add first minimal working BioTree and a few tests for it

.classpath

@@ -2,5 +2,6 @@
 <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="output" path="bin"/>
 </classpath>

src/biotree/BioTree.java

+package biotree;
+
+public class BioTree {
+	private static Species[] species;
+	private static int n;
+	
+	/**
+	 * Initialize species abstract object
+	 */
+	public static void init() {
+		species = new Species[500];
+		n = 0;
+	}
+
+	/**
+	 * TODO: Implement
+	 * 
+	 * @param fn
+	 *            Filename to read from
+	 */
+	public static void init(String fn) {
+
+	}
+
+	/**
+	 * TODO: Implement
+	 * 
+	 * @param fn
+	 *            Filename to write to
+	 */
+	public static void write(String fn) {
+
+	}
+
+	/**
+	 * Add a new species to the module
+	 * 
+	 * @param s
+	 *            New Species to add.
+	 * @return speciesid of new species entry
+	 */
+	public static int addSpecies(Species s) {
+		species[n++] = s;
+		return n;
+	}
+
+	/**
+	 * Update an existing species object.
+	 * 
+	 * @param i
+	 *            The index of the species to update.
+	 * @param s
+	 *            The new Species object to overwrite the old one with.
+	 */
+	public static void updateSpecies(int i, Species s) {
+		species[i] = s;
+	}
+
+	/**
+	 * Get the species at a given index (speciesid).
+	 * 
+	 * @param i
+	 *            The speciesid (index) of the species.
+	 * @return The Species object.
+	 */
+	public static Species getSpecies(int i) {
+		return species[i];
+	}
+
+	/**
+	 * Search for a species by name.
+	 * 
+	 * @param s
+	 *            The name of the species.
+	 * @return The speciesid of the species or -1 if it is not found.
+	 */
+	public static int findSpecies(String s) {
+		for (int i = 0; i < n; i++)
+			if (species[i].getSpecies() == s)
+				return i;
+		return -1;
+	}
+
+	/**
+	 * TODO: Implement
+	 * 
+	 * @param s
+	 *            The name of the genus.
+	 * @return Array of speciesid belonging to the genus.
+	 */
+	public static int[] findGenus(String s) {
+		int[] dummy = { 1, 2, 3 };
+		return dummy;
+	}
+
+	/**
+	 * TODO: Implement
+	 * 
+	 * @param s
+	 *            The name of the family.
+	 * @return Array of speciesid belonging to the family.
+	 */
+	public static int[] findFamily(String s) {
+		int[] dummy = { 1, 2, 3 };
+		return dummy;
+	}
+
+	/**
+	 * TODO: Implement
+	 * 
+	 * @param s
+	 *            The name of the order.
+	 * @return Array of speciesid belonging to the order.
+	 */
+	public static int[] findOrder(String s) {
+		int[] dummy = { 1, 2, 3 };
+		return dummy;
+	}
+
+}

src/biotree/TestBioTree.java

+package biotree;
+
+import static org.junit.Assert.*;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class TestBioTree {
+
+	@Before
+	public void setUp() throws Exception {
+		BioTree.init();
+		Species s0 = new Species("Actinopterygii","Perciformes","Moronidae","Morone","Morone chrysops");
+		Species s1 = new Species("Actinopterygii","Perciformes","Percidae","Perca","Perca flavescens");
+		BioTree.addSpecies(s0);
+		BioTree.addSpecies(s1);
+	}
+
+	@Test
+	public void testFindSpecies() {
+		assert BioTree.findSpecies("Morone chrysops") == 0;
+		assert BioTree.findSpecies("Perca flavescens") == 1;
+	}
+	
+	@Test
+	public void testGetSpecies() {
+		assert BioTree.getSpecies(0).getSpecies() == "Morone chrysops";
+		assert BioTree.getSpecies(1).getSpecies() == "Perca flavescens";
+	}
+
+}