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Addition of molecule-tracking for reaction in nearest neighbours, which also meant re-writing

a bit of the existing code to make it all look the same.
Worked on the compile time conditionals and fixed warningless compiles on OSX

davidfange 2015-05-18

Browse code at this revision

Parent: [r711]

Child: [r713]

changed /branches/MesoRD_MoleculeTracking/CMakeLists.txt
changed /branches/MesoRD_MoleculeTracking/config.h.in
changed /branches/MesoRD_MoleculeTracking/src/Compartment.cpp
changed /branches/MesoRD_MoleculeTracking/src/CompartmentTable.cpp
changed /branches/MesoRD_MoleculeTracking/src/CubicSubvolume.cpp
changed /branches/MesoRD_MoleculeTracking/src/CubicSubvolume.hpp
changed /branches/MesoRD_MoleculeTracking/src/CuboidSubvolume.cpp
changed /branches/MesoRD_MoleculeTracking/src/CuboidSubvolume.hpp
changed /branches/MesoRD_MoleculeTracking/src/Molecule.cpp
changed /branches/MesoRD_MoleculeTracking/src/Molecule.hpp
changed /branches/MesoRD_MoleculeTracking/src/OctahedricSubvolume.cpp
changed /branches/MesoRD_MoleculeTracking/src/OctahedricSubvolume.hpp
changed /branches/MesoRD_MoleculeTracking/src/ReactionTable.hpp
changed /branches/MesoRD_MoleculeTracking/src/Species.cpp
changed /branches/MesoRD_MoleculeTracking/src/Species.hpp
changed /branches/MesoRD_MoleculeTracking/src/SpeciesTable.cpp
changed /branches/MesoRD_MoleculeTracking/src/SpeciesTable.hpp
changed /branches/MesoRD_MoleculeTracking/src/Subvolume.cpp
changed /branches/MesoRD_MoleculeTracking/src/Subvolume.hpp
changed /branches/MesoRD_MoleculeTracking/src/System.cpp
changed /branches/MesoRD_MoleculeTracking/src/System.hpp
changed /branches/MesoRD_MoleculeTracking/src/reaction/ReactionNode.cpp
changed /branches/MesoRD_MoleculeTracking/src/test/molecule_tracking.xml
changed /branches/MesoRD_MoleculeTracking/src/ui/GetOpt.hpp
changed /branches/MesoRD_MoleculeTracking/src/ui/TextGetOpt.cpp
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/branches/MesoRD_MoleculeTracking/src/Compartment.cpp Diff Switch to side-by-side view
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/branches/MesoRD_MoleculeTracking/src/CubicSubvolume.cpp Diff Switch to side-by-side view
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/branches/MesoRD_MoleculeTracking/src/CuboidSubvolume.cpp Diff Switch to side-by-side view
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/branches/MesoRD_MoleculeTracking/src/Molecule.cpp Diff Switch to side-by-side view
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/branches/MesoRD_MoleculeTracking/src/OctahedricSubvolume.cpp Diff Switch to side-by-side view
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