Class StrongAmplifierGeometry

Object

AbstractGeometry

StrongAmplifierGeometry

public class StrongAmplifierGeometry
extends AbstractGeometry

Strong undirected amplifier graph based on Giakkoupis (2016).

See Also:

• Giakkoupis (2016) Amplifiers and Suppressors of Selection...

Field Summary

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
StrongAmplifierGeometry(EvoLudo engine)	Create a strong amplifier geometry tied to the given engine.

Method Summary

Modifier and Type	Method	Description
protected boolean	checkSettings()	Hook for subclasses to implement geometry specific checks.
void	init()	Generates a strong undirected amplifier of selection as described by Giakkoupis (2016).
private void	initRRGCore(RNGDistribution rng, int start, int end, int degree)	Initialise the random-regular core subgraph.
private boolean	rewireNeighbourEdge(RNGDistribution rng, int nodeA, int nodeB, int[] done, int nDone)	Attempt to rewire edges so that nodeA and nodeB can connect without duplicating links.

Methods inherited from class AbstractGeometry

addDirected, addEdgeAt, addLinkAt, addUndirected, alloc, check, clearLinksFrom, clearLinksTo, clone, create, create, decodeGeometry, deriveCompetitionGeometry, displaySingle, encodeGeometry, enforceSize, equals, getAddwire, getConnectivity, getEncodeKey, getFeatures, getLabel, getName, getNetwork2D, getNetwork3D, getRewire, getSize, getSpecs, getType, hashCode, isConsistent, isGraphConnected, isInterspecies, isLattice, isNeighborOf, isRegular, isRewired, isSingle, isType, isUndirected, isUnique, parse, 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

Constructor Details

StrongAmplifierGeometry

public StrongAmplifierGeometry(EvoLudo engine)

Create a strong amplifier geometry tied to the given engine.

Parameters:

engine - EvoLudo pacemaker

Method Details

init

public void init()

Generates a strong undirected amplifier of selection as described by Giakkoupis (2016). Population size satisfies \(N=n^3+(1+a)n^2\) with integer \(n\) and suitable \(a\geq 5\) and comprises three node types \(U=n^3\), \(V=n^2\) and \(W=N-U-V\). Nodes in \(U\) are leaves attached to nodes in \(V\) while nodes in \(V\) connect to \(n^2\) nodes in the regular core \(W\).

Specified by:

init in class AbstractGeometry

See Also:

• Giakkoupis (2016) Amplifiers and Suppressors of Selection...

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

initRRGCore

private void initRRGCore(RNGDistribution rng,
 int start,
 int end,
 int degree)

Initialise the random-regular core subgraph.

Parameters:

rng - random number generator

start - first node index of the core

end - (exclusive) end index of the core

degree - desired degree per node

rewireNeighbourEdge

private boolean rewireNeighbourEdge(RNGDistribution rng,
 int nodeA,
 int nodeB,
 int[] done,
 int nDone)

Attempt to rewire edges so that nodeA and nodeB can connect without duplicating links.

Parameters:

rng - random number generator

nodeA - first node needing neighbours

nodeB - second node needing neighbours

done - array of already satisfied nodes

nDone - number of valid entries in done

Returns:

true if rewiring succeeded