[jayes] inference benchmark

Change-Id: I59d8e0083512aed36b37b892d1f8bd3c7dfbe185
[jayes] evaluation: evaluation application

Change-Id: Ifb88a0a7fd28e0ec88ca25af68e45cc62ca57e58
[jayes] remove JunctionTreeBuilder.optimizeStructure

benchmarking says that this "optimization" does not help
the runtime (and only adds memory overhead) => remove it

Change-Id: I41fa412ea7f0c3cfdbe7affccfcc874689b89579
Merge "[jayes] evaluation: evaluation application"
[jayes] refactoring

- replace some jayes.utils usage and move classes that are
  not used by other projects and are not public API to
  an internal package
- moved arraywrapper package from *.utils to *.factor

Change-Id: Iee187c80ceb747985ce4bc044dbb7b9ed651f87f
[jayes] evaluation: diagram generation

added plugin.xml as additional wiring

Change-Id: I552570c7313a8bd8eaa747092d4a96f6b2527c29
[jayes] purge references to BayesNet from JunctionTreeAlgorithm
[jayes] add benchmark for stability

this is still very slow, but shows how Jayes will behave with many
nodes / low probabilities

Change-Id: Ide3928e3a6545091be8efe4d2121f846b1c615e8
[jayes] evaluation: product definition for console usage
Merge "[jayes] add benchmark for stability"
[jayes] inference benchmark using model transformation
[jayes] add .checkstyle and *.orig to .gitignore
[jayes] replace logThreshold by binary option

as i have never been able to show that this log threshold heuristic is
really any good, replace the option for now with a binary option (log
scale / not log scale). I kept the ability for JunctionTreeAlgorithm to
handle mixed normal / log scale factors for now, though.
[jayes] move triangulation logic out of JunctionTreeBuilder

this allows to transparently plug in more efficient elimination order
heuristics in the future

Change-Id: Ia4ad6c158d5f2cfb8d24930b3c3a53db85d8c91a
Merge "[jayes] move triangulation logic out of JunctionTreeBuilder"
Merge "[jayes] inference benchmark using model transformation"