To set up benchmarking:


1. In the jalview directory run 
  ant makedist

This builds a jalview.jar file and puts it into dist/


2. Make a lib directory in benchmarking/ if not already present.


3. In the benchmarking directory run:
  	mvn install:install-file -Dfile=../dist/jalview.jar -DgroupId=jalview.org -DartifactId=jalview -Dversion=1.0 -Dpackaging=jar -DlocalRepositoryPath=lib

to install the jalview.jar file in the local maven repository. The pom.xml in the benchmarking references this installation, so if you change the names the pom.xml file will also need to be updated.


4. Build and run jmh benchmarking. In the benchmarking directory:
  	mvn clean install
  	java -jar target/benchmarks.jar
  
  To get output as a json file use instead:
  	java -jar target/benchmarks.jar -rf json
  
  JSON files can be visualised using the viewer at http://jmh.morethan.io/
  
  To get help use the standard -h option:
  	java -jar target/benchmarks.jar -h
  	
  More information here:
  	http://openjdk.java.net/projects/code-tools/jmh/
  	http://java-performance.info/jmh/
  
  
 5. If you make changes to the jalview code everything will need to be refreshed, by calling:
  	mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false
  
  followed by steps 3 and 4 again.