introduced generics

dyoo · Jan 31, 2012 · 3c43ad9 · 3c43ad9
1 parent d53b22b
commit 3c43ad9
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Showing 7 changed files with 80 additions and 80 deletions.
diff --git a/src/org/arabidopsis/interval/FlankingFinder.java b/src/org/arabidopsis/interval/FlankingFinder.java
@@ -1,8 +1,7 @@
 package org.arabidopsis.interval;
 
-import java.util.List;
 import java.util.ArrayList;
-
+import java.util.List;
 import java.util.Map;
 import java.util.WeakHashMap;
 
@@ -16,22 +15,22 @@
  *
  */
 
-public class FlankingFinder {
-    private RbTree lows;
-    private RbTree highs;
+public class FlankingFinder<T> {
+    private final RbTree lows;
+    private final RbTree highs;
 
-    private Map lowRbNodeToObj;
-    private Map highRbNodeToObj;
+    private final Map<RbNode, T> lowRbNodeToObj;
+    private final Map<RbNode, T> highRbNodeToObj;
 
     public FlankingFinder() {
 	this.lows = new RbTree();
 	this.highs = new RbTree();
-	this.lowRbNodeToObj = new WeakHashMap();
-	this.highRbNodeToObj = new WeakHashMap();
+	this.lowRbNodeToObj = new WeakHashMap<RbNode, T>();
+	this.highRbNodeToObj = new WeakHashMap<RbNode, T>();
     }
 
 
-    public void add(Object obj, int low, int high) {
+    public void add(T obj, int low, int high) {
 	RbNode lowNode = new RbNode(low);
 	RbNode highNode = new RbNode(high);
 	this.lows.insert(lowNode);
@@ -43,9 +42,9 @@ public void add(Object obj, int low, int high) {
 
 
 
-    public List flankingLeft(int pos, int n) {
+    public List<T> flankingLeft(int pos, int n) {
 	if (this.highs.root.isNull())
-	    return new ArrayList();
+	    return new ArrayList<T>();
 
 	RbNode node = this.highs.root;
 	RbNode lastNode = node;
@@ -63,7 +62,7 @@ public List flankingLeft(int pos, int n) {
 	    lastNode = this.highs.predecessor(lastNode);
 	}
 
-	List results = new ArrayList();
+	List<T> results = new ArrayList<T>();
 	for (int i = 0; i < n && lastNode != RbNode.NIL; i++) {
 	    results.add(highRbNodeToObj.get(lastNode));
 	    lastNode = this.highs.predecessor(lastNode);
@@ -74,9 +73,9 @@ public List flankingLeft(int pos, int n) {
 
 
 
-    public List flankingRight(int pos, int n) {
+    public List<T> flankingRight(int pos, int n) {
 	if (this.lows.root.isNull())
-	    return new ArrayList();
+	    return new ArrayList<T>();
 
 	RbNode node = this.lows.root;
 	RbNode lastNode = node;
@@ -94,7 +93,7 @@ public List flankingRight(int pos, int n) {
 	    lastNode = this.lows.successor(lastNode);
 	}
 
-	List results = new ArrayList();
+	List<T> results = new ArrayList<T>();
 	for (int i = 0; i < n && lastNode != RbNode.NIL; i++) {
 	    results.add(lowRbNodeToObj.get(lastNode));
 	    lastNode = this.lows.successor(lastNode);

diff --git a/src/org/arabidopsis/interval/Interval.java b/src/org/arabidopsis/interval/Interval.java
@@ -1,7 +1,7 @@
 package org.arabidopsis.interval;
 
 // Quick and dirty interval class
-public class Interval implements Comparable {
+public class Interval implements Comparable<Interval> {
     private final int low;
     private final int high;
 
@@ -29,8 +29,7 @@ public int hashCode() {
     }
 
 
-    public int compareTo(Object o) {
-	Interval other = (Interval) o;
+    public int compareTo(final Interval other) {
 	if (this.low < other.low)
 	    return -1;
 	if (this.low > other.low)

diff --git a/src/org/arabidopsis/interval/IntervalTree.java b/src/org/arabidopsis/interval/IntervalTree.java
@@ -5,21 +5,22 @@
  */
 
