Class HierarchicalGeometry

Object

AbstractGeometry

AbstractLattice

HierarchicalGeometry

public class HierarchicalGeometry
extends AbstractLattice

Hierarchical meta-population structure implementation. Embeds well-mixed or square-lattice demes into recursive layers.

Field Summary

Fields

Modifier and Type	Field	Description
private int[]	hierarchy	The number of units at each hierarchical level.
private double	hierarchyWeight	Coupling strength between hierarchical levels.
private GeometryType	subType	The geometry of each hierarchical level.

Fields inherited from class AbstractLattice

fixedBoundary

Fields inherited from class AbstractGeometry

connectivity, EMPTY_LINKS, engine, features, in, isInterspecies, isRegular, isRewired, isSingle, isUndirected, isValid, kin, kout, logger, name, network2D, network3D, out, pAddwire, pRewire, size, specs, type

Constructor Summary

Constructors

Constructor	Description
HierarchicalGeometry(EvoLudo engine)	Create a hierarchical geometry tied to the given engine.

Method Summary

Modifier and Type	Method	Description
private void	addBoundaryLinks(int player, int fullside, int range, boolean interspecies, int uStep, int vStep)	Add links for a boundary player in a square deme.
private void	addSquareNeighborhood(int i, int j, int sideLen, int fullside, int offset, int range, boolean interspecies)	Add all neighbours for a player in the square deme.
private void	adjustMooreBoundaries(int sideLen, int fullside, int offset, boolean interspecies)	Adjust Moore neighbourhoods along fixed boundaries.
private void	adjustNeumann2ndBoundaries(int sideLen, int fullside, int offset, boolean interspecies)	Adjust second-neighbour von Neumann neighbourhoods along fixed boundaries.
private void	adjustNeumannBoundaries(int sideLen, int fullside, int offset, boolean interspecies)	Adjust von Neumann neighbourhoods along fixed boundaries.
private void	adjustSquareBoundaries(int sideLen, int fullside, int offset, int range, boolean interspecies)	Adjust arbitrary-range square neighbourhoods along fixed boundaries.
private int	calcSquareUnit(int nHierarchy)	Calculate the unit size for square-lattice hierarchies, adjusting each level to a perfect square with at least 2x2 units with at least 3x3 individuals each.
private boolean	calcUnitSize()	Process the hierarchy specifications to calculate the number of units and the size of each unit.
protected boolean	checkSettings()	Hook for subclasses to implement geometry specific checks.
HierarchicalGeometry	clone()	Clone geometry.
boolean	equals(Object obj)
int[]	getHierarchyLevels()	Retrieve a copy of the processed hierarchy definition (levels plus individuals per deme).
double	getHierarchyWeight()	Report the weight applied to inter-level interactions.
GeometryType	getSubType()	Retrieve the geometry used within each hierarchy level (e.g.
int	hashCode()
void	init()	Initialise the geometry.
private void	initHierarchy(int level, int start)	Utility method to generate hierarchical graphs.
private void	initHierarchyMeanfield(int start, int end)	Utility method to generate hierarchical well-mixed subpopulations (demes).
private void	initHierarchySquare(int start, int end)	Utility method to generate hierarchical square-lattice demes.
private void	initSquare(int sideLen, int fullside, int offset)	Initialize a square deme for arbitrary (odd) neighbourhood sizes.
private void	initSquareMoore(int sideLen, int fullside, int offset)	Initialize a square deme with Moore connectivity.
private void	initSquareVonNeumann(int sideLen, int fullside, int offset)	Initialize a square deme with von Neumann connectivity, optionally adjusting for boundary conditions.
private void	initSquareVonNeumann2nd(int sideLen, int fullside, int offset)	Initialize a square deme with second-neighbour von Neumann connectivity.
boolean	isSubtype(GeometryType type)	Check if the sub-geometry matches the given type.
boolean	isUnique()	Check if current geometry unique.
(package private) boolean	parse(String spec)	Parse geometry-specific CLI options.
private void	parseHierarchy()	Parse the hierarchy-related CLI spec, updating subtype, boundary flag and weight, and storing the raw hierarchy levels (without the computed leaf size).

