Introduces the PathwayMonitor, an abstraction which refactor the reaction recursion depth monitor, and fixes bugs for the monitors.
Adds PathwayMonitor and test.
Adds the layout file namer.
Adds pathway classes.
Changes in exec and new classes to accommodate use of pathways for layouts.
Merge branch 'release/1.0.4' into develop
Merge branch 'feature/pathwayBasedLay' into develop
Moves to 1.0.4-SNAPSHOTS, the first one with pathway support for PAMELA.
Refactors into modules, moves provisionally to 1.0.4.5-SNAPSHOT. Nearly there (just one glitch to solve regarding property files).
Fixes to have first version of refactored modules compiling.
Fixes issue with renderer SBW test.
Moves application properties to RheaDB
Adds a RheaConnectionManager to re-use connections. Minor refactoring in Rhea exec and RxnListRetriever.
Adds notice that no reaction/pathway was found. Modifies the MultiQueryPipeline to accommodate for the generation of pathways for the MTBL reference layer.
Merge branch 'feature/modules' into develop
Moves to 1.0.5
Merge branch 'release/1.0.5'