org.ginsim.service.tool.reg2dyn.priorityclass

Class PrioritySetDefinition

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<T>

org.ginsim.core.utils.data.NamedList<T>

org.ginsim.core.utils.data.ListenableNamedList<PriorityClass>

org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

All Implemented Interfaces:

Serializable, Cloneable, Iterable<PriorityClass>, Collection<PriorityClass>, List<PriorityClass>, RandomAccess, XMLize, NamedObject, UpdaterDefinition

public class PrioritySetDefinition
extends ListenableNamedList<PriorityClass>
implements UpdaterDefinition

Definition of a set of priority classes: store a list of classes and assign all nodes to one of them.

Author:

Aurelien Naldi

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DOWN
Map<RegulatoryNode,PriorityClass[]>	m_elt
static int	NONE
static int	UP

Fields inherited from class java.util.AbstractList

modCount

Fields inherited from interface org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinition

USE_BIOLQM_UPDATERS

Constructor Summary

Constructors

Constructor and Description
PrioritySetDefinition(List<RegulatoryNode> elts, String name)

Method Summary

Modifier and Type	Method and Description
int	add()
int	add(int i)
void	associate(RegulatoryNode node, PriorityClass cl)
void	associate(RegulatoryNode node, PriorityClass clUp, PriorityClass clDown)
int[][]	getMovingRows(int key, int[] index) when moving a selection of class, they must move with other class of the same priority.
String	getName()
int[][]	getPclass(List<org.colomoto.biolqm.NodeInfo> nodeOrder)
SimulationUpdater	getUpdater(org.colomoto.biolqm.LogicalModel model)
void	groupToggle(int[] ts) toggle the selection grouping: - if all selected items are part of the same group, it will be "ungrouped" - if selected items are part of several groups, they will be merged with the first one
boolean	match(String filter)
void	moveElementAt(int j, int pos)
boolean	moveSelection(int[] sel, int diff)
PriorityClass	remove(int idx)
boolean	remove(int[] t_index) Remove a group of items
boolean	remove(Object o)
void	removeNode(RegulatoryNode node)
void	setName(String name) change the name of this object
String	summary(List<org.colomoto.biolqm.NodeInfo> nodeOrder)
String	toString()
void	toXML(XMLWriter out) write the XML representation of this object to a file

Methods inherited from class org.ginsim.core.utils.data.ListenableNamedList

add, add, addListListener, fireAdded, fireChanged, fireRemoved, removeListListener

Methods inherited from class org.ginsim.core.utils.data.NamedList

findUniqueName, getByName, isNameValid, rename

Methods inherited from class java.util.ArrayList

addAll, addAll, clear, clone, contains, ensureCapacity, forEach, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

containsAll, equals, hashCode

Methods inherited from interface java.util.Collection

parallelStream, stream

Field Detail

UP

public static final int UP

See Also:

Constant Field Values

DOWN

public static final int DOWN

See Also:

Constant Field Values

NONE

public static final int NONE

See Also:

Constant Field Values

m_elt

public Map<RegulatoryNode,PriorityClass[]> m_elt

Constructor Detail

PrioritySetDefinition

public PrioritySetDefinition(List<RegulatoryNode> elts,
                             String name)

Method Detail

getUpdater

public SimulationUpdater getUpdater(org.colomoto.biolqm.LogicalModel model)

Specified by:

getUpdater in interface UpdaterDefinition

setName

public void setName(String name)

Description copied from interface: NamedObject

change the name of this object

Specified by:

setName in interface NamedObject

getName

public String getName()

Specified by:

getName in interface NamedObject

Returns:

the name of this object

toString

public String toString()

Overrides:

toString in class AbstractCollection<PriorityClass>

moveElementAt

public void moveElementAt(int j,
                          int pos)

associate

public void associate(RegulatoryNode node,
                      PriorityClass cl)

associate

public void associate(RegulatoryNode node,
                      PriorityClass clUp,
                      PriorityClass clDown)

remove

public PriorityClass remove(int idx)

Specified by:

remove in interface List<PriorityClass>

Overrides:

remove in class ListenableNamedList<PriorityClass>

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<PriorityClass>

Specified by:

remove in interface List<PriorityClass>

Overrides:

remove in class ArrayList<PriorityClass>

remove

public boolean remove(int[] t_index)

Remove a group of items

Parameters:

t_index -

Returns:

moveSelection

public boolean moveSelection(int[] sel,
                             int diff)

getMovingRows

public int[][] getMovingRows(int key,
                             int[] index)

when moving a selection of class, they must move with other class of the same priority. this checks the selection and compute a list of all really moving rows as ranges: start-stop for each selected clas

Parameters:

key -

index -

Returns:

moving ranges or null if nothing should move

toXML

public void toXML(XMLWriter out)
           throws IOException

Description copied from interface: XMLize

write the XML representation of this object to a file

Specified by:

toXML in interface XMLize

Throws:

IOException

getPclass

public int[][] getPclass(List<org.colomoto.biolqm.NodeInfo> nodeOrder)

Returns:

the compiled priority class. in the form of an int[][] each int[] represent a priority class: - the very first int is the class' priority - the second int is the class' mode (sync or async) - and all others are couples: index of node in the nodeOrder followed by transition filter. the "transition filter" is a bit hacky: add it to your transition (which should be either +1 or -1) and if the result is zero (0), then this transition shouldn't be followed. shortly: it is 0 for all transitions, 1 for negative transitions and -1 for positive ones

match

public boolean match(String filter)

add

public int add()

add

public int add(int i)

groupToggle

public void groupToggle(int[] ts)

toggle the selection grouping: - if all selected items are part of the same group, it will be "ungrouped" - if selected items are part of several groups, they will be merged with the first one

summary

public String summary(List<org.colomoto.biolqm.NodeInfo> nodeOrder)

Specified by:

summary in interface UpdaterDefinition

removeNode

public void removeNode(RegulatoryNode node)