Methods inherited from class AbstractLattice

isFixedBoundary, setFixedBoundary, stripBoundary

Methods inherited from class AbstractGeometry

addDirected, addEdgeAt, addLinkAt, addUndirected, alloc, check, clearLinksFrom, clearLinksTo, create, create, decodeGeometry, deriveCompetitionGeometry, displaySingle, encodeGeometry, enforceSize, getAddwire, getConnectivity, getEncodeKey, getFeatures, getLabel, getName, getNetwork2D, getNetwork3D, getRewire, getSize, getSpecs, getType, isConsistent, isGraphConnected, isInterspecies, isLattice, isNeighborOf, isRegular, isRewired, isSingle, isType, isUndirected, parse, removeEdgeAt, removeLinkAt, rewire, rewireDirected, rewireEdgeAt, rewireLinkAt, rewireUndirected, setAddwire, setConnectivity, setInterspecies, setName, setNetwork2D, setNetwork3D, setRewire, setSingle, setSize, setType, swapEdges, usage, warn

Methods inherited from class Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Details

subType

private GeometryType subType

The geometry of each hierarchical level.

hierarchy

private int[] hierarchy

The number of units at each hierarchical level.

hierarchyWeight

private double hierarchyWeight

Coupling strength between hierarchical levels.

Constructor Details

HierarchicalGeometry

public HierarchicalGeometry(EvoLudo engine)

Create a hierarchical geometry tied to the given engine.

Parameters:

engine - EvoLudo pacemaker

Method Details

parse

boolean parse(String spec)

Description copied from class: AbstractGeometry

Parse geometry-specific CLI options.

Overrides:

parse in class AbstractGeometry

Parameters:

spec - the argument string without the geometry key

Returns:

true if parsing succeeded, false if invalid

isSubtype

public boolean isSubtype(GeometryType type)

Check if the sub-geometry matches the given type.

Parameters:

type - the geometry type to check against

Returns:

true if the sub-geometry matches the given type

getSubType

public GeometryType getSubType()

Retrieve the geometry used within each hierarchy level (e.g. square or well-mixed).

Returns:

the geometry used within each hierarchy level (e.g. square or well-mixed)

getHierarchyWeight

public double getHierarchyWeight()

Report the weight applied to inter-level interactions.

Returns:

the weight applied to inter-level interactions

getHierarchyLevels

public int[] getHierarchyLevels()

Retrieve a copy of the processed hierarchy definition (levels plus individuals per deme).

Returns:

a copy of the processed hierarchy definition (levels plus individuals per deme)

checkSettings

protected boolean checkSettings()

Description copied from class: AbstractGeometry

Hook for subclasses to implement geometry specific checks.

Overrides:

checkSettings in class AbstractGeometry

Returns:

true if adjustments require a reset

calcUnitSize

private boolean calcUnitSize()

Process the hierarchy specifications to calculate the number of units and the size of each unit. On each level there must be at least 2 units for well-mixed hierarchies and each unit must contain at least 2 individuals. For hierarchies with square lattices each level must ahev at least 2x2 units with at least 3x3 individuals each.

Returns:

true if the size was adjusted and resetting is required

calcSquareUnit

private int calcSquareUnit(int nHierarchy)

Calculate the unit size for square-lattice hierarchies, adjusting each level to a perfect square with at least 2x2 units with at least 3x3 individuals each.

Parameters:

nHierarchy - the number of hierarchy levels

Returns:

the total size of the graph

init

public void init()

Initialise the geometry.

Requirements/notes:

Only well-mixed (complete) or square lattice graphs are currently supported.

Specified by:

init in class AbstractGeometry

initHierarchy

private void initHierarchy(int level,
 int start)

Utility method to generate hierarchical graphs.

Parameters:

level - the hierarchical level

start - the index of the first node to process

initHierarchyMeanfield

private void initHierarchyMeanfield(int start,
 int end)

Utility method to generate hierarchical well-mixed subpopulations (demes).

