Add metadata parser, phylogenetic tree, and semantic zooming

.gitattributes

@@ -0,0 +1 @@
+*.gfa filter=lfs diff=lfs merge=lfs -text

README.md

@@ -33,21 +33,21 @@ Not officially supported.
     git clone https://github.com/ProgrammingLife2016/PL1-2016.git
     cd PL1-2016
     mvn package
-    java -cp target/byzantinegenerals-0.1.3.jar io.github.programminglife2016.pl1_2016.Launcher
+    java -cp target/byzantinegenerals-0.2.0.jar io.github.programminglife2016.pl1_2016.Launcher
 
 ### Subsequent runs
 
 Go to the `PL1-2016` directory.
 
     git pull
     mvn package
-    java -cp target/byzantinegenerals-0.1.3.jar io.github.programminglife2016.pl1_2016.Launcher
+    java -cp target/byzantinegenerals-0.2.0.jar io.github.programminglife2016.pl1_2016.Launcher
 
 ## Usage
 
 The server is running on `http://localhost:8081`.
 
-Open the web app at `http://localhost:8081/static/index.html`.
+Open the web app at `http://localhost:8081`.
 
 If you are a developer, you might be interested in interacting with the server
 directly. In that case, consult the API documentation below.

code.java

@@ -0,0 +1,8 @@
+
+    public static void main(String[] args) {
+        TokenIterator it = new TokenIterator("cbbaaacabaa", "bc");
+        while (it.hasNext()) {
+            System.out.println("next: " + it.next());
+        }
+    }
+

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>io.github.programminglife2016.pl1_2016</groupId>
     <artifactId>byzantinegenerals</artifactId>
-    <version>0.1.3</version>
+    <version>0.2.0</version>
 
     <build>
         <plugins>

src/main/java/io/github/programminglife2016/pl1_2016/Launcher.java

@@ -1,7 +1,9 @@
 package io.github.programminglife2016.pl1_2016;
 
-import io.github.programminglife2016.pl1_2016.parser.JsonSerializable;
-import io.github.programminglife2016.pl1_2016.parser.SimpleParser;
+import io.github.programminglife2016.pl1_2016.parser.phylotree.TreeNodeCollection;
+import io.github.programminglife2016.pl1_2016.parser.nodes.NodeCollection;
+import io.github.programminglife2016.pl1_2016.parser.nodes.SegmentParser;
+import io.github.programminglife2016.pl1_2016.parser.phylotree.PhyloGeneticTreeParser;
 import io.github.programminglife2016.pl1_2016.server.api.RestServer;
 import io.github.programminglife2016.pl1_2016.server.Server;
 
@@ -12,6 +14,7 @@
  * Reads the input and launches the server.
  */
 public final class Launcher {
+    private static final double NANOSECONDS_PER_SECOND = 1000000000.0;
     private Launcher() {
     }
     /**
@@ -20,9 +23,16 @@ private Launcher() {
      * @throws IOException thrown if the port is in use.
      */
     public static void main(String[] args) throws IOException {
-        InputStream is = Launcher.class.getResourceAsStream("/genomes/TB10_200.gfa");
-        JsonSerializable jsonSerializable = new SimpleParser().parse(is);
-        Server server = new RestServer(jsonSerializable);
+        System.out.println("Started loading.");
+        long startTime = System.nanoTime();
+        InputStream is = Launcher.class.getResourceAsStream("/genomes/TB10.gfa");
+        NodeCollection nodeCollection = new SegmentParser().parse(is);
+        long endTime = System.nanoTime();
+        System.out.println(String.format("Loading time: %f s.", (endTime - startTime)
+                / NANOSECONDS_PER_SECOND));
+        InputStream nwk = Launcher.class.getResourceAsStream("/genomes/TB10.nwk");
+        TreeNodeCollection treeNodes = new PhyloGeneticTreeParser().parse(nwk);
+        Server server = new RestServer(nodeCollection, treeNodes.getRoot());
         server.startServer();
     }
 }

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

@@ -0,0 +1,23 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import io.github.programminglife2016.pl1_2016.parser.phylotree.TreeNode;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class ClosestGenomeSelectionStrategy implements GenomeSelectionStrategy {
+    @Override
+    public Collection<String> genomes(TreeNode rootNode, int level) {
+        List<TreeNode> treeNodes = rootNode.flatten().stream().collect(Collectors.toList());
+        Collection<String> genomes = new ArrayList<>();
+        for (int i = 0; i < Math.min(Math.pow(2, level), treeNodes.size()); i++) {
+            genomes.add(treeNodes.get(i).getName());
+        }
+//        return genomes;
+        return Arrays.asList("TKK 02 0007", "TKK 02 0006");
+    }
+
+}

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

@@ -0,0 +1,29 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import io.github.programminglife2016.pl1_2016.parser.phylotree.TreeNode;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Optional;
+
+public class FurthestGenomeSelectionStrategy implements GenomeSelectionStrategy {
+    @Override
+    public Collection<String> genomes(TreeNode rootNode, int level) {
+        if (level == 0) {
+            Optional<TreeNode> treeNode = rootNode.flatten().stream().findFirst();
+            return Collections.singletonList(treeNode.get().getName());
+        }
+        if (rootNode.getChildren().isEmpty()) {
+            return Collections.singletonList(rootNode.getName());
+        } else {
+            Collection<TreeNode> children = rootNode.getChildren();
+            Collection<String> allGenomes = new ArrayList<>();
+            for (TreeNode child : children) {
+                Collection<String> genomes = genomes(child, level - 1);
+                allGenomes.addAll(genomes);
+            }
+            return allGenomes;
+        }
+    }
+}

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

@@ -0,0 +1,9 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import io.github.programminglife2016.pl1_2016.parser.phylotree.TreeNode;
+
+import java.util.Collection;
+
+public interface GenomeSelectionStrategy {
+    Collection<String> genomes(TreeNode rootNode, int level);
+}

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/NodeReductionStrategy.java

@@ -0,0 +1,7 @@
+package io.github.programminglife2016.pl1_2016.parser;
+
+import io.github.programminglife2016.pl1_2016.parser.nodes.NodeCollection;
+
+public interface NodeReductionStrategy {
+    NodeCollection reduce(NodeCollection original);
+}