AbstractGraph (GINsim 3.0.0b-SNAPSHOT API)

java.lang.Object
- org.ginsim.core.graph.AbstractGraph<V,E>

Type Parameters:

V - the type of vertices

E - the type of edges

All Implemented Interfaces:

Graph<V,E>, GraphModel<V,E>, GraphViewListener

Direct Known Subclasses:

AbstractDerivedGraph, RegulatoryGraphImpl, TreeImpl
```
public abstract class AbstractGraph<V,E extends Edge<V>>
extends Object
implements Graph<V,E>, GraphViewListener
```
Base class for graphs using a storage backend: it provides generic methods and storage abstraction. The actual structure is stored in the graph backend, and classes deriving from this one can provide specialised methods.

Author:

Lionel Spinelli, Aurelien Naldi

Field Summary

Fields
Modifier and Type Field and Description

protected Map<String,String> attributes

protected Annotation graphAnnotation

protected String graphName

static String ZIP_PREFIX

Fields
Modifier and Type	Field and Description
`protected Map<String,String>`	`attributes`
`protected Annotation`	`graphAnnotation`
`protected String`	`graphName`
`static String`	`ZIP_PREFIX`

Constructor Summary

Constructors
Modifier Constructor and Description

protected AbstractGraph(GraphFactory factory)
Create a new graph with the default back-end.

Constructors
Modifier	Constructor and Description
`protected`	`AbstractGraph(GraphFactory factory)` Create a new graph with the default back-end.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addEdge(E edge)` Add an edge to this graph structure.
`boolean`	`addNode(V node)` Add a node to this graph structure
`void`	`addViewListener(GraphViewListener listener)` Add a listener for view change events.
`boolean`	`containsEdge(V from, V to)`
`boolean`	`containsNode(V node)`
`void`	`copyView(Graph<V,E> src, ViewCopyHelper<Graph<V,E>,V,E> helper)` Transfer view settings from a related graph.
`void`	`damage(Object o)`
`protected abstract List<?>`	`doMerge(Graph<V,E> graph)` Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level
`protected void`	`doSave(OutputStreamWriter osw, Collection<V> nodes, Collection<E> edges)` save implementation for a specific graph type.
`void`	`fireGraphChange(GraphChangeType type, Object data)` The graph has changed, all listeners will be notified.
`void`	`fireMetaChange()`
`Annotation`	`getAnnotation()` Give access to the annotation associated with this graph.
`Map<String,String>`	`getAttributes()` Retrieve graph-level attributes
`protected EdgeAttributesReader`	`getCachedEdgeAttributeReader()`
`protected NodeAttributesReader`	`getCachedNodeAttributeReader()`
`Dimension`	`getDimension()` Get the global bounds of the graph.
`String`	`getDisplayName(V node)` Retrieve the name to use when displaying a graph node.
`E`	`getEdge(V source, V target)`
`EdgeAttributesReader`	`getEdgeAttributeReader()` Give access to the attribute reader of edges
`Collection<E>`	`getEdges()`
`V`	`getExistingNode(V node)`
`protected GINMLWriter`	`getGINMLWriter()`
`String`	`getGraphName()` Give access to the name of the graph
`protected String`	`getGraphZipName()` Return the zip extension for the graph type
`Collection<E>`	`getIncomingEdges(V node)`
`NodeAttributesReader`	`getNodeAttributeReader()` Give access to the attribute reader of vertices
`V`	`getNodeByName(String id)` Give access to the node named with the given name
`int`	`getNodeCount()` Return the number of node in this graph
`abstract int`	`getNodeOrderSize()` Return the size of the node order
`Collection<V>`	`getNodes()` Return the Collection of the graph nodes
`Collection<E>`	`getOutgoingEdges(V node)`
`List<E>`	`getShortestPath(V source, V target)` Find the shortest path between the two given vertices
`List<Set<V>>`	`getStronglyConnectedComponents()` Return a list of set of node, each set containing a strongly connected component of the graph
`StyleManager<V,E>`	`getStyleManager()` Retrieve the style manager for this graph.
`abstract Graph<V,E>`	`getSubgraph(Collection<V> node, Collection<E> edges)` Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph
`boolean`	`isEmpty()`
`List<?>`	`merge(Graph<V,E> graph)` Launch the merge method on the specialized graph level, merging the current graph with the given one and fire a graph change event
`void`	`refresh(Object o)` Declare an object visual setting change
`boolean`	`removeEdge(E edge)` Remove an edge from the graph.
`boolean`	`removeNode(V node)` Remove a node from the graph.
`void`	`repaint()` The full view was changed.
`void`	`save(String save_path)` Save this graph.
`void`	`save(String save_path, Collection<V> vertices, Collection<E> edges)` Save some components of this graph.
`List<V>`	`searchNodes(String regexp)` Search the vertices with ID matching the given regular expression.
`void`	`setAttribute(String name, String value)`
`void`	`setGraphName(String graph_name)` changes (if success) the name associated with this graph.

