RegulatoryNode (GINsim 3.0.0b-SNAPSHOT API)

java.lang.Object
- org.ginsim.core.graph.regulatorygraph.RegulatoryNode

All Implemented Interfaces:

org.colomoto.biolqm.NodeInfoHolder, ToolTipsable
```
public class RegulatoryNode
extends Object
implements ToolTipsable, org.colomoto.biolqm.NodeInfoHolder
```
A node in the Regulatory graph, representing a regulatory component. A component has:
- a maxValue
- an annotation (comment and URLs)
- a dynamical behaviour defined by logical parameters or functions.
Author:

Aurelien Naldi.

Field Summary

Fields
Modifier and Type Field and Description

static int MAXVALUE

Fields
Modifier and Type	Field and Description
`static int`	`MAXVALUE`

Constructor Summary

Constructors
Constructor and Description
`RegulatoryNode(int num, RegulatoryGraph graph)`
`RegulatoryNode(String id, RegulatoryGraph graph)` Constructs an empty vector and set the baseValue (0) and the maxValue (1)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addLogicalParameter(LogicalParameter I, boolean manual)` Adds the specified interaction I to the interactions of the node
`void`	`cleanupInteraction()` update logical parameters when an interaction is deleted.
`void`	`cleanupInteractionForNewGraph(Map copyMap)`
`RegulatoryNode`	`clone(RegulatoryGraph graph)`
`boolean`	`equals(Object obj)` Compare the object to the given one, using the internal NodeInfo.
`Annotation`	`getAnnotation()` get notes on this gene.
`String`	`getDisplayName()`
`String`	`getId()`
`LogicalParameter`	`getInteraction(int index)` Returns the interaction at the specified position index
`TreeInteractionsModel`	`getInteractionsModel()`
`byte`	`getMaxValue()`
`int`	`getMDD(RegulatoryGraph graph, org.colomoto.mddlib.MDDManager factory)` Experimental: Get the MDD for this node function using the new MDD toolkit.
`String`	`getName()` get the long name of the node.
`org.colomoto.biolqm.NodeInfo`	`getNodeInfo()`
`LogicalParameterList`	`getV_logicalParameters()`
`int`	`hashCode()`
`void`	`incomingEdgeAdded(RegulatoryMultiEdge me)`
`int`	`interactionCount()` Returns the number of the interaction in the node.
`boolean`	`isInput()`
`boolean`	`isOutput()`
`void`	`removeEdgeFromInteraction(RegulatoryMultiEdge multiEdge)` when an incoming edge is deleted, we don't want to see it appear in interactions anymore.
`void`	`removeEdgeFromInteraction(RegulatoryMultiEdge multiEdge, int index)` when an incoming edge is deleted, we don't want to see it appear in interactions anymore.
`void`	`removeInteraction(LogicalParameter I)` Removes the specified interaction to the interactions of the node
`void`	`saveInteractionsModel(XMLWriter out)`
`void`	`setGsa(Annotation annotation)`
`boolean`	`setId(String id, RegulatoryGraph graph)` change the id of this node.
`void`	`setInput(boolean input, Graph graph)`
`void`	`setInteractionsModel(TreeInteractionsModel model)`
`void`	`setMaxValue(byte max, RegulatoryGraph graph)` Sets the max value to the node
`void`	`setName(String name, RegulatoryGraph graph)` set the name of the gene.
`void`	`setOutput(boolean output, Graph graph)`
`String`	`toString()`
`String`	`toToolTip()` retrieve the tooltip text
`void`	`toXML(XMLWriter out)`
`void`	`updateInteraction(int index, List edges)` change an interaction's list of edges: we have to check that the new list of edges is not in an existing interaction.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - MAXVALUE
```
public static final int MAXVALUE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RegulatoryNode
```
public RegulatoryNode(String id,
                      RegulatoryGraph graph)
```
    Constructs an empty vector and set the baseValue (0) and the maxValue (1)
    
    Parameters:
    
    id -
  - RegulatoryNode
```
public RegulatoryNode(int num,
                      RegulatoryGraph graph)
```
    Parameters:
    
    num - number of the gene.
- Method Detail
  - isInput
```
public boolean isInput()
```
  - setInput
```
public void setInput(boolean input,
                     Graph graph)
```
  - isOutput
```
public boolean isOutput()
```
  - setOutput
```
public void setOutput(boolean output,
                      Graph graph)
```
  - getMaxValue
```
public byte getMaxValue()
```
    Returns:
    
    the max value of the node
  - setMaxValue
```
public void setMaxValue(byte max,
                        RegulatoryGraph graph)
```
    Sets the max value to the node
    
    Parameters:
    
    max - the new max value
    
    graph - the graph (to propagate changes if needed)
  - getId
```
public String getId()
```
    Returns:
    
    the id of this node.
  - setId
```
public boolean setId(String id,
                     RegulatoryGraph graph)
```
    change the id of this node.
    
    Parameters:
    
    id - the new id.
  - addLogicalParameter
```
public boolean addLogicalParameter(LogicalParameter I,
                                   boolean manual)
```
    Adds the specified interaction I to the interactions of the node
    
