From cc56c66bb10c1d3cf714ca1c02abb24aa0f6c43d Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 5 Feb 2018 09:52:38 +0000
Subject: [PATCH] JAL-2778 Sequence width benchmark

---
 .../main/java/org/jalview/SeqWidthBenchmark.java   |   96 ++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java

diff --git a/benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java b/benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java
new file mode 100644
index 0000000..a92d4f0
--- /dev/null
+++ b/benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java
@@ -0,0 +1,96 @@
+/*
+ * 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.jalview.HiddenColumnsBenchmark.HiddenColsAndStartState;
+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.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.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+/*
+ * 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 SeqWidthBenchmark {
+
+	/*
+	 * State with multiple hidden columns and a start position set
+	 */
+	@State(Scope.Thread)
+	public static class AlignmentState
+	{
+		@Param({"100", "1000", "10000", "100000"})
+		public int numSeqs;
+		
+		Random rand = new Random();
+		
+		AlignmentI al;
+		
+		@Setup
+		public void setup()
+		{
+			rand.setSeed(1234);
+			
+			SequenceI[] seqs = new Sequence[numSeqs];
+		    for (int i = 0; i < numSeqs; i++)
+		    {
+		      int count = rand.nextInt(10000); 
+		      StringBuilder aas = new StringBuilder();
+		      for (int j=0; j<count; j++)
+		      {
+		    	 aas.append("a");
+		      }
+
+		      seqs[i] = new Sequence("Sequence" + i, aas.toString());
+		    }
+			al = new Alignment(seqs);
+		}
+	}
+	
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchSeqGetWidth(AlignmentState tstate)
+	{
+		return tstate.al.getWidth();
+	}
+	
+}
-- 
1.7.10.2