Add JSON serializer for treenode

src/main/java/io/github/programminglife2016/pl1_2016/parser/BaseTreeNode.java

@@ -7,8 +7,10 @@
 /**
  * Class for representing a node in the phylogenetic tree.
  */
-public class BaseTreeNode implements JsonSerializable, TreeNode {
-    private String id;
+public class BaseTreeNode implements TreeNode {
+    private static int STATIC_ID = 1;
+    private int id;
+    private String name;
     private double weight;
     private List<TreeNode> children;
     private TreeNode parent;
@@ -22,22 +24,23 @@ public BaseTreeNode() {
 
     /**
      * Create a Tree Node Object.
-     * @param id id of the tree node.
+     * @param name name of the tree node.
      * @param weight weight of the tree node.
      */
-    public BaseTreeNode(String id, double weight) {
-        this(id, weight, new ArrayList<>(), null);
+    public BaseTreeNode(String name, double weight) {
+        this(name, weight, new ArrayList<>(), null);
     }
 
     /**
      * Create a BaseTreeNode object.
-     * @param id id of the treenode.
+     * @param name name of the treenode.
      * @param weight weight of the tree node.
      * @param children list of children tree nodes.
      * @param parent parent tree node of this tree node.
      */
-    public BaseTreeNode(String id, double weight, List<TreeNode> children, TreeNode parent) {
-        this.id = id;
+    public BaseTreeNode(String name, double weight, List<TreeNode> children, TreeNode parent) {
+        this.id = STATIC_ID++;
+        this.name = name;
         this.weight = weight;
         this.children = children;
         this.parent = parent;
@@ -60,11 +63,21 @@ public void setChildren(List<TreeNode> children) {
     }
 
     /**
-     * Set the id of the tree node.
-     * @param id value of the id.
+     * Get the id of the tree node.
+     *
+     * @return id of the tree node
      */
-    public void setId(String id) {
-        this.id = id;
+    @Override
+    public int getId() {
+        return id;
+    }
+
+    /**
+     * Set the name of the tree node.
+     * @param name value of the name.
+     */
+    public void setName(String name) {
+        this.name = name;
     }
 
     /**
@@ -76,11 +89,11 @@ public void setWeight(double weight) {
     }
 
     /**
-     * Get id of tree node.
-     * @return id of tree.
+     * Get name of tree node.
+     * @return name of tree.
      */
-    public String getId() {
-        return id;
+    public String getName() {
+        return name;
     }
 
     /**
@@ -113,7 +126,7 @@ public void setParent(TreeNode parent) {
      */
     @Override
     public String toString() {
-        return "[" + this.getId() + " " + this.getWeight()
+        return "[" + this.getName() + " " + this.getWeight()
                 + " {" + children.stream()
                                  .map(Object::toString)
                                  .collect(joining(", ")) + "}]";

src/main/java/io/github/programminglife2016/pl1_2016/parser/JsonSerializable.java

@@ -1,22 +1,9 @@
 package io.github.programminglife2016.pl1_2016.parser;
 
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-
 /**
  * Data is sent by the server in JSON format. Classes extending this method can convert their
  * representation to JSON.
  */
 public interface JsonSerializable {
-    /**
-     * Convert the representation to JSON.
-     *
-     * @return JSON representation of this object.
-     */
-    default String toJson() {
-        Gson gson = new GsonBuilder()
-                .registerTypeAdapter(NodeList.class, new NodeCollectionSerializer())
-                .registerTypeAdapter(NodeMap.class, new NodeCollectionSerializer()).create();
-        return gson.toJson(this);
-    }
+    String toJson();
 }

src/main/java/io/github/programminglife2016/pl1_2016/parser/NodeList.java

@@ -1,5 +1,8 @@
 package io.github.programminglife2016.pl1_2016.parser;
 
