/*
* 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 .
* 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