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

- Field Detail
  - ZIP_PREFIX
```
public static final String ZIP_PREFIX
```
    See Also:
    
    Constant Field Values
  - graphName
```
protected String graphName
```
  - attributes
```
protected Map<String,String> attributes
```
  - graphAnnotation
```
protected Annotation graphAnnotation
```
- Constructor Detail
  - AbstractGraph
```
protected AbstractGraph(GraphFactory factory)
```
    Create a new graph with the default back-end.
- Method Detail
  - getGraphName
```
public String getGraphName()
```
    Give access to the name of the graph
    
    Specified by:
    
    getGraphName in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    the name associated with this graph.
  - setGraphName
```
public void setGraphName(String graph_name)
                  throws GsException
```
    changes (if success) the name associated with this graph. By default only valid xmlid are accepted.
    
    Specified by:
    
    setGraphName in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    graph_name - the new name.
    
    Throws:
    
    GsException - if the name is invalid.
  - getDisplayName
```
public String getDisplayName(V node)
```
    Description copied from interface: Graph
    
    Retrieve the name to use when displaying a graph node.
    
    Specified by:
    
    getDisplayName in interface Graph<V,E extends Edge<V>>
    
    Returns:
  - getAttributes
```
public Map<String,String> getAttributes()
```
    Description copied from interface: Graph
    
    Retrieve graph-level attributes
    
    Specified by:
    
    getAttributes in interface Graph<V,E extends Edge<V>>
    
    Returns:
    
    a map of attribute values, it can be empty but should not be null
  - setAttribute
```
public void setAttribute(String name,
                         String value)
```
    Specified by:
    
    setAttribute in interface Graph<V,E extends Edge<V>>
  - getGraphZipName
```
protected String getGraphZipName()
```
    Return the zip extension for the graph type
    
    Returns:
    
    the zip extension for the graph type
  - addNode
```
public boolean addNode(V node)
```
    Add a node to this graph structure
    
    Specified by:
    
    addNode in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    node -
    
    Returns:
    
    the created node
  - addEdge
```
public boolean addEdge(E edge)
```
    Add an edge to this graph structure.
    
    Specified by:
    
    addEdge in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    edge -
    
    Returns:
    
    the created edge
  - removeNode
```
public boolean removeNode(V node)
```
    Remove a node from the graph.
    
    Specified by:
    
    removeNode in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    node -
    
    Returns:
    
    true if the node was effectively removed
  - removeEdge
```
public boolean removeEdge(E edge)
```
    Remove an edge from the graph.
    
    Specified by:
    
    removeEdge in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    edge -
    
    Returns:
    
    true if the edge was effectively removed
  - getNodeCount
```
public int getNodeCount()
```
    Description copied from interface: GraphModel
    
    Return the number of node in this graph
    
    Specified by:
    
    getNodeCount in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    the number of node in this graph.
  - getEdge
```
public E getEdge(V source,
                 V target)
```
    Specified by:
    
    getEdge in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    source -
    
    target -
    
    Returns:
    
    the edge between source and target or null if not found.
  - getEdges
```
public Collection<E> getEdges()
```
    Specified by:
    
    getEdges in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    a Collection of the graph edges.
  - getNodes
```
public Collection<V> getNodes()
```
    Description copied from interface: GraphModel
    
