X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=benchmarking%2Fsrc%2Fmain%2Fjava%2Forg%2Fjalview%2FHiddenColumnsBenchmark.java;h=ae2d628125af331c402e2a495a76d50052c56bf2;hb=4d3cf3e91660d6b1c5bcdee4bef34c2747ac7023;hp=ffeb6131a4648049d671af336c77a859b4667abd;hpb=26f91aeb379024f7b3585bda7ee587e1b57af6b3;p=jalview.git

diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
index ffeb613..ae2d628 100644
--- a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
+++ b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
@@ -1,83 +1,157 @@
 /*
- * Copyright (c) 2014, Oracle America, Inc.
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- *  * Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
- *
- *  * Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the distribution.
- *
- *  * Neither the name of Oracle nor the names of its contributors may be used
- *    to endorse or promote products derived from this software without
- *    specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- * THE POSSIBILITY OF SUCH DAMAGE.
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 
 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
-    public boolean benchIsVisibleLastCol(ThreadState tstate) 
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.findColumnPosition(tstate.visibleColumn);
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public int benchGetSize(HiddenColsAndStartState tstate)
     {
-    	return tstate.h.isVisible(tstate.MAXCOLS - 3); 
+		return tstate.h.getSize();
     }
-    
-    @Benchmark
-    public boolean benchIsVisibleFirstCol(ThreadState tstate)
+*/
+   @Benchmark
+    @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchHideCols(HiddenColsAndStartState tstate) 
     {
-    	return tstate.h.isVisible(1);
+    	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); 
+    }
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchReveal(HiddenColsAndStartState tstate) 
+    {
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+    	return tstate.h;
+    }
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate) 
+    {
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealAllHiddenColumns(sel);
+    	return tstate.h;
+    }
+	*/
+	
+}
\ No newline at end of file