (x.left), height(x.right)) + 1;
 	}
+	
+	public void writeToFile(String fn) {
+		try {
+	         FileOutputStream fileOut =
+	        		 new FileOutputStream(fn);
+	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
+	         out.writeObject(this);
+	         out.close();
+	         fileOut.close();
+	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      }
+	}
 }

src/sort/KDT.java

@@ -65,17 +65,7 @@ public class KDT<KeyVal extends Comparable<KeyVal>> implements Serializable {
 
 		System.out.println(kdt.toString());
 		
-		try {
-	         FileOutputStream fileOut =
-	        		 new FileOutputStream("kdtree.ser");
-	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
-	         out.writeObject(kdt);
-	         out.close();
-	         fileOut.close();
-	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
-	      } catch (IOException i) {
-	         i.printStackTrace();
-	      }
+		kdt.writeToFile("kdtree.ser");
 	}
 	
 	private class KDNode implements Serializable{
@@ -114,6 +104,7 @@ public class KDT<KeyVal extends Comparable<KeyVal>> implements Serializable {
 	         System.out.println("Employee class not found");
 	         c.printStackTrace();
 	      }
+		//https://stackoverflow.com/questions/26327956/set-this-in-a-class
 		this.root = kdt.root;
 		this.axes = kdt.axes;
 	}
@@ -201,6 +192,20 @@ public class KDT<KeyVal extends Comparable<KeyVal>> implements Serializable {
 		return toString(root, "");
 	}
 	
+	public void writeToFile(String fn) {
+		try {
+	         FileOutputStream fileOut =
+	        		 new FileOutputStream(fn);
+	         ObjectOutputStream out = new ObjectOutputStream(fileOut);
+	         out.writeObject(this);
+	         out.close();
+	         fileOut.close();
+	         System.out.printf("Serialized data is saved in /tmp/kdtree.ser");
+	      } catch (IOException i) {
+	         i.printStackTrace();
+	      }
+	}
+	
 	private String toString(KDNode x, String depth) {
 		if (x == null) return depth + "null\n";
 		String result = "";