BEAST2 and Intellij

BEAST2.4.0 and Intellij

Updated from what I wrote in Jun 2015. The following is what I did on 2016-02-24. Intellij 15.0.2. BEAST 2.4.0.

Download BEAST2 source

I downloaded zip from https://github.com/CompEvol/beast2 and unpacked as beast2p4p0.

New STACEY version

(This is my primitive branching procedure. Next time, perhaps, I'll understand git.)

Copied files from directory for old STACEY version. Copy called STACEY240
I left src directory unchanged.
I left Package directory mainly unchanged, but:
- I deleted stacey.src.jar, lib\stacey.jar
- I updated version.xml
I deleted Git and Intellij files:

Directory out
Directory .git
Directory .idea
File STACEYDevMyBeastOpUnions.iml

I deleted some other files to tidy up. Experimental code, Findbugs settings, etc

Make BEAST2 in Intellij

Close any projects. Choose "Import project".
Select folder beast2p4p0.
Leave "Create project from existing sources" ticked, Next.
Accept name, location, Next.
Accept source folders, Next.
Accept libraries, Next.
Accept module structure, Next.
Choose JDK 1.8, Next. Finish.
Project Structure. set Project language level to 8.
Menu - Build - Make project. 2 warnings.

I suspect the above is not necessary, but maybe best to make sure this works first. I can't seem to persuade Intellij I want language level 8 as default.

Set up project for new STACEY version

Close BEAST2 project. Create New Java Project. Name it STACEY240, to match directory exactly.
File - New... - Module from existing sources. Choose beast2p4p0. Reuse .iml.
Project Structure. Select Modules, STACEY240, dependencies tab. Make STACEY240 depend on beast2p3p0. (Click on green +.)
Build.
Project Structure. Artifacts. Make empty jar, name it stacey. Choose STACEY240 compile output. Double click to add it. Output directory = STACEY240\Package\lib. Build on make = true.
Project Structure. Artifacts. Make empty jar, name it stacey.src. Green arrow below Output Layout, add directory content, choose ...\STACEY240\src. Build on make = true. Output directory = STACEY240\Package.

If the artifacts are not empty jars, I can't change the names from automatically supplied and wrong ones.

Intellij errors when compiling STACEY 1.1.1 against BEAST 2.4.0pre

Error:(121, 17) java: cannot find symbol
Information:Using javac 1.8.0_66 to compile java sources
Information:java: Errors occurred while compiling module 'STACEY240'
Information:Modules "STACEY240", "beast2p4p0" were fully rebuilt due to project configuration/dependencies changes
Information:24/02/2016 08:39 - Compilation completed with 8 errors and 2 warnings in 13s 202ms
C:\Users\Work\AAA\Programming\biology\beast2p4p0\src\beast\evolution\tree\TraitSet.java
Warning:(187, 49) java: parse(java.lang.String) in java.util.Date has been deprecated
C:\Users\Work\AAA\Programming\biology\beast2p4p0\src\beast\app\beauti\TipDatesInputEditor.java
Warning:(465, 33) java: parse(java.lang.String) in java.util.Date has been deprecated
C:\Users\Work\AAA\Programming\biology\beast2p4p0\src\beast\evolution\operators\DeltaExchangeOperator.java
Information:java: C:\Users\Work\AAA\Programming\biology\beast2p4p0\src\beast\evolution\operators\DeltaExchangeOperator.java uses unchecked or unsafe operations.
Information:java: Recompile with -Xlint:unchecked for details.

BEAST.

C:\Users\Work\AAA\Programming\biology\STACEY240\src\stacey\PopSampleStatistic.java
Error:(60, 17) java: init(java.io.PrintStream) in stacey.PopSampleStatistic cannot implement init(java.io.PrintStream) in beast.core.Loggable
  overridden method does not throw java.lang.Exception

Removed throw.

C:\Users\Work\AAA\Programming\biology\STACEY240\src\stacey\PIOMSCoalescentDistribution.java
Error:(188, 17) java: initAndValidate() in stacey.PIOMSCoalescentDistribution cannot implement initAndValidate() in beast.core.BEASTInterface
  overridden method does not throw java.lang.Exception

Removed throw.

C:\Users\Work\AAA\Programming\biology\STACEY240\src\stacey\BirthDeathCollapseModel.java
Error:(76, 17) java: initAndValidate() in stacey.BirthDeathCollapseModel cannot implement initAndValidate() in beast.core.BEASTInterface
  overridden method does not throw java.lang.Exception

Removed throw.

C:\Users\Work\AAA\Programming\biology\STACEY240\src\stacey\GtreeAndCoalFactorInputEditor.java
Error:(51, 9) java: cannot find symbol
  symbol:   variable m_plugin
  location: class stacey.GtreeAndCoalFactorInputEditor
Error:(76, 17) java: cannot find symbol
  symbol: variable m_plugin
Error:(120, 42) java: cannot find symbol
  symbol:   variable m_plugin
  location: class stacey.GtreeAndCoalFactorInputEditor
Error:(121, 17) java: cannot find symbol
  symbol:   variable m_plugin
  location: class stacey.GtreeAndCoalFactorInputEditor

m_input -> m_beastObject

C:\Users\Work\AAA\Programming\biology\STACEY240\src\stacey\BirthDeathCollapseNClustersStatistic.java
Error:(58, 17) java: init(java.io.PrintStream) in stacey.BirthDeathCollapseNClustersStatistic cannot implement init(java.io.PrintStream) in beast.core.Loggable
  overridden method does not throw java.lang.Exception

Removed throw.