HierarchicalNode (GINsim 3.0.0b-SNAPSHOT API)

java.lang.Object
- org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

All Implemented Interfaces:

Comparable<Object>, Dotify
```
public class HierarchicalNode
extends Object
implements Comparable<Object>, Dotify
```
Define the nodes of the Hierarchical Transition Graph.

A node has a unique id uid, a type defining the kind of Strongly Connected Component it contains and statesSet, the set of all the states it contains.

Author:

Duncan Berenguier

Field Summary

Fields
Modifier and Type	Field and Description
`StatesSet`	`statesSet` The set of states
`static Color`	`TYPE_EDEN_TRANSIENT_COMPONENT_COLOR`
`static byte`	`TYPE_STABLE_STATE`
`static Color`	`TYPE_STABLE_STATE_COLOR`
`static String`	`TYPE_STABLE_STATE_STRING`
`static byte`	`TYPE_TERMINAL_CYCLE`
`static Color`	`TYPE_TERMINAL_CYCLE_COLOR`
`static String`	`TYPE_TERMINAL_CYCLE_STRING`
`static byte`	`TYPE_TRANSIENT_COMPONENT`
`static Color`	`TYPE_TRANSIENT_COMPONENT_ALONE_COLOR`
`static Color`	`TYPE_TRANSIENT_COMPONENT_COLOR`
`static String`	`TYPE_TRANSIENT_COMPONENT_STRING`
`static byte`	`TYPE_TRANSIENT_CYCLE`
`static Color`	`TYPE_TRANSIENT_CYCLE_COLOR`
`static String`	`TYPE_TRANSIENT_CYCLE_STRING`

Constructor Summary

Constructors
Constructor and Description

HierarchicalNode(HierarchicalTransitionGraph htg)
Default constructor.

Constructors
Constructor and Description
`HierarchicalNode(HierarchicalTransitionGraph htg)` Default constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAllTheStatesInQueue()` Perform a mergeMultiple on all the omdd in the pile and the root.
`boolean`	`addEdgeTo(HierarchicalNode to)` Add an edge between to a node
`void`	`addState(byte[] state, int status)` Add the state directly to the stateSet.
`void`	`addStateToThePile(byte[] state)` Add a new state to the pile.
`int`	`compareTo(Object arg0)`
`boolean`	`contains(byte[] state)` Indicates if the HierarchicalNode contains a state by searching both the pile and the omdd
`StringBuffer`	`firstStatesToString()` Return a string representation of the first state in the node.
`Set<HierarchicalNode>`	`getIn()`
`String`	`getLongId()`
`Set<HierarchicalNode>`	`getOut()`
`String`	`getShortId()`
`HierarchicalSigmaSet`	`getSigma()` return the set sigma
`int`	`getSize()`
`byte`	`getType()`
`long`	`getUniqueId()` Return the long identifying this node "uniquely" (if in the range of long)
`int`	`hashcode()`
`boolean`	`isCycle()`
`boolean`	`isStable()`
`boolean`	`isTerminal()`
`boolean`	`isTransient()`
`void`	`merge(HierarchicalNode slaveNode, Collection<HierarchicalNode> nodeSet, HierarchicalSigmaSetFactory sigmaSetFactory, HierarchicalTransitionGraph htg)` Merge the slave (or its master) node into this (or its master).
`void`	`parse(String parse)`
`void`	`releaseEdges()`
`void`	`setIn(Set<HierarchicalNode> in)`
`void`	`setLabelCount(short intValue)`
`void`	`setOut(Set<HierarchicalNode> out)`
`void`	`setSigma(HierarchicalSigmaSet sigma)` return the set sigma
`void`	`setType(byte type)`
`void`	`setTypeFromString(String type)` Set the type from a string
`List<byte[]>`	`statesToList()` Initialize and fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1).
`String`	`statesToString()`
`String`	`statesToString(boolean addValue)`
`String`	`toDot()` Return a dot representation of the object as a String
`String`	`toDot(Object to)` Return a dot representation of the edge as a String The object is the source of the edge, the first parameter is the target.
`String`	`toLongString()`
`String`	`toString()`
`static byte`	`typeFromString(String type)` Return an int representation for a given string
`String`	`typeToString()` Return a string representation for the type of this node.
`static String`	`typeToString(int type)` Return a string representation for a given type.
`void`	`updateSize()` Compute the size.
`String`	`write()`

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

- Field Detail
  - TYPE_TRANSIENT_COMPONENT
```
public static final byte TYPE_TRANSIENT_COMPONENT
```
    See Also:
    