Parameters:

start - the index of the first node to process

end - the index of the last node to process

initHierarchySquare

private void initHierarchySquare(int start,
 int end)

Utility method to generate hierarchical square-lattice demes.

Parameters:

start - the index of the first node to process

end - the index of the last node to process

initSquareVonNeumann

private void initSquareVonNeumann(int sideLen,
 int fullside,
 int offset)

Initialize a square deme with von Neumann connectivity, optionally adjusting for boundary conditions.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

adjustNeumannBoundaries

private void adjustNeumannBoundaries(int sideLen,
 int fullside,
 int offset,
 boolean interspecies)

Adjust von Neumann neighbourhoods along fixed boundaries.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

interspecies - true if interspecific interactions allow self-links

initSquareVonNeumann2nd

private void initSquareVonNeumann2nd(int sideLen,
 int fullside,
 int offset)

Initialize a square deme with second-neighbour von Neumann connectivity.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

adjustNeumann2ndBoundaries

private void adjustNeumann2ndBoundaries(int sideLen,
 int fullside,
 int offset,
 boolean interspecies)

Adjust second-neighbour von Neumann neighbourhoods along fixed boundaries.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

interspecies - true if interspecific interactions allow self-links

initSquareMoore

private void initSquareMoore(int sideLen,
 int fullside,
 int offset)

Initialize a square deme with Moore connectivity.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

adjustMooreBoundaries

private void adjustMooreBoundaries(int sideLen,
 int fullside,
 int offset,
 boolean interspecies)

Adjust Moore neighbourhoods along fixed boundaries.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

interspecies - true if interspecific interactions allow self-links

initSquare

private void initSquare(int sideLen,
 int fullside,
 int offset)

Initialize a square deme for arbitrary (odd) neighbourhood sizes.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

addSquareNeighborhood

private void addSquareNeighborhood(int i,
 int j,
 int sideLen,
 int fullside,
 int offset,
 int range,
 boolean interspecies)

Add all neighbours for a player in the square deme.

Parameters:

i - row index within the deme

j - column index within the deme

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

range - neighbour range

interspecies - true if interspecific interactions allow self-links

adjustSquareBoundaries

private void adjustSquareBoundaries(int sideLen,
 int fullside,
 int offset,
 int range,
 boolean interspecies)

Adjust arbitrary-range square neighbourhoods along fixed boundaries.

Parameters:

sideLen - side length of the deme

fullside - side length of the full lattice

offset - index offset of the deme

range - neighbour range

interspecies - true if interspecific interactions allow self-links

addBoundaryLinks

private void addBoundaryLinks(int player,
 int fullside,
 int range,
 boolean interspecies,
 int uStep,
 int vStep)

Add links for a boundary player in a square deme.

Parameters:

player - the player at the boundary

fullside - the side length of the full lattice

range - the neighbour range

interspecies - true for interspecific interactions

uStep - the step size in the u direction

vStep - the step size in the v direction

isUnique

public boolean isUnique()

Description copied from class: AbstractGeometry

Check if current geometry unique. Only unique geomteries need to be encoded.

Requirements/notes:

1. Lattices etc. are not unique because they can be identically recreated.
2. Complete graphs, stars, wheels, etc. are not unique.
3. All geometries involving random elements are unique.
4. All rewired geometries are unique.
5. Hierarchical geometries require recursive checks of uniqueness.

Overrides:

isUnique in class AbstractGeometry

Returns:

true if geometry is unique

clone

public HierarchicalGeometry clone()

Description copied from class: AbstractGeometry

Clone geometry.

Requirements/notes:

1. Overrides clone() in Object but conflicts with GWT's aversion to clone()ing...
2. Remove @SuppressWarnings("all") to ensure that no other issues crept in when modifying method.

Overrides:

clone in class AbstractLattice

Returns:

clone of geometry

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractLattice

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractLattice

parseHierarchy

private void parseHierarchy()

Parse the hierarchy-related CLI spec, updating subtype, boundary flag and weight, and storing the raw hierarchy levels (without the computed leaf size).