edu.uci.ics.jung.io.GraphMLReader<G,V,E>

All Implemented Interfaces:: ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class GraphMLReader<G extends Hypergraph<V,E>,V,E> extends DefaultHandler

Reads in data from a GraphML-formatted file and generates graphs based on that data. Currently supports the following parts of the GraphML specification:

graphs and hypergraphs
directed and undirected edges
graph, vertex, edge data
graph, vertex, edge descriptions and data descriptions
vertex and edge IDs

Each of these is exposed via appropriate get methods. Does not currently support nested graphs or ports.

Note that the user is responsible for supplying a graph Factory that can support the edge types in the supplied GraphML file. If the graph generated by the Factory is not compatible (for example: if the graph does not accept directed edges, and the GraphML file contains a directed edge) then the results are graph-implementation-dependent.

See Also:

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

protected static enum

GraphMLReader.KeyType

protected static enum

GraphMLReader.TagState
Field Summary

Fields

Modifier and Type

Field

Description

protected E

current_edge

protected G

current_graph

protected String

current_key

protected LinkedList<GraphMLReader.TagState>

current_states

protected StringBuilder

current_text

protected V

current_vertex

protected EdgeType

default_edgetype

protected Map<E,String>

edge_desc

protected com.google.common.base.Supplier<E>

edge_factory

protected com.google.common.collect.BiMap<E,String>

edge_ids

protected Map<String,GraphMLMetadata<E>>

edge_metadata

protected Map<G,String>

graph_desc

protected com.google.common.base.Supplier<G>

graph_factory

protected Map<String,GraphMLMetadata<G>>

graph_metadata

protected List<G>

graphs

protected Collection<V>

hyperedge_vertices

protected GraphMLReader.KeyType

key_type

protected SAXParser

saxp

protected com.google.common.collect.BiMap<String,GraphMLReader.TagState>

tag_state

protected Map<V,String>

vertex_desc

protected com.google.common.base.Supplier<V>

vertex_factory

protected com.google.common.collect.BiMap<V,String>

vertex_ids

protected Map<String,GraphMLMetadata<V>>

vertex_metadata
Constructor Summary

Constructors

Constructor

Description

GraphMLReader()

Creates a GraphMLReader instance that assigns the vertex and edge id strings to be the vertex and edge objects, as well as their IDs.

GraphMLReader(com.google.common.base.Supplier<V> vertex_factory, com.google.common.base.Supplier<E> edge_factory)

Creates a GraphMLReader instance with the specified vertex and edge factories.
Method Summary

Modifier and Type

Method

Description

protected <T> void

addDatum(Map<String,GraphMLMetadata<T>> metadata, T current_elt, String text)

protected void

assignEdgeSourceTarget(E e, Attributes atts, Map<String,String> edge_atts)

void

characters(char[] ch, int start, int length)

protected void

clearData()

protected void

createEdge(Attributes atts, GraphMLReader.TagState state)

protected void

createKey(Attributes atts)

protected void

createVertex(Attributes atts)

void

endElement(String uri, String name, String qName)

protected Map<String,String>

getAttributeMap(Attributes atts)

Map<E,String>

getEdgeDescriptions()

com.google.common.collect.BiMap<E,String>

getEdgeIDs()

Returns a bidirectional map relating edges and IDs.

Map<String,GraphMLMetadata<E>>

getEdgeMetadata()

Map<G,String>

getGraphDescriptions()

Map<String,GraphMLMetadata<G>>

getGraphMetadata()

Map<V,String>

getVertexDescriptions()

com.google.common.collect.BiMap<V,String>

getVertexIDs()

Map<String,GraphMLMetadata<V>>

getVertexMetadata()

protected void

handleData(Attributes atts)

protected void

initializeData()

This is separate from initialize() because these data structures are shared among all graphs loaded (i.e., they're defined inside graphml rather than graph.

void

load(Reader reader, G g)

Populates the specified graph with the data parsed from the reader.

void

load(String filename, G g)

Populates the specified graph with the data parsed from the specified file.

List<G>

loadMultiple(Reader reader, com.google.common.base.Supplier<G> graph_factory)

Returns a list of the graphs parsed from the specified reader, as created by the specified Supplier.

