public abstract class CylinderSubstrate extends Substrate
Modifier and Type | Field and Description |
---|---|
Cylinder[] |
cylinder |
a, border, factor, intersectsBoundary, spatialOptInitialised, voxToObjects
Constructor and Description |
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CylinderSubstrate(double[] L,
SimulationParams simParams,
boolean useSpaceOpt) |
Modifier and Type | Method and Description |
---|---|
boolean |
crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a walker's step will take it across a membrane or not.
|
Cylinder[] |
getCylinders() |
abstract double |
getPeakCoord() |
abstract double[] |
getSubstrateSize() |
void |
init()
initialiser for substrate.
|
boolean |
intracellular(Walker walker)
checks if a walker is in intracellular (true) or
extracellular (false) space
|
static void |
main(java.lang.String[] args) |
void |
setSubstrateDims(double[] L)
change the substrate dimensions
|
amend, getBottomLeft, getDiffusivityAt, getLogMagnetisationChange, getN, getSubsObj, getSubstrateCoords, getSubVoxelIndex, getUpperRight, initBoundaryIntersectionArrays, initCandidates, initialiseSpatialOptimisation, mapStepIntoSubstrate, moreCandidates, nextCandidate, testAmendment, testStepAmendment, unmapStepFromSubstrate, voxelContains
public Cylinder[] cylinder
public CylinderSubstrate(double[] L, SimulationParams simParams, boolean useSpaceOpt)
public boolean crossesMembrane(Walker walker, double[] offset, double[] stepVector, double[] normal, double[] d, boolean skipCurrent, double origLength, boolean[] in, double[] p)
crossesMembrane
in class Substrate
walker
- the walker to checkoffset
- offset from current walker position for beginning of stepstepVector
- the step being madenormal
- space to store the normal if a barrier is crossedd
- space to store barrier distance from origin dotted with normalskipCurrent
- flag indicating we're sitting on a barrier and should
ignore the closest one.originLength
- the original length of the step vector;public abstract double[] getSubstrateSize()
getSubstrateSize
in class Substrate
public abstract double getPeakCoord()
getPeakCoord
in class Substrate
public void init()
Substrate
public void setSubstrateDims(double[] L)
L
- the new dimensionspublic boolean intracellular(Walker walker)
Substrate
intracellular
in class Substrate
walker
- the walker to checkpublic final Cylinder[] getCylinders()
public static void main(java.lang.String[] args)