JAL-3253-applet JAL-3397

[jalview.git] / test / intervalstore / nonc / IntervalStoreTest.java

diff --git a/test/intervalstore/nonc/IntervalStoreTest.java b/test/intervalstore/nonc/IntervalStoreTest.java
index 7c1a921..581f5f4 100644 (file)
--- a/test/intervalstore/nonc/IntervalStoreTest.java
+++ b/test/intervalstore/nonc/IntervalStoreTest.java
@@ -46,10 +46,21 @@ import intervalstore.api.IntervalStoreI;
 
 public class IntervalStoreTest
 {
+
+  public static void main(String[] args)
+  {
+    new IntervalStoreTest().defaultTests();
+  }
+
+  private void defaultTests()
+  {
+    testAddAndQueryTiming();
+  }
+
   @Test(groups = "Functional")
   public void testFindOverlaps_nonNested()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 20);
     // same range different description
     SimpleFeature sf2 = new SimpleFeature(10, 20, "desc");
@@ -89,7 +100,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testFindOverlaps_nested()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 50);
     SimpleFeature sf2 = add(store, 10, 40);
     SimpleFeature sf3 = add(store, 20, 30);
@@ -127,7 +138,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testFindOverlaps_mixed()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 50);
     SimpleFeature sf2 = add(store, 1, 15);
     SimpleFeature sf3 = add(store, 20, 30);
@@ -184,7 +195,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testRemove()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 20);
     assertTrue(store.contains(sf1));
 
@@ -274,7 +285,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testAdd()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
 
     assertFalse(store.add(null));
 
@@ -304,7 +315,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testAdd_noDuplicates()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
 
     SimpleFeature sf1 = new SimpleFeature(10, 20, "Cath");
     SimpleFeature sf2 = new SimpleFeature(10, 20, "Cath");
@@ -320,7 +331,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testIsEmpty()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     assertTrue(store.isEmpty());
     assertEquals(store.size(), 0);
 
@@ -373,7 +384,7 @@ public class IntervalStoreTest
     /*
      * add a feature and a nested feature
      */
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 20);
     // sf2 is nested in sf1 so will be stored in nestedFeatures
     SimpleFeature sf2 = add(store, 12, 14);
@@ -399,7 +410,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testContains()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = new SimpleFeature(10, 20, "Cath");
     SimpleFeature sf2 = new SimpleFeature(10, 20, "Pfam");
 
@@ -436,7 +447,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testFindOverlaps_resultsArg_mixed()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 50);
     SimpleFeature sf2 = add(store, 1, 15);
     SimpleFeature sf3 = add(store, 20, 30);
@@ -499,7 +510,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testFindOverlaps_resultsArg_nested()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 50);
     SimpleFeature sf2 = add(store, 10, 40);
     SimpleFeature sf3 = add(store, 20, 30);
@@ -541,7 +552,7 @@ public class IntervalStoreTest
   @Test(groups = "Functional")
   public void testFindOverlaps_resultsArg_nonNested()
   {
-    IntervalStore<SimpleFeature> store = new IntervalStore<>();
+    IntervalStore<SimpleFeature> store = new IntervalStoreImpl();
     SimpleFeature sf1 = add(store, 10, 20);
     // same range different description
     SimpleFeature sf2 = new SimpleFeature(10, 20, "desc");
@@ -592,13 +603,32 @@ public class IntervalStoreTest
   @Test(groups = "Timing")
   public void testAddAndQueryTiming()
   {
-    IntervalStoreI<SimpleFeature> store = new intervalstore.impl.IntervalStore<>();
-    System.out.println("IntervalStoreJ");
-    testAddAndQueryTiming(store);
+    testAddAndQuery(1, 20000000, 10, 20);
+    testAddAndQuery(0, 0, 10, 20);
+
+    testAddAndQuery(1, 20000000, 10, 200);
+    testAddAndQuery(0, 0, 10, 200);
+
+    testAddAndQuery(1, 20000000, 10, 2000);
+    testAddAndQuery(0, 0, 10, 2000);
+
+    testAddAndQuery(1, 20000000, -2000000, 2000000);
+    testAddAndQuery(0, 0, -2000000, 2000000);
+  }
 
