From 321dc2877e7da49e61364180a84f353e67982578 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 20 Sep 2017 11:28:01 +0100
Subject: [PATCH] JAL-2662 Adjustments to hidden columns benchmark

---
 .../java/org/jalview/HiddenColumnsBenchmark.java   |  142 ++++++++++++++++----
 1 file changed, 118 insertions(+), 24 deletions(-)

diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
index 2518494..eb35e3b 100644
--- a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
+++ b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
@@ -22,57 +22,151 @@
 package org.jalview;
 
 import org.openjdk.jmh.annotations.Benchmark;
+import org.openjdk.jmh.annotations.BenchmarkMode;
+import org.openjdk.jmh.annotations.Fork;
+import org.openjdk.jmh.annotations.Measurement;
+import org.openjdk.jmh.annotations.Mode;
 import org.openjdk.jmh.annotations.Setup;
 import org.openjdk.jmh.annotations.State;
-import org.openjdk.jmh.annotations.TearDown;
+import org.openjdk.jmh.annotations.Warmup;
 import org.openjdk.jmh.annotations.Scope;
+import org.openjdk.jmh.annotations.Param;
+
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Random;
+import java.util.concurrent.TimeUnit;
 
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 
 /*
  * A class to benchmark hidden columns performance
  */
+@Warmup(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Fork(1)
 public class HiddenColumnsBenchmark 
-{
+{	
+	/*
+	 * State with multiple hidden columns and a start position set
+	 */
 	@State(Scope.Thread)
-	public static class ThreadState
+	public static class HiddenColsAndStartState
 	{
+		@Param({"300", "10000", "100000"})
+		public int maxcols;
+		
+		@Param({"1", "50", "90"})
+		public int startpcnt; // position as percentage of maxcols
+		
+		@Param({"1","15","100"})
+		public int hide;
+		
 		HiddenColumns h = new HiddenColumns();
-		int MAXCOLS = 100000;
 		Random rand = new Random();
+		
+		public int hiddenColumn;
+		public int visibleColumn;
 	
 		@Setup
 		public void setup()
 		{
 			rand.setSeed(1234);
-	    	for (int i=0; i<MAXCOLS; ++i)
+			int lastcol = 0;
+	    	while (lastcol < maxcols)
 	    	{
-	    		int col = rand.nextInt(MAXCOLS); 
-	    		h.hideColumns(col, col+1);
+	    		int count = rand.nextInt(100); 
+	    		lastcol += count;
+	    		h.hideColumns(lastcol, lastcol+hide);
+	    		lastcol+=hide;
 	    	}
+	    	
+	    	// make sure column at start is hidden
+	    	hiddenColumn = (int)(maxcols * startpcnt/100.0);
+	    	h.hideColumns(hiddenColumn, hiddenColumn);
+	    	
+	    	// and column <hide> after start is visible
+	    	ColumnSelection sel = new ColumnSelection();
+	    	h.revealHiddenColumns(hiddenColumn+hide, sel);
+	    	visibleColumn = hiddenColumn+hide;
+	    	
+	    	System.out.println("Maxcols: " + maxcols + " HiddenCol: " + hiddenColumn + " Hide: " + hide);
+	    	System.out.println("Number of hidden columns: " + h.getSize());
 		}
+	}
 	
-		@TearDown
-		public void tearDown()
-		{
-			
-		}
+	/* Convention: functions in alphabetical order */
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.findColumnPosition(tstate.visibleColumn);
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public List<Integer> benchFindHiddenRegionPositions(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.findHiddenRegionPositions();
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public ArrayList<int[]> benchGetHiddenColumnsCopy(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.getHiddenColumnsCopy();
+	}
+	
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public int benchGetSize(HiddenColsAndStartState tstate)
+    {
+		return tstate.h.getSize();
+    }
+
+   @Benchmark
+    @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchHideCols(HiddenColsAndStartState tstate) 
+    {
+    	tstate.h.hideColumns(tstate.visibleColumn,
+    			tstate.visibleColumn+2000); 
+    	return tstate.h;
+    }
+   
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public boolean benchIsVisible(HiddenColsAndStartState tstate) 
+    {
+    	return tstate.h.isVisible(tstate.hiddenColumn); 
     }
 	
-	/*
-	 * isVisible benchmarking
-	 */
-    @Benchmark
-    public boolean benchIsVisibleLastCol(ThreadState tstate) 
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchReveal(HiddenColsAndStartState tstate) 
     {
-    	return tstate.h.isVisible(tstate.MAXCOLS - 3); 
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+    	return tstate.h;
     }
-    
-    @Benchmark
-    public boolean benchIsVisibleFirstCol(ThreadState tstate)
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate) 
     {
-    	return tstate.h.isVisible(1);
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealAllHiddenColumns(sel);
+    	return tstate.h;
     }
-
-}
+	
+	
+}
\ No newline at end of file
-- 
1.7.10.2