    Parameters:
    
    I -
    
    Returns:
    
    true if the logical parameter has been added
  - removeInteraction
```
public void removeInteraction(LogicalParameter I)
```
    Removes the specified interaction to the interactions of the node
    
    Parameters:
    
    I -
  - getInteraction
```
public LogicalParameter getInteraction(int index)
```
    Returns the interaction at the specified position index
    
    Parameters:
    
    index -
    
    Returns:
    
    LogicalParameter
  - updateInteraction
```
public void updateInteraction(int index,
                              List edges)
```
    change an interaction's list of edges: we have to check that the new list of edges is not in an existing interaction.
    
    Parameters:
    
    index -
    
    edges -
  - interactionCount
```
public int interactionCount()
```
    Returns the number of the interaction in the node.
    
    Returns:
    
    the number of user defined interactions on this node
  - getName
```
public String getName()
```
    get the long name of the node.
    
    Returns:
    
    the name
  - setName
```
public void setName(String name,
                    RegulatoryGraph graph)
```
    set the name of the gene.
    
    Parameters:
    
    name - the new name
  - getAnnotation
```
public Annotation getAnnotation()
```
    get notes on this gene.
    
    Returns:
    
    the annotation associated to this node
  - getV_logicalParameters
```
public LogicalParameterList getV_logicalParameters()
```
    Returns:
    
    the list of all interactions on this gene.
  - getMDD
```
public int getMDD(RegulatoryGraph graph,
                  org.colomoto.mddlib.MDDManager factory)
```
    Experimental: Get the MDD for this node function using the new MDD toolkit.
    
    Parameters:
    
    factory -
    
    Returns:
  - toToolTip
```
public String toToolTip()
```
    Description copied from interface: ToolTipsable
    
    retrieve the tooltip text
    
    Specified by:
    
    toToolTip in interface ToolTipsable
    
    Returns:
    
    the string to be displayed in the tooltip
  - toXML
```
public void toXML(XMLWriter out)
           throws IOException
```
    Throws:
    
    IOException
  - setGsa
```
public void setGsa(Annotation annotation)
```
    Parameters:
    
    annotation - for this node.
  - clone
```
public RegulatoryNode clone(RegulatoryGraph graph)
```
  - cleanupInteraction
```
public void cleanupInteraction()
```
    update logical parameters when an interaction is deleted.
  - removeEdgeFromInteraction
```
public void removeEdgeFromInteraction(RegulatoryMultiEdge multiEdge,
                                      int index)
```
    when an incoming edge is deleted, we don't want to see it appear in interactions anymore. This will remove a subedge. NOTE: ALL interaction involving the deleted subedge will be suppressed.
    
    Parameters:
    
    multiEdge -
    
    index -
  - removeEdgeFromInteraction
```
public void removeEdgeFromInteraction(RegulatoryMultiEdge multiEdge)
```
    when an incoming edge is deleted, we don't want to see it appear in interactions anymore. This will remove all subedges of a multiedge. NOTE: ALL interaction involving the deleted multiedge will be suppressed.
    
    Parameters:
    
    multiEdge -
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getDisplayName
```
public String getDisplayName()
```
  - cleanupInteractionForNewGraph
```
public void cleanupInteractionForNewGraph(Map copyMap)
```
    Parameters:
    
    copyMap -
  - setInteractionsModel
```
public void setInteractionsModel(TreeInteractionsModel model)
```
  - getInteractionsModel
```
public TreeInteractionsModel getInteractionsModel()
```
  - saveInteractionsModel
```
public void saveInteractionsModel(XMLWriter out)
                           throws IOException
```
    Throws:
    
    IOException
  - incomingEdgeAdded
```
public void incomingEdgeAdded(RegulatoryMultiEdge me)
```
  - equals
```
public boolean equals(Object obj)
```
    Compare the object to the given one, using the internal NodeInfo.
    
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - getNodeInfo
```
public org.colomoto.biolqm.NodeInfo getNodeInfo()
```
    Specified by:
    
    getNodeInfo in interface org.colomoto.biolqm.NodeInfoHolder

Class RegulatoryNode

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAXVALUE

Constructor Detail

RegulatoryNode

RegulatoryNode

Method Detail

isInput

setInput

isOutput

setOutput

getMaxValue

setMaxValue

getId

setId

addLogicalParameter

removeInteraction

getInteraction

updateInteraction

interactionCount

getName

setName

getAnnotation

getV_logicalParameters

getMDD

toToolTip

toXML

setGsa

clone

cleanupInteraction

removeEdgeFromInteraction

removeEdgeFromInteraction

toString

getDisplayName

cleanupInteractionForNewGraph

setInteractionsModel

getInteractionsModel

saveInteractionsModel

incomingEdgeAdded

equals

hashCode

getNodeInfo