List<G>

loadMultiple(String filename, com.google.common.base.Supplier<G> graph_factory)

Returns a list of the graphs parsed from the specified file, as created by the specified Supplier.

protected void

parse(Reader reader)

void

startElement(String uri, String name, String qName, Attributes atts)

Methods inherited from class org.xml.sax.helpers.DefaultHandler
endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

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

Methods inherited from interface org.xml.sax.ContentHandler
declaration

Field Details
- saxp
  
  protected SAXParser saxp
- default_edgetype
  
  protected EdgeType default_edgetype
- current_graph
  
  protected G extends Hypergraph<V,E> current_graph
- current_vertex
  
  protected V current_vertex
- current_edge
  
  protected E current_edge
- current_key
  
  protected String current_key
- current_states
  
  protected LinkedList<GraphMLReader.TagState> current_states
- tag_state
  
  protected com.google.common.collect.BiMap<String,GraphMLReader.TagState> tag_state
- graph_factory
  
  protected com.google.common.base.Supplier<G extends Hypergraph<V,E>> graph_factory
- vertex_factory
  
  protected com.google.common.base.Supplier<V> vertex_factory
- edge_factory
  
  protected com.google.common.base.Supplier<E> edge_factory
- vertex_ids
  
  protected com.google.common.collect.BiMap<V,String> vertex_ids
- edge_ids
  
  protected com.google.common.collect.BiMap<E,String> edge_ids
- graph_metadata
  
  protected Map<String,GraphMLMetadata<G extends Hypergraph<V,E>>> graph_metadata
- vertex_metadata
  
  protected Map<String,GraphMLMetadata<V>> vertex_metadata
- edge_metadata
  
  protected Map<String,GraphMLMetadata<E>> edge_metadata
- vertex_desc
  
  protected Map<V,String> vertex_desc
- edge_desc
  
  protected Map<E,String> edge_desc
- graph_desc
  
  protected Map<G extends Hypergraph<V,E>,String> graph_desc
- key_type
  
  protected GraphMLReader.KeyType key_type
- hyperedge_vertices
  
  protected Collection<V> hyperedge_vertices
- graphs
  
  protected List<G extends Hypergraph<V,E>> graphs
- current_text
  
  protected StringBuilder current_text
Constructor Details
- GraphMLReader
  
  public GraphMLReader(com.google.common.base.Supplier<V> vertex_factory, com.google.common.base.Supplier<E> edge_factory) throws ParserConfigurationException, SAXException
  
  Creates a GraphMLReader instance with the specified vertex and edge factories.
  
  Parameters:
  
  vertex_factory - the vertex supplier to use to create vertex objects
  
  edge_factory - the edge supplier to use to create edge objects
  
  Throws:
  
  ParserConfigurationException - if a SAX parser cannot be constructed
  
  SAXException - if the SAX parser factory cannot be constructed
- GraphMLReader
  
  public GraphMLReader() throws ParserConfigurationException, SAXException
  
  Creates a GraphMLReader instance that assigns the vertex and edge id strings to be the vertex and edge objects, as well as their IDs. Note that this requires that (a) each edge have a valid ID, which is not normally a requirement for edges in GraphML, and (b) that the vertex and edge types be assignment-compatible with String.
  
  Throws:
  
  ParserConfigurationException - if a SAX parser cannot be constructed
  
  SAXException - if the SAX parser factory cannot be constructed
Method Details
- loadMultiple
  
  public List<G> loadMultiple(Reader reader, com.google.common.base.Supplier<G> graph_factory) throws IOException
  
  Returns a list of the graphs parsed from the specified reader, as created by the specified Supplier.
  
  Parameters:
  
  reader - the source of the graph data in GraphML format
  
  graph_factory - used to build graph instances
  
  Returns:
  
  the graphs parsed from the specified reader
  
  Throws:
  
  IOException - if an error is encountered while parsing the graph
- loadMultiple
  
  public List<G> loadMultiple(String filename, com.google.common.base.Supplier<G> graph_factory) throws IOException
  
  Returns a list of the graphs parsed from the specified file, as created by the specified Supplier.
  
  Parameters:
  
  filename - the source of the graph data in GraphML format
  
  graph_factory - used to build graph instances
  
  Returns:
  
  the graphs parsed from the specified file
  
  Throws:
  
  IOException - if an error is encountered while parsing the graph
- load
  
  public void load(Reader reader, G g) throws IOException
  
  Populates the specified graph with the data parsed from the reader.
  
  Parameters:
  
  reader - the source of the graph data in GraphML format
  
  g - the graph instance to populate
  
  Throws:
  
  IOException - if an error is encountered while parsing the graph
- load
  
  public void load(String filename, G g) throws IOException
  
  Populates the specified graph with the data parsed from the specified file.
  
