--- /dev/null
+<!--
+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.
+-->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.jalview</groupId>
+ <artifactId>benchmarking</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <packaging>jar</packaging>
+
+ <name>JMH benchmark sample: Java</name>
+
+ <!--
+ This is the demo/sample template build script for building Java benchmarks with JMH.
+ Edit as needed.
+ -->
+
+ <repositories>
+ <repository>
+ <id>lib</id>
+ <url>file://${project.basedir}/lib</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.openjdk.jmh</groupId>
+ <artifactId>jmh-core</artifactId>
+ <version>${jmh.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.openjdk.jmh</groupId>
+ <artifactId>jmh-generator-annprocess</artifactId>
+ <version>${jmh.version}</version>
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>jalview.org</groupId>
+ <artifactId>jalview</artifactId>
+ <version>1.0</version>
+ </dependency>
+ </dependencies>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+
+ <!--
+ JMH version to use with this project.
+ -->
+ <jmh.version>1.19</jmh.version>
+
+ <!--
+ Java source/target to use for compilation.
+ -->
+ <javac.target>1.8</javac.target>
+
+ <!--
+ Name of the benchmark Uber-JAR to generate.
+ -->
+ <uberjar.name>benchmarks</uberjar.name>
+ </properties>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>3.1</version>
+ <configuration>
+ <compilerVersion>${javac.target}</compilerVersion>
+ <source>${javac.target}</source>
+ <target>${javac.target}</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.2</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ <configuration>
+ <finalName>${uberjar.name}</finalName>
+ <transformers>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <mainClass>org.openjdk.jmh.Main</mainClass>
+ </transformer>
+ </transformers>
+ <filters>
+ <filter>
+ <!--
+ Shading signed JARs will fail without this.
+ http://stackoverflow.com/questions/999489/invalid-signature-file-when-attempting-to-run-a-jar
+ -->
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ <pluginManagement>
+ <plugins>
+ <plugin>
+ <artifactId>maven-clean-plugin</artifactId>
+ <version>2.5</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-deploy-plugin</artifactId>
+ <version>2.8.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-install-plugin</artifactId>
+ <version>2.5.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.4</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.9.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.6</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-site-plugin</artifactId>
+ <version>3.3</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>2.2.1</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.17</version>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+
+</project>
--- /dev/null
+/*
+ * 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.Setup;
+import org.openjdk.jmh.annotations.State;
+import org.openjdk.jmh.annotations.TearDown;
+import org.openjdk.jmh.annotations.Scope;
+import java.util.Random;
+
+import jalview.datamodel.HiddenColumns;
+
+/*
+ * A class to benchmark hidden columns performance
+ */
+public class HiddenColumnsBenchmark
+{
+ @State(Scope.Thread)
+ public static class ThreadState
+ {
+ HiddenColumns h = new HiddenColumns();
+ int MAXCOLS = 100000;
+ Random rand = new Random();
+
+ @Setup
+ public void setup()
+ {
+ rand.setSeed(1234);
+ for (int i=0; i<MAXCOLS; ++i)
+ {
+ int col = rand.nextInt(MAXCOLS);
+ h.hideColumns(col, col+1);
+ }
+ }
+
+ @TearDown
+ public void tearDown()
+ {
+
+ }
+ }
+
+ /*
+ * isVisible benchmarking
+ */
+ @Benchmark
+ public boolean benchIsVisibleLastCol(ThreadState tstate)
+ {
+ return tstate.h.isVisible(tstate.MAXCOLS - 3);
+ }
+
+ @Benchmark
+ public boolean benchIsVisibleFirstCol(ThreadState tstate)
+ {
+ return tstate.h.isVisible(1);
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff