From: kiramt Date: Mon, 5 Feb 2018 09:52:38 +0000 (+0000) Subject: JAL-2778 Sequence width benchmark X-Git-Tag: Release_2_10_4~67^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc56c66bb10c1d3cf714ca1c02abb24aa0f6c43d;p=jalview.git JAL-2778 Sequence width benchmark --- 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 . + * 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