org.ginsim.service.tool.reg2dyn.updater

Class BaseSimulationUpdater

java.lang.Object

org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

All Implemented Interfaces:

Iterator, SimulationUpdater

Direct Known Subclasses:

SynchronousSimulationUpdater

public abstract class BaseSimulationUpdater
extends Object
implements SimulationUpdater

This is the part of the simulation in charge for generating the following states. supported methods are:

• synchronous search: all changes at once, each state has at most one successor
• asynchronous search: changes one by one, each state can have many successors
• by priority class: genes are classed by priority groups.
  • only changes on the higher priority group(s) containing changing genes will be applied.
  • if this concerns several groups, changes corresponding to each group will be applied asynchronously
  • each group can be either synchronous or asynchronous, changes will be applied all at once or one by one, depending on the group!
  • +1 and -1 transitions can be separated to create really fine-tuned groups

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	cur_state
protected int	depth
protected int	length
protected org.ginsim.service.tool.reg2dyn.updater.ModelHelper	modelHelper
protected boolean	multiple
protected byte[]	next
protected Object	node

Constructor Summary

Constructors

Constructor and Description
BaseSimulationUpdater(org.colomoto.biolqm.LogicalModel model)
BaseSimulationUpdater(org.ginsim.service.tool.reg2dyn.updater.ModelHelper helper)

Method Summary

Modifier and Type	Method and Description
SimulationUpdater	cloneForState(byte[] state)
protected abstract void	doBuildNext()
protected abstract SimulationUpdater	doClone()
protected abstract void	doSetState()
static SimulationUpdater	getAsynchronousInstance(org.colomoto.biolqm.LogicalModel model)
static SimulationUpdater	getInstance(org.colomoto.biolqm.LogicalModel model, PrioritySetDefinition pcdef)
static SimulationUpdater	getSynchronousInstance(org.colomoto.biolqm.LogicalModel model)
boolean	hasNext()
Object	next()
byte[]	nextState()
protected int	nodeChange(byte[] initState, int i) get change step for a gene
void	remove()
void	setState(byte[] state, int depth, Object node) set the state which should be used as basis.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

length

protected final int length

cur_state

protected byte[] cur_state

next

protected byte[] next

depth

protected int depth

node

protected Object node

multiple

protected boolean multiple

modelHelper

protected org.ginsim.service.tool.reg2dyn.updater.ModelHelper modelHelper

Constructor Detail

BaseSimulationUpdater

public BaseSimulationUpdater(org.colomoto.biolqm.LogicalModel model)

BaseSimulationUpdater

public BaseSimulationUpdater(org.ginsim.service.tool.reg2dyn.updater.ModelHelper helper)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

next

public Object next()

Specified by:

next in interface Iterator

nextState

public byte[] nextState()

Specified by:

nextState in interface SimulationUpdater

remove

public void remove()

Specified by:

remove in interface Iterator

setState

public void setState(byte[] state,
                     int depth,
                     Object node)

set the state which should be used as basis.

Specified by:

setState in interface SimulationUpdater

Parameters:

node -

depth -

state -

doSetState

protected abstract void doSetState()

doBuildNext

protected abstract void doBuildNext()

doClone

protected abstract SimulationUpdater doClone()

cloneForState

public SimulationUpdater cloneForState(byte[] state)

Specified by:

cloneForState in interface SimulationUpdater

nodeChange

protected int nodeChange(byte[] initState,
                         int i)

get change step for a gene

Parameters:

initState -

i - index of the gene to test

Returns:

the direction in which the gene want to change: 0 for no change, 1 for increase and -1 for decrease

getAsynchronousInstance

public static SimulationUpdater getAsynchronousInstance(org.colomoto.biolqm.LogicalModel model)

getSynchronousInstance

public static SimulationUpdater getSynchronousInstance(org.colomoto.biolqm.LogicalModel model)

getInstance

public static SimulationUpdater getInstance(org.colomoto.biolqm.LogicalModel model,
                                            PrioritySetDefinition pcdef)