    Return the Collection of the graph nodes
    
    Specified by:
    
    getNodes in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    a Collection of the graph vertices.
  - getStronglyConnectedComponents
```
public List<Set<V>> getStronglyConnectedComponents()
```
    Return a list of set of node, each set containing a strongly connected component of the graph
    
    Specified by:
    
    getStronglyConnectedComponents in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    a list of set of node, each set containing a strongly connected component of the graph
  - getNodeByName
```
public V getNodeByName(String id)
```
    Give access to the node named with the given name
    
    Specified by:
    
    getNodeByName in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    id - name of a node
    
    Returns:
    
    the node corresponding to this unique id or null if not found.
  - getNodeOrderSize
```
public abstract int getNodeOrderSize()
```
    Return the size of the node order
    
    Specified by:
    
    getNodeOrderSize in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    the size of the node order
  - searchNodes
```
public List<V> searchNodes(String regexp)
```
    Search the vertices with ID matching the given regular expression. Other kind of graph could overwrite this method.
    
    Specified by:
    
    searchNodes in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    regexp - the regular expression node ID must match to be selected
    
    Returns:
    
    a List of vertices
  - containsNode
```
public boolean containsNode(V node)
```
    Specified by:
    
    containsNode in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    true if the node is in the graph, false if not.
  - getExistingNode
```
public V getExistingNode(V node)
```
    Specified by:
    
    getExistingNode in interface GraphModel<V,E extends Edge<V>>
  - containsEdge
```
public boolean containsEdge(V from,
                            V to)
```
    Specified by:
    
    containsEdge in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    true if an edge between the two provided vertices exists in the graph, false if not.
  - getIncomingEdges
```
public Collection<E> getIncomingEdges(V node)
```
    Specified by:
    
    getIncomingEdges in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    incoming edges of the given node.
  - getOutgoingEdges
```
public Collection<E> getOutgoingEdges(V node)
```
    Specified by:
    
    getOutgoingEdges in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    outgoing edges of the given node.
  - getShortestPath
```
public List<E> getShortestPath(V source,
                               V target)
```
    Description copied from interface: GraphModel
    
    Find the shortest path between the two given vertices
    
    Specified by:
    
    getShortestPath in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    source - the node at the beginning of the searched path
    
    target - the node at the end of the searched path
    
    Returns:
    
    the list of edges composing the shortest path
  - addViewListener
```
public void addViewListener(GraphViewListener listener)
```
    Description copied from interface: Graph
    
    Add a listener for view change events. Note: only one listener is supported: the GraphGUI
    
    Specified by:
    
    addViewListener in interface Graph<V,E extends Edge<V>>
  - refresh
```
public void refresh(Object o)
```
    Declare an object visual setting change
    
    Specified by:
    
    refresh in interface GraphViewListener
    
    Parameters:
    
    o -
  - repaint
```
public void repaint()
```
    Description copied from interface: GraphViewListener
    
    The full view was changed.
    
    Specified by:
    
    repaint in interface GraphViewListener
  - damage
```
public void damage(Object o)
```
  - getStyleManager
```
public StyleManager<V,E> getStyleManager()
```
    Description copied from interface: Graph
    
    Retrieve the style manager for this graph.
    
    Specified by:
    
    getStyleManager in interface Graph<V,E extends Edge<V>>
    
    Returns:
    
    the style manager
  - getEdgeAttributeReader
```
public EdgeAttributesReader getEdgeAttributeReader()
```
    Description copied from interface: Graph
    
    Give access to the attribute reader of edges
    
    Specified by:
    
    getEdgeAttributeReader in interface Graph<V,E extends Edge<V>>
    
    Returns:
    
    the attribute reader of edges
  - getNodeAttributeReader
```
public NodeAttributesReader getNodeAttributeReader()
```
    Description copied from interface: Graph
    
    Give access to the attribute reader of vertices
    
    Specified by:
    
    getNodeAttributeReader in interface Graph<V,E extends Edge<V>>
    
    Returns:
    
    the attribute reader of vertices
  - getCachedEdgeAttributeReader
```
protected EdgeAttributesReader getCachedEdgeAttributeReader()
```
  - getCachedNodeAttributeReader
```
protected NodeAttributesReader getCachedNodeAttributeReader()
```
  - getDimension
```
public Dimension getDimension()
```
    Description copied from interface: Graph
    
    Get the global bounds of the graph.
    