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.stream.Collectors;
@@ -62,4 +65,10 @@ public boolean containsKey(Object id) {
     public Collection<Node> getNodes() {
         return Arrays.asList(array).stream().filter(x -> x != null).collect(Collectors.toList());
     }
+
+    @Override
+    public String toJson() {
+        Gson gson = new GsonBuilder().registerTypeAdapter(NodeList.class, new NodeCollectionSerializer()).create();
+        return gson.toJson(this);
+    }
 }

src/main/java/io/github/programminglife2016/pl1_2016/parser/NodeMap.java

@@ -1,5 +1,8 @@
 package io.github.programminglife2016.pl1_2016.parser;
 
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
 import java.util.Collection;
 import java.util.HashMap;
 
@@ -24,4 +27,10 @@ public NodeMap(int initialCapacity) {
     public Collection<Node> getNodes() {
         return values();
     }
+
+    @Override
+    public String toJson() {
+        Gson gson = new GsonBuilder().registerTypeAdapter(NodeMap.class, new NodeCollectionSerializer()).create();
+        return gson.toJson(this);
+    }
 }

src/main/java/io/github/programminglife2016/pl1_2016/parser/PhyloGeneticTreeParser.java

@@ -1,10 +1,6 @@
 package io.github.programminglife2016.pl1_2016.parser;
 
-import io.github.programminglife2016.pl1_2016.Launcher;
-
-import java.io.ByteArrayInputStream;
 import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
 import java.util.*;
 
 
@@ -16,8 +12,7 @@ public class PhyloGeneticTreeParser implements Parser {
     @Override
     public JsonSerializable parse(InputStream inputStream) {
         String s = inputStreamToString(inputStream);
-        Collection<TreeNode> nodes = parseTokensFromString(s);
-        return null;
+        return parseTokensFromString(s);
     }
 
     private String inputStreamToString(InputStream inputStream) {
@@ -32,9 +27,9 @@ private String inputStreamToString(InputStream inputStream) {
      * @param s string representin the tree.
      * @return root of tree
      */
-    public Collection<TreeNode> parseTokensFromString(String s) {
+    public TreeNodeCollection parseTokensFromString(String s) {
         StringTokenizer tokenizer = new StringTokenizer(s, "(:,);", true);
-        Collection<TreeNode> nodes = construct(tokenizer);
+        TreeNodeCollection nodes = construct(tokenizer);
         return nodes;
     }
 
@@ -43,10 +38,11 @@ public Collection<TreeNode> parseTokensFromString(String s) {
      * @param tokenizer tokenizer with the contents of the .nwk file.
      * @return parsed Tree Node object.
      */
-    public Collection<TreeNode> construct(StringTokenizer tokenizer) {
-        Collection<TreeNode> nodes = new ArrayList<TreeNode>();
+    public TreeNodeCollection construct(StringTokenizer tokenizer) {
+        TreeNodeCollection nodes = new TreeNodeList();
         TreeNode root = new BaseTreeNode();
         nodes.add(root);
+        nodes.setRoot(root);
         TreeNode current = root;
         while (tokenizer.hasMoreTokens()) {
             String currentToken = tokenizer.nextToken();
@@ -76,7 +72,7 @@ public Collection<TreeNode> construct(StringTokenizer tokenizer) {
                 case ";":
                     break;
                 default:
-                    current.setId(currentToken);
+                    current.setName(currentToken);
                     break;
             }
         }

src/main/java/io/github/programminglife2016/pl1_2016/parser/TreeNode.java

@@ -7,12 +7,18 @@
  * Created by ravishivam on 6-5-16.
  */
 public interface TreeNode {
+    /**
+     * Get the id of the tree node.
+     *
+     * @return id of the tree node
+     */
+    int getId();
 
     /**
-     * Set the id of the tree node.
-     * @param id value of the id.
+     * Set the name of the tree node.
+     * @param name value of the name.
      */
-    void setId(String id);
+    void setName(String name);
 
     /**
      * Set the list of children tree nodes.
@@ -24,7 +30,7 @@ public interface TreeNode {
      * Get id of tree node.
      * @return id of tree.
      */
-    String getId();
+    String getName();
 
     /**
      * Return weight of this node.