 
-import java.util.WeakHashMap;
-import java.util.Map;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.WeakHashMap;
+
 import org.apache.log4j.Logger;
 
 public class IntervalTree {
-    private StatisticUpdate updater;
-    private RbTree tree;
+    private final StatisticUpdate updater;
+    private final RbTree tree;
 
-    private Map intervals;
-    private Map max;
-    private Map min;
+	private final Map<RbNode, Interval> intervals;
+	private final Map<RbNode, Integer> max;
+	private final Map<RbNode, Integer> min;
 
-    private Logger logger;
+    private final Logger logger;
 
 
     public IntervalTree() {
@@ -28,12 +29,12 @@ public IntervalTree() {
 
 	this.logger = Logger.getLogger(this.getClass());
 
-	this.intervals = new WeakHashMap();
+	this.intervals = new WeakHashMap<RbNode, Interval>();
 	this.intervals.put(RbNode.NIL, null);
 
-	this.max = new WeakHashMap();
+	this.max = new WeakHashMap<RbNode, Integer>();
 	this.max.put(RbNode.NIL, new Integer(Integer.MIN_VALUE));
-	this.min = new WeakHashMap();
+	this.min = new WeakHashMap<RbNode, Integer>();
 	this.min.put(RbNode.NIL, new Integer(Integer.MAX_VALUE));
     }
 
@@ -93,22 +94,22 @@ private boolean canOverlapOnRightSide(Interval interval,
 
 
     // Returns all matches as a list of Intervals
-    public List searchAll(Interval interval) {
+    public List<Interval> searchAll(Interval interval) {
 	logger.debug("Starting search for " + interval);
 
 	if (tree.root().isNull()) {
-	    return new ArrayList();
+	    return new ArrayList<Interval>();
 	}
 	return this._searchAll(interval, tree.root());
     }
 
 
-    private List _searchAll(Interval interval, RbNode node) {
+    private List<Interval> _searchAll(Interval interval, RbNode node) {
 	assert (! node.isNull());
 
 	logger.debug("Looking at " + getInterval(node));
 
-	List results = new ArrayList();
+	List<Interval> results = new ArrayList<Interval>();
 	if (getInterval(node).overlaps(interval)) {
 	    results.add(getInterval(node));
 	    logger.debug("match");
@@ -136,15 +137,15 @@ public Interval getInterval(RbNode node) {
 
 	assert (this.intervals.containsKey(node));
 
-	return (Interval) this.intervals.get(node);
+	return this.intervals.get(node);
     }
 
 
     public int getMax(RbNode node) {
 	assert (node != null);
 	assert (this.intervals.containsKey(node));
 
-	return ((Integer) this.max.get(node)).intValue();
+	return (this.max.get(node)).intValue();
     }
 
 
@@ -157,7 +158,7 @@ public int getMin(RbNode node) {
 	assert (node != null);
 	assert (this.intervals.containsKey(node));
 
-	return ((Integer) this.min.get(node)).intValue();
+	return (this.min.get(node)).intValue();
     }
 
 

diff --git a/src/org/arabidopsis/interval/OrderStatisticTree.java b/src/org/arabidopsis/interval/OrderStatisticTree.java
@@ -5,12 +5,12 @@
 
 
 public class OrderStatisticTree {
-    private RbTree tree;
-    private Map sizes;		// RbNode -> size
-    private OrderStatisticUpdate updater;
+    private final RbTree tree;
+    private final Map<RbNode, Integer> sizes;		// RbNode -> size
+    private final OrderStatisticUpdate updater;
 
     public OrderStatisticTree() {
-	this.sizes = new WeakHashMap();
+	this.sizes = new WeakHashMap<RbNode, Integer>();
 	this.sizes.put(RbNode.NIL, new Integer(0));
 	this.updater = new OrderStatisticUpdate();
 	this.tree = new RbTree(this.updater);
@@ -43,7 +43,7 @@ private RbNode _select(RbNode node, int i) {
     // Returns the size of a node.
     public int size(RbNode node) {
 	assert this.sizes.containsKey(node);
-	return ((Integer) this.sizes.get(node)).intValue();
+	return (this.sizes.get(node)).intValue();
     }
 
 

diff --git a/src/org/arabidopsis/interval/TestAll.java b/src/org/arabidopsis/interval/TestAll.java
@@ -12,13 +12,13 @@
  * @see
  */
 
