Index

A

AdhesionDisplacements (C++ class) AdhesionDisplacements::AdhesionDisplacements (C++ function), [1] AdhesionDisplacements::annihilated (C++ member) AdhesionDisplacements::source (C++ member) AdhesionDisplacements::target (C++ member) AdhesionIndex (C++ class) AdhesionIndex::get_adhesions (C++ function) AdhesionIndex::get_cell_ecm_interactions (C++ function) AdhesionIndex::move_adhesions (C++ function)

AdhesionIndex::rebuild (C++ function) AdhesionIndex::remove_adhesions (C++ function) AdhesionIndex::reset_cell_ecm_interactions (C++ function) AdhesionMover (C++ class) AdhesionMover::AdhesionMover (C++ function) AdhesionMover::commit_move (C++ function) AdhesionMover::get_cell_ecm_interactions (C++ function) AdhesionMover::move_dh (C++ function) AdhesionMover::reset_cell_ecm_interactions (C++ function) AdhesionMover::update (C++ function)

C

Cell (C++ class) Cell::AddToGrad (C++ function) Cell::AliveP (C++ function) Cell::Apoptose (C++ function) Cell::Area (C++ function) Cell::Cell (C++ function), [1] Cell::CellBirth (C++ function) Cell::ClearGrad (C++ function) Cell::ClearJ (C++ function) Cell::Colour (C++ function) Cell::ColourOfBirth (C++ function) Cell::DateOfBirth (C++ function) Cell::Daughter (C++ function) Cell::DecrementAdhesiveArea (C++ function) Cell::DecrementTargetArea (C++ function) Cell::GetGrad (C++ function) Cell::GetJ (C++ function) Cell::getTau (C++ function) Cell::GradX (C++ function) Cell::GradY (C++ function) Cell::IncrementAdhesiveArea (C++ function) Cell::IncrementTargetArea (C++ function) Cell::MaxSigma (C++ function) Cell::MeasureCellSize (C++ function) Cell::Mother (C++ function) Cell::operator= (C++ function) Cell::PrintInertia (C++ function) Cell::SetColour (C++ function) Cell::SetGrad (C++ function) Cell::SetJ (C++ function) Cell::SetTargetArea (C++ function) Cell::SetTargetLength (C++ function) Cell::setTau (C++ function) Cell::Sigma (C++ function) Cell::TargetArea (C++ function) Cell::TimesDivided (C++ function) CellularPotts (C++ class) CellularPotts::Act_AmoebaeMove (C++ function) CellularPotts::AddCell (C++ function) CellularPotts::AllocateMatrix (C++ function) CellularPotts::AllocateSigma (C++ function) CellularPotts::AmoebaeMove (C++ function) CellularPotts::anneal (C++ function) CellularPotts::CellDensity (C++ function) CellularPotts::CellularPotts (C++ function) CellularPotts::Compactness (C++ function)

CellularPotts::ConstructInitCells (C++ function) CellularPotts::DivideCells (C++ function), [1] CellularPotts::DrawConvexHull (C++ function) CellularPotts::FindBoundingBox (C++ function) CellularPotts::FindCellDirections (C++ function) CellularPotts::get_annealed_sigma (C++ function) CellularPotts::GetActLevel (C++ function) CellularPotts::GetCellECMInteractions (C++ function) CellularPotts::GetMatrixLevel (C++ function) CellularPotts::GetNewPerimeterIfXYWereAdded (C++ function) CellularPotts::GetNewPerimeterIfXYWereRemoved (C++ function) CellularPotts::GrowAndDivideCells (C++ function) CellularPotts::GrowInCells (C++ function), [1] CellularPotts::InitialiseEdgeList (C++ function) CellularPotts::IsingMove (C++ function) CellularPotts::KawasakiMove (C++ function) CellularPotts::linePlotPos (C++ function) CellularPotts::Mass (C++ function) CellularPotts::MeanCellArea (C++ function) CellularPotts::MeasureCellPerimeters (C++ function) CellularPotts::MeasureCellSizes (C++ function) CellularPotts::Plot (C++ function) CellularPotts::PlotIsing (C++ function) CellularPotts::plotPos (C++ function) CellularPotts::PlotSigma (C++ function) CellularPotts::PottsMove (C++ function) CellularPotts::PottsNeighbourMove (C++ function) CellularPotts::RandomSigma (C++ function) CellularPotts::RandomSpins (C++ function) CellularPotts::ReadZygotePicture (C++ function) CellularPotts::ResetCellECMInteractions (C++ function) CellularPotts::ResetTargetLengths (C++ function) CellularPotts::SearchNandPlot (C++ function) CellularPotts::SearchNandPlotClear (C++ function) CellularPotts::SearchNeighbours (C++ function) CellularPotts::SearchNeighboursMatrix (C++ function) CellularPotts::SetECMBoundaryState (C++ function) CellularPotts::SetLambdaPerimeter (C++ function) CellularPotts::SetRandomTypes (C++ function) CellularPotts::SetTargetPerimeter (C++ function) CellularPotts::ShowDirections (C++ function) CellularPotts::Sigma (C++ function) CellularPotts::SizeX (C++ function) CellularPotts::SizeY (C++ function) CellularPotts::SquareCell (C++ function) CellularPotts::ThrowInCells (C++ function) CellularPotts::Time (C++ function)

D

Dish (C++ class) Dish::Area (C++ function) Dish::CellGrowthAndDivision (C++ function) Dish::CountCells (C++ function) Dish::Erase (C++ function) Dish::getCell (C++ function)

Dish::Init (C++ function) Dish::Plot (C++ function) Dish::SizeX (C++ function) Dish::SizeY (C++ function) Dish::TargetArea (C++ function) Dish::Time (C++ function)

P

PDE (C++ class) PDE::AbsorbingBoundaries (C++ function) PDE::addtoValue (C++ function) PDE::ContourPlot (C++ function) PDE::cuHorizontalADIstep (C++ function) PDE::cuODEstep (C++ function) PDE::cuPDEsteps (C++ function) PDE::cuVerticalADIstep (C++ function) PDE::DerivativesPDE (C++ function) PDE::Diffuse (C++ function) PDE::ForwardEulerStep (C++ function) PDE::get_PDEvars (C++ function) PDE::GetChemAmount (C++ function) PDE::GradC (C++ function) PDE::InitialiseAgeLayer (C++ function) PDE::InitialiseCuda (C++ function) PDE::InitialiseDiffusionCoefficients (C++ function) PDE::InitialisePDE (C++ function)

PDE::InitialisePDEvars (C++ function) PDE::InitLinearYGradient (C++ function) PDE::Layers (C++ function) PDE::Max (C++ function) PDE::Min (C++ function) PDE::NoFluxBoundaries (C++ function) PDE::PDE (C++ function) PDE::PeriodicBoundaries (C++ function) PDE::Plot (C++ function), [1] PDE::plotPos (C++ function) PDE::PlotVectorField (C++ function) PDE::ReactionDiffusion (C++ function) PDE::Secrete (C++ function) PDE::SetSpeciesName (C++ function) PDE::setValue (C++ function) PDE::SizeX (C++ function) PDE::SizeY (C++ function) PDE::TheTime (C++ function)