Merge remote-tracking branch 'origin/task/JAL-2662' into develop

Conflicts:
	benchmarking/README

diff --combined benchmarking/README
index fac0bf6,4011e5a..ccf53c1
--- 1/benchmarking/README
--- 2/benchmarking/README
+++ b/benchmarking/README
@@@ -1,27 -1,40 +1,40 @@@
  To set up benchmarking:
  
 +You will need to install Maven: https://maven.apache.org/install.html
  
 -1. In the jalview directory run 
 +1. Run the makedist target of build.xml in Eclipse, or 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.
 +2. Make a lib directory in benchmarking/ if not already present and cd into this directory.
  
+ 
 -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
 +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.
  
+ 
 -4. Build and run jmh benchmarking. In the benchmarking directory:
 -      mvn clean install
 -      java -jar target/benchmarks.jar
 +5. 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
 +  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/
 -  JSON files can be visualised using the viewer at http://jmh.morethan.io/
++  JSON output can be viewed quickly by drag-dropping on 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.
 -  
++ 6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again.