    Constant Field Values
  - TYPE_TRANSIENT_CYCLE
```
public static final byte TYPE_TRANSIENT_CYCLE
```
    See Also:
    
    Constant Field Values
  - TYPE_TERMINAL_CYCLE
```
public static final byte TYPE_TERMINAL_CYCLE
```
    See Also:
    
    Constant Field Values
  - TYPE_STABLE_STATE
```
public static final byte TYPE_STABLE_STATE
```
    See Also:
    
    Constant Field Values
  - TYPE_TRANSIENT_COMPONENT_STRING
```
public static final String TYPE_TRANSIENT_COMPONENT_STRING
```
    See Also:
    
    Constant Field Values
  - TYPE_TERMINAL_CYCLE_STRING
```
public static final String TYPE_TERMINAL_CYCLE_STRING
```
    See Also:
    
    Constant Field Values
  - TYPE_TRANSIENT_CYCLE_STRING
```
public static final String TYPE_TRANSIENT_CYCLE_STRING
```
    See Also:
    
    Constant Field Values
  - TYPE_STABLE_STATE_STRING
```
public static final String TYPE_STABLE_STATE_STRING
```
    See Also:
    
    Constant Field Values
  - TYPE_TRANSIENT_COMPONENT_ALONE_COLOR
```
public static final Color TYPE_TRANSIENT_COMPONENT_ALONE_COLOR
```
  - TYPE_TRANSIENT_COMPONENT_COLOR
```
public static final Color TYPE_TRANSIENT_COMPONENT_COLOR
```
  - TYPE_TRANSIENT_CYCLE_COLOR
```
public static final Color TYPE_TRANSIENT_CYCLE_COLOR
```
  - TYPE_EDEN_TRANSIENT_COMPONENT_COLOR
```
public static final Color TYPE_EDEN_TRANSIENT_COMPONENT_COLOR
```
  - TYPE_TERMINAL_CYCLE_COLOR
```
public static final Color TYPE_TERMINAL_CYCLE_COLOR
```
  - TYPE_STABLE_STATE_COLOR
```
public static final Color TYPE_STABLE_STATE_COLOR
```
  - statesSet
```
public StatesSet statesSet
```
    The set of states
- Constructor Detail
  - HierarchicalNode
```
public HierarchicalNode(HierarchicalTransitionGraph htg)
```
    Default constructor. Initialize a new node with a good uid, and type TYPE_TRANSIENT_COMPONENT By default the state set is not initialized
- Method Detail
  - addAllTheStatesInQueue
```
public void addAllTheStatesInQueue()
```
    Perform a mergeMultiple on all the omdd in the pile and the root.
  - addStateToThePile
```
public void addStateToThePile(byte[] state)
```
    Add a new state to the pile. Note the new state is not added to the HierarchicalNode omdd aiming to add several omdd at the same time.
    
    Parameters:
    
    state - the state to add
  - addState
```
public void addState(byte[] state,
                     int status)
```
    Add the state directly to the stateSet. Set the leaf value to status
    
    Parameters:
    
    state -
    
    status -
  - contains
```
public boolean contains(byte[] state)
```
    Indicates if the HierarchicalNode contains a state by searching both the pile and the omdd
    
    Parameters:
    
    state -
    
    Returns:
    
    true if it contains the state
  - merge
```
public void merge(HierarchicalNode slaveNode,
                  Collection<HierarchicalNode> nodeSet,
                  HierarchicalSigmaSetFactory sigmaSetFactory,
                  HierarchicalTransitionGraph htg)
```
    Merge the slave (or its master) node into this (or its master). All the function call on the slave are redirected to this. The states of the slave are merged with this (or its master)
    
    Parameters:
    
    slaveNode -
    
    nodeSet -
    
    htg -
  - getSize
```
public int getSize()
```
  - updateSize
```
public void updateSize()
```
    Compute the size. This function reduce the stateSet but doesn't add the states in the queue to the stateSet.
  - addEdgeTo
```
public boolean addEdgeTo(HierarchicalNode to)
```
    Add an edge between to a node
    
    Parameters:
    
    to -
    
    Returns:
    
    true if an edge was added (no autoregulation)
  - setOut
```
public void setOut(Set<HierarchicalNode> out)
```
    Parameters:
    
    out - the out to set
  - getOut
```
public Set<HierarchicalNode> getOut()
```
    Returns:
    
    the out
  - setIn
```
public void setIn(Set<HierarchicalNode> in)
```
    Parameters:
    
    in - the in to set
  - getIn
```
public Set<HierarchicalNode> getIn()
```
    Returns:
    
    the in
  - releaseEdges
```
public void releaseEdges()
```
  - getSigma
```
public HierarchicalSigmaSet getSigma()
```
    return the set sigma
  - setSigma
```
public void setSigma(HierarchicalSigmaSet sigma)
```
    return the set sigma
  - getUniqueId
```
public long getUniqueId()
```
    Return the long identifying this node "uniquely" (if in the range of long)
    