-    System.out.println("\nnonc.IntervalStore");
+  private void testAddAndQuery(int addstart, int addend, int start, int end)
+  {
+    System.out.println("\nadd: " + addstart + " " + addend + " query: "
+            + start + "  " + end);
+    StringBuffer sb = new StringBuffer();
+    IntervalStoreI<SimpleFeature> store;
     store = new intervalstore.nonc.IntervalStore<>();
-    testAddAndQueryTiming(store);
+    testAddAndQueryTiming(store, false, sb, addstart, addend, start, end);
+
+    store = new intervalstore.impl.IntervalStore<>();
+    testAddAndQueryTiming(store, true, sb, addstart, addend, start, end);
+
+    System.out.println(sb);
   }
 
   /**
@@ -608,30 +638,44 @@ public class IntervalStoreTest
    * 
    * @param store
    */
-  private void testAddAndQueryTiming(IntervalStoreI<SimpleFeature> store)
+  private void testAddAndQueryTiming(IntervalStoreI<SimpleFeature> store,
+          boolean isNCList, StringBuffer sb, int addstart, int addend,
+          int start, int end)
   {
     final int seqlen = 100000; // e.g. length of gene sequence
     final int repeats = 20;
     final int K = 1000;
     final int warmups = 5;
-    final int[] scales = new int[] { 10 * K, 100 * K, K * K };
+    final int[] scales = new int[] { 10 * K, 100 * K, 1000 * K };// , 10000 * K
+                                                       // };
 
     Random r = new Random(732); // fixed seed = repeatable test
     int counter = 0; // to ensure a distinct description for each feature
 
-    System.out.println("Scale\titeration\tmicrosecs");
+    // System.out.println("Scale\titeration\tmicrosecs");
     
     for (int scale : scales)
     {
       /*
        * add 'scale' features to the store
        */
+      long ntimeLoad = System.nanoTime();
       for (int i = 0; i < scale; i++)
       {
-        SimpleFeature sf = makeFeature(seqlen, r, counter);
+        SimpleFeature sf;
+        sf = makeFeature(seqlen, r, counter);
         counter++;
         store.add(sf);
       }
+      if (!isNCList)
+      {
+        ((intervalstore.nonc.IntervalStore) store).revalidate();
+      }
+      String line = "time to load " + (isNCList ? "NClist " : "NCArray ")
+              + (System.nanoTime() - ntimeLoad) / K / K + " ms scale "
+              + scale;
+      // System.out.println(line);
+      sb.append(line);
 
       /*
        * do "add then query" and log the time taken for the query
@@ -640,20 +684,32 @@ public class IntervalStoreTest
       long total = 0L;
       for (int i = 0; i < repeats + warmups; i++)
       {
-        SimpleFeature sf = makeFeature(seqlen, r, counter);
-        store.add(sf);
+        SimpleFeature sf;
+        if (addstart == 0)
+        {
+          sf = makeFeature(seqlen, r, counter++);
+        }
+        else
+        {
+          sf = new SimpleFeature(addstart, addend, "desc" + counter++);
+        }
+        System.gc();
         long t1 = System.nanoTime();
-        store.findOverlaps(10, 20);
+        store.add(sf);
+        store.findOverlaps(start, end);
         long elapsed = System.nanoTime() - t1;
         if (i >= warmups)
         {
           total += elapsed;
-          System.out.println(
-                  String.format("%d\t%d\t%d", scale, i - warmups,
-                          elapsed / K));
+          // System.out.println(
+          // String.format("%d\t%d\t%d", scale, i - warmups,
+          // elapsed / K));
         }
       }
-      System.out.println("average " + (total / (K * repeats)));
+      sb.append(
+              " add+query "
+                      + (isNCList ? "NCList " : "NCArray ")
+                      + (total / (K * repeats)) + " microseconds\n");
     }
   }