  Parameters:
  
  filename - the source of the graph data in GraphML format
  
  g - the graph instance to populate
  
  Throws:
  
  IOException - if an error is encountered while parsing the graph
- clearData
  
  protected void clearData()
- initializeData
  
  protected void initializeData()
  
  This is separate from initialize() because these data structures are shared among all graphs loaded (i.e., they're defined inside graphml rather than graph.
- parse
  
  protected void parse(Reader reader) throws IOException
  
  Throws:
  
  IOException
- startElement
  
  public void startElement(String uri, String name, String qName, Attributes atts) throws SAXNotSupportedException
  
  Specified by:
  
  startElement in interface ContentHandler
  
  Overrides:
  
  startElement in class DefaultHandler
  
  Throws:
  
  SAXNotSupportedException
- characters
  
  public void characters(char[] ch, int start, int length) throws SAXNotSupportedException
  
  Specified by:
  
  characters in interface ContentHandler
  
  Overrides:
  
  characters in class DefaultHandler
  
  Throws:
  
  SAXNotSupportedException
- addDatum
  
  protected <T> void addDatum(Map<String,GraphMLMetadata<T>> metadata, T current_elt, String text) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- endElement
  
  public void endElement(String uri, String name, String qName) throws SAXNotSupportedException
  
  Specified by:
  
  endElement in interface ContentHandler
  
  Overrides:
  
  endElement in class DefaultHandler
  
  Throws:
  
  SAXNotSupportedException
- getAttributeMap
  
  protected Map<String,String> getAttributeMap(Attributes atts)
- handleData
  
  protected void handleData(Attributes atts) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- createKey
  
  protected void createKey(Attributes atts) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- createVertex
  
  protected void createVertex(Attributes atts) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- createEdge
  
  protected void createEdge(Attributes atts, GraphMLReader.TagState state) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- assignEdgeSourceTarget
  
  protected void assignEdgeSourceTarget(E e, Attributes atts, Map<String,String> edge_atts) throws SAXNotSupportedException
  
  Throws:
  
  SAXNotSupportedException
- getVertexIDs
  
  public com.google.common.collect.BiMap<V,String> getVertexIDs()
  
  Returns:
  
  a bidirectional map relating vertices and IDs.
- getEdgeIDs
  
  public com.google.common.collect.BiMap<E,String> getEdgeIDs()
  
  Returns a bidirectional map relating edges and IDs. This is not guaranteed to always be populated (edge IDs are not required in GraphML files.
  
  Returns:
  
  a bidirectional map relating edges and IDs.
- getGraphMetadata
  
  public Map<String,GraphMLMetadata<G>> getGraphMetadata()
  
  Returns:
  
  a map from graph type name to type metadata
- getVertexMetadata
  
  public Map<String,GraphMLMetadata<V>> getVertexMetadata()
  
  Returns:
  
  a map from vertex type name to type metadata
- getEdgeMetadata
  
  public Map<String,GraphMLMetadata<E>> getEdgeMetadata()
  
  Returns:
  
  a map from edge type name to type metadata
- getGraphDescriptions
  
  public Map<G,String> getGraphDescriptions()
  
  Returns:
  
  a map from graphs to graph descriptions
- getVertexDescriptions
  
  public Map<V,String> getVertexDescriptions()
  
  Returns:
  
  a map from vertices to vertex descriptions
- getEdgeDescriptions
  
  public Map<E,String> getEdgeDescriptions()
  
  Returns:
  
  a map from edges to edge descriptions

Class GraphMLReader<G extends Hypergraph<V,E>,V,E>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.xml.sax.helpers.DefaultHandler

Methods inherited from class java.lang.Object

Methods inherited from interface org.xml.sax.ContentHandler

Field Details

saxp

default_edgetype

current_graph

current_vertex

current_edge

current_key

current_states

tag_state

graph_factory

vertex_factory

edge_factory

vertex_ids

edge_ids

graph_metadata

vertex_metadata

edge_metadata

vertex_desc

edge_desc

graph_desc

key_type

hyperedge_vertices

graphs

current_text

Constructor Details

GraphMLReader

GraphMLReader

Method Details

loadMultiple

loadMultiple

load

load

clearData

initializeData

parse

startElement

characters

addDatum

endElement

getAttributeMap

handleData

createKey

createVertex

createEdge

assignEdgeSourceTarget

getVertexIDs

getEdgeIDs

getGraphMetadata

getVertexMetadata

getEdgeMetadata

getGraphDescriptions

getVertexDescriptions

getEdgeDescriptions