    Returns:
  - hashcode
```
public int hashcode()
```
  - parse
```
public void parse(String parse)
           throws SAXException
```
    Throws:
    
    SAXException
  - setLabelCount
```
public void setLabelCount(short intValue)
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - toLongString
```
public String toLongString()
```
  - getShortId
```
public String getShortId()
```
  - getLongId
```
public String getLongId()
```
  - write
```
public String write()
```
  - statesToString
```
public String statesToString()
```
  - statesToString
```
public String statesToString(boolean addValue)
```
  - statesToList
```
public List<byte[]> statesToList()
```
    Initialize and fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1). Note the order in the list is relative to the omdd structure.
    
    Returns:
    
    a list made of all the states as schemata (using *)
  - firstStatesToString
```
public StringBuffer firstStatesToString()
```
    Return a string representation of the first state in the node.
  - isStable
```
public boolean isStable()
```
  - isTransient
```
public boolean isTransient()
```
  - isCycle
```
public boolean isCycle()
```
  - isTerminal
```
public boolean isTerminal()
```
  - setType
```
public void setType(byte type)
```
  - getType
```
public byte getType()
```
  - typeToString
```
public String typeToString()
```
    Return a string representation for the type of this node.
    
    Returns:
    
    the string reprensetation
  - typeToString
```
public static String typeToString(int type)
```
    Return a string representation for a given type.
    
    Parameters:
    
    type - is either TYPE_STABLE_STATEG or TYPE_TERMINAL_CYCLE or TYPE_TRANSIENT_COMPONENT
    
    Returns:
    
    the string reprensetation
  - setTypeFromString
```
public void setTypeFromString(String type)
```
    Set the type from a string
    
    Parameters:
    
    type - a string from the constants TYPE_STABLE_STATE_STRING, TYPE_TERMINAL_CYCLE_STRING...
  - typeFromString
```
public static byte typeFromString(String type)
```
    Return an int representation for a given string
    
    Parameters:
    
    type - is either TYPE_STABLE_STATE_STRING or TYPE_TERMINAL_CYCLE_STRING or TYPE_TRANSIENT_COMPONENT_STRING OR TYPE_CYCLE_STRING
    
    Returns:
    
    the type constant
  - toDot
```
public String toDot()
```
    Description copied from interface: Dotify
    
    Return a dot representation of the object as a String
    
    Specified by:
    
    toDot in interface Dotify
    
    Returns:
    
    a String
  - toDot
```
public String toDot(Object to)
```
    Description copied from interface: Dotify
    
    Return a dot representation of the edge as a String The object is the source of the edge, the first parameter is the target.
    
    Specified by:
    
    toDot in interface Dotify
    
    Returns:
    
    a String
  - compareTo
```
public int compareTo(Object arg0)
```
    Specified by:
    
    compareTo in interface Comparable<Object>

Class HierarchicalNode

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TYPE_TRANSIENT_COMPONENT

TYPE_TRANSIENT_CYCLE

TYPE_TERMINAL_CYCLE

TYPE_STABLE_STATE

TYPE_TRANSIENT_COMPONENT_STRING

TYPE_TERMINAL_CYCLE_STRING

TYPE_TRANSIENT_CYCLE_STRING

TYPE_STABLE_STATE_STRING

TYPE_TRANSIENT_COMPONENT_ALONE_COLOR

TYPE_TRANSIENT_COMPONENT_COLOR

TYPE_TRANSIENT_CYCLE_COLOR

TYPE_EDEN_TRANSIENT_COMPONENT_COLOR

TYPE_TERMINAL_CYCLE_COLOR

TYPE_STABLE_STATE_COLOR

statesSet

Constructor Detail

HierarchicalNode

Method Detail

addAllTheStatesInQueue

addStateToThePile

addState

contains

merge

getSize

updateSize

addEdgeTo

setOut

getOut

setIn

getIn

releaseEdges

getSigma

setSigma

getUniqueId

hashcode

parse

setLabelCount

toString

toLongString

getShortId

getLongId

write

statesToString

statesToString

statesToList

firstStatesToString

isStable

isTransient

isCycle

isTerminal

setType

getType

typeToString

typeToString

setTypeFromString

typeFromString

toDot

toDot

compareTo