From 26f91aeb379024f7b3585bda7ee587e1b57af6b3 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 11 Aug 2017 14:41:40 +0100
Subject: [PATCH] JAL-2662 First attempt to set up JMH hidden columns
 benchmark

---
 benchmarking/.classpath                            |   28 ++++
 benchmarking/.gitignore                            |    1 +
 .../.settings/org.eclipse.core.resources.prefs     |    3 +
 benchmarking/.settings/org.eclipse.jdt.core.prefs  |    5 +
 benchmarking/.settings/org.eclipse.m2e.core.prefs  |    4 +
 benchmarking/pom.xml                               |  171 ++++++++++++++++++++
 .../java/org/jalview/HiddenColumnsBenchmark.java   |   83 ++++++++++
 7 files changed, 295 insertions(+)
 create mode 100644 benchmarking/.classpath
 create mode 100644 benchmarking/.gitignore
 create mode 100644 benchmarking/.settings/org.eclipse.core.resources.prefs
 create mode 100644 benchmarking/.settings/org.eclipse.jdt.core.prefs
 create mode 100644 benchmarking/.settings/org.eclipse.m2e.core.prefs
 create mode 100644 benchmarking/pom.xml
 create mode 100644 benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java

diff --git a/benchmarking/.classpath b/benchmarking/.classpath
new file mode 100644
index 0000000..131ff24
--- /dev/null
+++ b/benchmarking/.classpath
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry combineaccessrules="false" kind="src" path="/Jalview Release 2.7"/>
+	<classpathentry kind="lib" path="/Jalview Release 2.7/jalviewApplet.jar"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/benchmarking/.gitignore b/benchmarking/.gitignore
new file mode 100644
index 0000000..b83d222
--- /dev/null
+++ b/benchmarking/.gitignore
@@ -0,0 +1 @@
+/target/
diff --git a/benchmarking/.settings/org.eclipse.core.resources.prefs b/benchmarking/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000..e9441bb
--- /dev/null
+++ b/benchmarking/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,3 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding/<project>=UTF-8
diff --git a/benchmarking/.settings/org.eclipse.jdt.core.prefs b/benchmarking/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000..714351a
--- /dev/null
+++ b/benchmarking/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8
diff --git a/benchmarking/.settings/org.eclipse.m2e.core.prefs b/benchmarking/.settings/org.eclipse.m2e.core.prefs
new file mode 100644
index 0000000..f897a7f
--- /dev/null
+++ b/benchmarking/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
diff --git a/benchmarking/pom.xml b/benchmarking/pom.xml
new file mode 100644
index 0000000..5ca96f6
--- /dev/null
+++ b/benchmarking/pom.xml
@@ -0,0 +1,171 @@
+<!--
+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.
+    -->
+
+    <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>
+    </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>
diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
new file mode 100644
index 0000000..ffeb613
--- /dev/null
+++ b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
@@ -0,0 +1,83 @@
+/*
+ * 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.
+ */
+
+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;
+
+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()
+		{
+			
+		}
+    }
+	
+	
+    @Benchmark
+    public boolean benchIsVisibleLastCol(ThreadState tstate) 
+    {
+    	return tstate.h.isVisible(tstate.MAXCOLS - 3); 
+    }
+    
+    @Benchmark
+    public boolean benchIsVisibleFirstCol(ThreadState tstate)
+    {
+    	return tstate.h.isVisible(1);
+    }
+
+}
-- 
1.7.10.2