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. Purge any previous maven dependencies:
   mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false

4. 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.

5. Build and run jmh benchmarking. In the benchmarking directory:
  mvn clean install
  java -jar target/benchmarks.jar
  
  To get JSON output instead use:
  java -jar target/benchmarks.jar -rf json
  
  JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/