-import junit.runner.TestCollector;
-import junit.runner.LoadingTestCollector;
-import junit.framework.TestSuite;
-import junit.framework.TestCase;
-
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
+
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import junit.runner.LoadingTestCollector;
+import junit.runner.TestCollector;
 
 
 public class TestAll extends TestCase {
@@ -36,9 +36,9 @@ public TestAll(String name) {
     public static TestSuite suite() throws Exception {
         TestSuite suite = new TestSuite();
 
-	List allTestClasses = getAllTestClasses();
+	List<Class<? extends TestCase>> allTestClasses = getAllTestClasses();
 	for(int i = 0 ; i < allTestClasses.size(); i++) {
-	    suite.addTestSuite((Class)allTestClasses.get(i));
+	    suite.addTestSuite(allTestClasses.get(i));
 	}
 
         return suite;
@@ -57,13 +57,14 @@ public static TestSuite suite() throws Exception {
      * @exception
      * @see
      */
-    private static List getAllTestClasses() throws ClassNotFoundException {
-	TestCollector collector = new LoadingTestCollector();
-	java.util.Enumeration e = collector.collectTests();
-	List testClasses = new ArrayList();
+    private static List<Class<? extends TestCase>> getAllTestClasses() throws ClassNotFoundException {
+	final TestCollector collector = new LoadingTestCollector();
+	@SuppressWarnings("unchecked")
+	final java.util.Enumeration<String> e = collector.collectTests();
+	final List<Class<? extends TestCase>> testClasses = new ArrayList<Class<? extends TestCase>>();
 	while (e.hasMoreElements()) {
-	    String className = (String) e.nextElement();
-	    Class c = Class.forName(className);
+	    final String className = e.nextElement();
+	    final Class<? extends TestCase> c = Class.forName(className).asSubclass(TestCase.class);
 	    // don't add ourself
 	    if (isSelfClass(c) || isClassNotInMyPackage(c)) {
 		continue;
@@ -75,14 +76,14 @@ private static List getAllTestClasses() throws ClassNotFoundException {
 
 
     // Returns true if the given class is ourself.
-    private static boolean isSelfClass(Class c) {
+    private static boolean isSelfClass(Class<?> c) {
 	return c.equals(TestAll.class);
     }
 
 
     // Returns true if the class c is not within the same package
     // hierarchy as ourselves.
-    private static boolean isClassNotInMyPackage(Class c) {
+    private static boolean isClassNotInMyPackage(Class<?> c) {
 	return (! c.getPackage().getName().startsWith
 		(TestAll.class.getPackage().getName()));
     }

diff --git a/src/org/arabidopsis/interval/TestFlankingFinder.java b/src/org/arabidopsis/interval/TestFlankingFinder.java
@@ -1,41 +1,41 @@
 package org.arabidopsis.interval;
 
-import junit.framework.TestCase;
-
-import java.util.List;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
+
+import junit.framework.TestCase;
 
 
 public class TestFlankingFinder extends TestCase {
-    private FlankingFinder finder;
+    private FlankingFinder<String> finder;
 
 
     public void setUp() {
-	this.finder = new FlankingFinder();
+	this.finder = new FlankingFinder<String>();
     }
 
 
     public void testEmptyCase() {
-	assertEquals(new ArrayList(),
+	assertEquals(new ArrayList<String>(),
 		     this.finder.flankingLeft(42, 1));
-	assertEquals(new ArrayList(),
+	assertEquals(new ArrayList<String>(),
 		     this.finder.flankingRight(42, 1));
     }
 
 
     public void testNoFinding() {
 	this.finder.add("hello", 10, 20);
-	assertEquals(new ArrayList(),
+	assertEquals(new ArrayList<String>(),
 		     this.finder.flankingLeft(9, 1));
-	assertEquals(new ArrayList(),
+	assertEquals(new ArrayList<String>(),
 		     this.finder.flankingRight(21, 1));
     }
 
 
     public void testSimpleFinding() {
 	this.finder.add("hello", 10, 20);
-	List expected = new ArrayList();
+	List<String> expected = new ArrayList<String>();
 	expected.add("hello");
 	assertEquals(expected,
 		     this.finder.flankingLeft(21, 1));