Class LinearGeometry

Object

AbstractGeometry

AbstractLattice

LinearGeometry

public class LinearGeometry
extends AbstractLattice

Linear (1D lattice) geometry that supports asymmetric neighbourhoods and optional fixed boundaries.

Field Summary

Fields

Modifier and Type	Field	Description
private int	linearAsymmetry	Difference between the number of neighbours on the left vs right.

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
LinearGeometry(EvoLudo engine)	Create a linear (1D lattice) geometry attached to the given engine.

Method Summary

Modifier and Type	Method	Description
protected boolean	checkSettings()	Hook for subclasses to implement geometry specific checks.
LinearGeometry	clone()	Clone geometry.
boolean	equals(Object obj)
int	getLinearAsymmetry()	Get the current left-right neighbour difference.
int	hashCode()
void	init()	Generates a linear chain (1D lattice).
boolean	parse(String arg)	Parse geometry-specific CLI options.
void	setLinearAsymmetry(int asymmetry)	Set the left-right neighbour difference.

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, isUnique, 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

linearAsymmetry

private int linearAsymmetry

Difference between the number of neighbours on the left vs right.

Constructor Details

LinearGeometry

public LinearGeometry(EvoLudo engine)

Create a linear (1D lattice) geometry attached to the given engine.

Parameters:

engine - EvoLudo pacemaker

Method Details

parse

public boolean parse(String arg)

Description copied from class: AbstractGeometry

Parse geometry-specific CLI options.

Overrides:

parse in class AbstractGeometry

Parameters:

arg - the argument string without the geometry key

Returns:

true if parsing succeeded, false if invalid

init

public void init()

Generates a linear chain (1D lattice). With asymmetric neighbours and fixed boundaries this represents the simplest suppressor of selection.

Requirements/notes:

1. Supports different numbers of neighbours to the left and right.
2. For inter-species interactions connectivities are incremented by one and a connectivity of 1 is admissible.
3. Boundaries can be fixed or periodic (default).

Specified by:

init in class AbstractGeometry

setLinearAsymmetry

public void setLinearAsymmetry(int asymmetry)

Set the left-right neighbour difference.

Parameters:

asymmetry - positive values favour neighbours on the left

getLinearAsymmetry

public int getLinearAsymmetry()

Get the current left-right neighbour difference.

Returns:

the left-right neighbour difference

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

clone

public LinearGeometry 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