SimulationFile Member List

This is the complete list of members for SimulationFile, including all inherited members.

appendDsToGroup(H5MetaData *header, byte *data)	SimulationFile	protected
appendLattice(unsigned int replicate, lm::io::Lattice *lattice, byte *latticeData, size_t latticeDataSize)	SimulationFile	virtual
appendLattice_U32LE(unsigned int replicate, lm::io::Lattice *lattice, uint32_t *latticeData, size_t latticeDataSize)	SimulationFile	virtual
appendParameterValues(unsigned int replicate, lm::io::ParameterValues *parameterValues)	SimulationFile	virtual
appendSites(unsigned int replicate, lm::io::Lattice *lattice, uint8_t *siteData, size_t siteDataSize)	SimulationFile	virtual
appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts *speciesCounts)	SimulationFile	virtual
appendToDataset(H5MetaData *header, byte *data)	SimulationFile	protected
arbitraryH5(byte *ptr)	SimulationFile	virtual
arbitraryH5Lookup(byte *in, byte *&out, size_t &out_sz)	SimulationFile	virtual
checkpoint()	SimulationFile	virtual
close()	SimulationFile	virtual
closeAllReplicates()	SimulationFile	virtual
closeReplicate(unsigned int replicate)	SimulationFile	virtual
closeReplicateHandles(ReplicateHandles *handles)	SimulationFile	protectedvirtual
create(const string filename)	SimulationFile	static
create(const char *filename)	SimulationFile	static
create(const string filename, unsigned int numberSpecies)	SimulationFile	static
create(const char *filename, unsigned int numberSpecies)	SimulationFile	static
create(const char *filename, bool initializeModel, unsigned int numberSpecies=0)	SimulationFile	static
createReplicateHandles(string replicateString)	SimulationFile	protectedvirtual
CURRENT_VERSION	SimulationFile	static
file	SimulationFile	protected
filename	SimulationFile	protected
flush()	SimulationFile	virtual
getDiffusionModel(lm::io::DiffusionModel *diffusionModel)	SimulationFile	virtual
getDiffusionModelLattice(lm::io::DiffusionModel *diffusionModel, byte *lattice, size_t latticeMaxSize, byte *latticeSites, size_t latticeSitesMaxSize)	SimulationFile	virtual
getDiffusionModelLattice(lm::io::DiffusionModel *diffusionModel, lm::rdme::Lattice *lattice)	SimulationFile	virtual
getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice *lattice)	SimulationFile	virtual
getLatticeTimes(unsigned int replicate)	SimulationFile	virtual
getParameter(string key, string defaultValue="")	SimulationFile	virtual
getParameters()	SimulationFile	virtual
getParticleCounts(unsigned int replicate, unsigned int latticeIndex)	SimulationFile
getReactionModel(lm::io::ReactionModel *reactionModel)	SimulationFile	virtual
getSiteTypeNames()	SimulationFile
getSpatialModel(lm::io::SpatialModel *model)	SimulationFile	virtual
getSpeciesCounts(unsigned int replicate)	SimulationFile
getSpeciesCountTimes(unsigned int replicate)	SimulationFile
getSpeciesNames()	SimulationFile
isValidFile(const string filename)	SimulationFile	static
isValidFile(const char *filename)	SimulationFile	static
loadModel()	SimulationFile	protectedvirtual
loadParameters()	SimulationFile	protectedvirtual
makeNewDataset(H5MetaData *header, byte *data)	SimulationFile	protected
MAX_REACTION_RATE_CONSTANTS	SimulationFile	static
MAX_SHAPE_PARAMETERS	SimulationFile	static
MIN_VERSION	SimulationFile	static
modelGroup	SimulationFile	protected
modelLoaded	SimulationFile	protected
numberSpecies	SimulationFile	protected
open()	SimulationFile	protectedvirtual
openGroups()	SimulationFile	protectedvirtual
openReplicate(unsigned int replicate)	SimulationFile	virtual
openReplicateHandles(unsigned int replicate)	SimulationFile	protectedvirtual
openReplicates	SimulationFile	protected
parameterMap	SimulationFile	protected
parametersGroup	SimulationFile	protected
parseParameter(hid_t location_id, const char *attr_name, const H5A_info_t *ainfo, void *op_data)	SimulationFile	protectedstatic
readAttr(H5Lookup *req, byte *&data, size_t &sz)	SimulationFile	protected
readDataset(H5Lookup *req, byte *&data, size_t &sz)	SimulationFile	protected
replicateExists(unsigned int replicate)	SimulationFile	virtual
setDiffusionModel(lm::io::DiffusionModel *diffusionModel)	SimulationFile	virtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, uint8_t *lattice, uint8_t *latticeSites)	SimulationFile	virtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, uint32_t *lattice, uint8_t *latticeSites)	SimulationFile	virtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, lm::rdme::ByteLattice *lattice)	SimulationFile	virtual
setDiffusionModelLattice(lm::io::DiffusionModel *m, lm::rdme::IntLattice *lattice)	SimulationFile	virtual
setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes *speciesCounts)	SimulationFile	virtual
setParameter(string key, string value)	SimulationFile	virtual
setReactionModel(lm::io::ReactionModel *reactionModel)	SimulationFile	virtual
setSpatialModel(lm::io::SpatialModel *model)	SimulationFile	virtual
SimulationFile(const string filename)	SimulationFile
SimulationFile(const char *filename)	SimulationFile
simulationsGroup	SimulationFile	protected
version	SimulationFile	protected
write3DLattice_U8LE(const char *path, uint8_t *data, unsigned int x, unsigned int y, unsigned int z)	SimulationFile	protected
writeParticleLattice_U32LE(hid_t handle, const char *path, unsigned int *data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)	SimulationFile	protected
writeParticleLattice_U8LE(const char *path, uint8_t *data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)	SimulationFile	protected
~SimulationFile()	SimulationFile	virtual