src/main/java/io/github/programminglife2016/pl1_2016/parser/TreeNodeCollection.java

@@ -0,0 +1,8 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import java.util.Collection;
+
+public interface TreeNodeCollection extends Collection<TreeNode>, JsonSerializable {
+    TreeNode getRoot();
+    void setRoot(TreeNode root);
+}

src/main/java/io/github/programminglife2016/pl1_2016/parser/TreeNodeCollectionSerializer.java

@@ -0,0 +1,36 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonPrimitive;
+import com.google.gson.JsonSerializationContext;
+import com.google.gson.JsonSerializer;
+
+import java.lang.reflect.Type;
+
+public class TreeNodeCollectionSerializer implements JsonSerializer<TreeNodeCollection> {
+    @Override
+    public JsonElement serialize(TreeNodeCollection treeNodeCollection, Type type, JsonSerializationContext jsonSerializationContext) {
+        JsonObject jsonObject = new JsonObject();
+        JsonArray treeNodes = new JsonArray();
+        for (TreeNode treeNode : treeNodeCollection) {
+            JsonObject treeNodeObject = new JsonObject();
+            treeNodeObject.add("id", new JsonPrimitive(treeNode.getId()));
+            treeNodeObject.add("name", new JsonPrimitive(treeNode.getName()));
+            JsonArray children = new JsonArray();
+            treeNode.getChildren().stream().map(TreeNode::getName).forEach(children::add);
+            treeNodeObject.add("children", children);
+            if (treeNode.getParent() != null) {
+                treeNodeObject.add("parent", new JsonPrimitive(treeNode.getParent().getId()));
+            } else {
+                treeNodeObject.add("parent", new JsonPrimitive("null"));
+            }
+            treeNodeObject.add("weight", new JsonPrimitive(treeNode.getWeight()));
+            treeNodes.add(treeNodeObject);
+        }
+        jsonObject.add("treeNodes", treeNodes);
+        jsonObject.add("root", new JsonPrimitive(treeNodeCollection.getRoot().getName()));
+        return jsonObject;
+    }
+}

src/main/java/io/github/programminglife2016/pl1_2016/parser/TreeNodeList.java

@@ -0,0 +1,26 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+
+import java.util.ArrayList;
+
+public class TreeNodeList extends ArrayList<TreeNode> implements TreeNodeCollection {
+    private TreeNode root;
+
+    @Override
+    public String toJson() {
+        Gson gson = new GsonBuilder().registerTypeAdapter(TreeNodeList.class, new TreeNodeCollectionSerializer()).create();
+        return gson.toJson(this);
+    }
+
+    @Override
+    public TreeNode getRoot() {
+        return root;
+    }
+
+    @Override
+    public void setRoot(TreeNode root) {
+        this.root = root;
+    }
+}

src/test/java/io/github/programminglife2016/pl1_2016/parser/PhyloGeneticTreeParserTest.java

@@ -26,8 +26,8 @@ public void setUp() {
     public void testTreeWithSingleNode() {
         PhyloGeneticTreeParser parser = new PhyloGeneticTreeParser();
         String s = "(B:6.0,A:5.0);";
-        TreeNode node  = parser.parseTokensFromString(s);
-        assertEquals("B", node.getId());
+        TreeNodeCollection node  = parser.parseTokensFromString(s);
+        assertEquals("B", node.getRoot().getChildren().get(0).getName());
     }
 
     /**
@@ -37,8 +37,8 @@ public void testTreeWithSingleNode() {
     public void testTreeWithOneNestedLevel() {
         PhyloGeneticTreeParser parser = new PhyloGeneticTreeParser();
         String s = "(B:6.0,(A:5.0,(Z:9.0,T:10):3.0,E:4.0):5.0,D:11.0);";
-        TreeNode node = parser.parseTokensFromString(s);
-        assertEquals("B", node.getId());
+        TreeNodeCollection node = parser.parseTokensFromString(s);
+        assertEquals("B", node.getRoot().getChildren().get(0).getName());
     }
 
     /**