    Specified by:
    
    getDimension in interface Graph<V,E extends Edge<V>>
    
    Returns:
  - isEmpty
```
public boolean isEmpty()
```
    Returns:
    
    true if the graph is empty
  - merge
```
public List<?> merge(Graph<V,E> graph)
```
    Launch the merge method on the specialized graph level, merging the current graph with the given one and fire a graph change event
    
    Specified by:
    
    merge in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    graph - the graph to merge with the current one
    
    Returns:
  - doMerge
```
protected abstract List<?> doMerge(Graph<V,E> graph)
```
    Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level
    
    Parameters:
    
    graph -
    
    Returns:
  - getSubgraph
```
public abstract Graph<V,E> getSubgraph(Collection<V> node,
                                       Collection<E> edges)
```
    Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph
    
    Specified by:
    
    getSubgraph in interface GraphModel<V,E extends Edge<V>>
    
    Parameters:
    
    node - the list of node to include in the desired sub-graph
    
    edges - the list of edges to include in the sub-graph
    
    Returns:
    
    a Graph containing clones of initial vertices and edges structured as they are in the current graph
  - getAnnotation
```
public Annotation getAnnotation()
```
    Give access to the annotation associated with this graph.
    
    Specified by:
    
    getAnnotation in interface GraphModel<V,E extends Edge<V>>
    
    Returns:
    
    the association associated with this graph
  - save
```
public void save(String save_path)
          throws GsException
```
    Description copied from interface: Graph
    
    Save this graph.
    
    Specified by:
    
    save in interface Graph<V,E extends Edge<V>>
    
    Throws:
    
    GsException
  - save
```
public void save(String save_path,
                 Collection<V> vertices,
                 Collection<E> edges)
          throws GsException
```
    Description copied from interface: Graph
    
    Save some components of this graph.
    
    Specified by:
    
    save in interface Graph<V,E extends Edge<V>>
    
    Throws:
    
    GsException
  - copyView
```
public void copyView(Graph<V,E> src,
                     ViewCopyHelper<Graph<V,E>,V,E> helper)
```
    Description copied from interface: Graph
    
    Transfer view settings from a related graph. The position and styles of matching nodes and edges will be copied from the source graph to the current one
    
    Specified by:
    
    copyView in interface Graph<V,E extends Edge<V>>
    
    Parameters:
    
    src - the source graph
  - doSave
```
protected final void doSave(OutputStreamWriter osw,
                            Collection<V> nodes,
                            Collection<E> edges)
                     throws GsException
```
    save implementation for a specific graph type.
    
    Parameters:
    
    osw - stream writer
    
    nodes - vertices that should be saved (can not be null)
    
    edges - edges that should be saved (can not be null)
    
    Throws:
    
    GsException
  - getGINMLWriter
```
protected GINMLWriter getGINMLWriter()
```
  - fireMetaChange
```
public void fireMetaChange()
```
  - fireGraphChange
```
public void fireGraphChange(GraphChangeType type,
                            Object data)
```
    Description copied from interface: Graph
    
    The graph has changed, all listeners will be notified. It will also be marked as unsaved.
    
    Specified by:
    
    fireGraphChange in interface Graph<V,E extends Edge<V>>

Class AbstractGraph<V,E extends Edge<V>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ZIP_PREFIX

graphName

attributes

graphAnnotation

Constructor Detail

AbstractGraph

Method Detail

getGraphName

setGraphName

getDisplayName

getAttributes

setAttribute

getGraphZipName

addNode

addEdge

removeNode

removeEdge

getNodeCount

getEdge

getEdges

getNodes

getStronglyConnectedComponents

getNodeByName

getNodeOrderSize

searchNodes

containsNode

getExistingNode

containsEdge

getIncomingEdges

getOutgoingEdges

getShortestPath

addViewListener

refresh

repaint

damage

getStyleManager

getEdgeAttributeReader

getNodeAttributeReader

getCachedEdgeAttributeReader

getCachedNodeAttributeReader

getDimension

isEmpty

merge

doMerge

getSubgraph

getAnnotation

save

save

copyView

doSave

getGINMLWriter

fireMetaChange

fireGraphChange