Package edu.uci.ics.jung.io

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

  • All Implemented Interfaces:
    org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
    public class GraphMLReader<G extends Hypergraph<V,​E>,​V,​E>
extends org.xml.sax.helpers.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:
    "http://graphml.graphdrawing.org/specification.html"

    • 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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected <T> void addDatum​(java.util.Map<java.lang.String,​GraphMLMetadata<T>> metadata, T current_elt, java.lang.String text)  
      private <T> void addExtraData​(java.util.Map<java.lang.String,​java.lang.String> atts, java.util.Map<java.lang.String,​GraphMLMetadata<T>> metadata_map, T current_elt)  
      protected void assignEdgeSourceTarget​(E e, org.xml.sax.Attributes atts, java.util.Map<java.lang.String,​java.lang.String> edge_atts)  
      void characters​(char[] ch, int start, int length)  
      protected void clearData()  
      protected void createEdge​(org.xml.sax.Attributes atts, GraphMLReader.TagState state)  
      protected void createKey​(org.xml.sax.Attributes atts)  
      protected void createVertex​(org.xml.sax.Attributes atts)  
      void endElement​(java.lang.String uri, java.lang.String name, java.lang.String qName)  
      protected java.util.Map<java.lang.String,​java.lang.String> getAttributeMap​(org.xml.sax.Attributes atts)  
      java.util.Map<E,​java.lang.String> getEdgeDescriptions()  
      com.google.common.collect.BiMap<E,​java.lang.String> getEdgeIDs()
      Returns a bidirectional map relating edges and IDs.
      java.util.Map<java.lang.String,​GraphMLMetadata<E>> getEdgeMetadata()  
      java.util.Map<G,​java.lang.String> getGraphDescriptions()  
      java.util.Map<java.lang.String,​GraphMLMetadata<G>> getGraphMetadata()  
      java.util.Map<V,​java.lang.String> getVertexDescriptions()  
      com.google.common.collect.BiMap<V,​java.lang.String> getVertexIDs()  
      java.util.Map<java.lang.String,​GraphMLMetadata<V>> getVertexMetadata()  
      protected void handleData​(org.xml.sax.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​(java.io.Reader reader, G g)
      Populates the specified graph with the data parsed from the reader.
      void load​(java.lang.String filename, G g)
      Populates the specified graph with the data parsed from the specified file.
      java.util.List<G> loadMultiple​(java.io.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.
      java.util.List<G> loadMultiple​(java.lang.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​(java.io.Reader reader)  
      void startElement​(java.lang.String uri, java.lang.String name, java.lang.String qName, org.xml.sax.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

    • Field Detail

      • saxp

        protected javax.xml.parsers.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 java.lang.String current_key

      • 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,​java.lang.String> vertex_ids

      • edge_ids

        protected com.google.common.collect.BiMap<E,​java.lang.String> edge_ids

      • vertex_metadata

        protected java.util.Map<java.lang.String,​GraphMLMetadata<V>> vertex_metadata

      • edge_metadata

        protected java.util.Map<java.lang.String,​GraphMLMetadata<E>> edge_metadata

      • vertex_desc

        protected java.util.Map<V,​java.lang.String> vertex_desc

      • edge_desc

        protected java.util.Map<E,​java.lang.String> edge_desc

      • graph_desc

        protected java.util.Map<G extends Hypergraph<V,​E>,​java.lang.String> graph_desc

      • hyperedge_vertices

        protected java.util.Collection<V> hyperedge_vertices

      • graphs

        protected java.util.List<G extends Hypergraph<V,​E>> graphs

      • current_text

        protected java.lang.StringBuilder current_text

    • Constructor Detail

      • GraphMLReader

        public GraphMLReader​(com.google.common.base.Supplier<V> vertex_factory,
                     com.google.common.base.Supplier<E> edge_factory)
              throws javax.xml.parsers.ParserConfigurationException,
                     org.xml.sax.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:
        javax.xml.parsers.ParserConfigurationException - if a SAX parser cannot be constructed
        org.xml.sax.SAXException - if the SAX parser factory cannot be constructed

      • GraphMLReader

        public GraphMLReader()
              throws javax.xml.parsers.ParserConfigurationException,
                     org.xml.sax.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:
        javax.xml.parsers.ParserConfigurationException - if a SAX parser cannot be constructed
        org.xml.sax.SAXException - if the SAX parser factory cannot be constructed

    • Method Detail

      • loadMultiple

        public java.util.List<G> loadMultiple​(java.io.Reader reader,
                                      com.google.common.base.Supplier<G> graph_factory)
                               throws java.io.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:
        java.io.IOException - if an error is encountered while parsing the graph

      • loadMultiple

        public java.util.List<G> loadMultiple​(java.lang.String filename,
                                      com.google.common.base.Supplier<G> graph_factory)
                               throws java.io.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:
        java.io.IOException - if an error is encountered while parsing the graph

      • load

        public void load​(java.io.Reader reader,
                 G g)
          throws java.io.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:
        java.io.IOException - if an error is encountered while parsing the graph

      • load

        public void load​(java.lang.String filename,
                 G g)
          throws java.io.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:
        java.io.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​(java.io.Reader reader)
              throws java.io.IOException
        Throws:
        java.io.IOException

      • startElement

        public void startElement​(java.lang.String uri,
                         java.lang.String name,
                         java.lang.String qName,
                         org.xml.sax.Attributes atts)
                  throws org.xml.sax.SAXNotSupportedException
        Specified by:
        startElement in interface org.xml.sax.ContentHandler
        Overrides:
        startElement in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXNotSupportedException

      • addExtraData

        private <T> void addExtraData​(java.util.Map<java.lang.String,​java.lang.String> atts,
                              java.util.Map<java.lang.String,​GraphMLMetadata<T>> metadata_map,
                              T current_elt)
        Type Parameters:
        T -
        Parameters:
        atts -
        metadata_map -
        current_elt -

      • characters

        public void characters​(char[] ch,
                       int start,
                       int length)
                throws org.xml.sax.SAXNotSupportedException
        Specified by:
        characters in interface org.xml.sax.ContentHandler
        Overrides:
        characters in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXNotSupportedException

      • addDatum

        protected <T> void addDatum​(java.util.Map<java.lang.String,​GraphMLMetadata<T>> metadata,
                            T current_elt,
                            java.lang.String text)
                     throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • endElement

        public void endElement​(java.lang.String uri,
                       java.lang.String name,
                       java.lang.String qName)
                throws org.xml.sax.SAXNotSupportedException
        Specified by:
        endElement in interface org.xml.sax.ContentHandler
        Overrides:
        endElement in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXNotSupportedException

      • getAttributeMap

        protected java.util.Map<java.lang.String,​java.lang.String> getAttributeMap​(org.xml.sax.Attributes atts)

      • handleData

        protected void handleData​(org.xml.sax.Attributes atts)
                   throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • createKey

        protected void createKey​(org.xml.sax.Attributes atts)
                  throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • createVertex

        protected void createVertex​(org.xml.sax.Attributes atts)
                     throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • createEdge

        protected void createEdge​(org.xml.sax.Attributes atts,
                          GraphMLReader.TagState state)
                   throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • assignEdgeSourceTarget

        protected void assignEdgeSourceTarget​(E e,
                                      org.xml.sax.Attributes atts,
                                      java.util.Map<java.lang.String,​java.lang.String> edge_atts)
                               throws org.xml.sax.SAXNotSupportedException
        Throws:
        org.xml.sax.SAXNotSupportedException

      • getVertexIDs

        public com.google.common.collect.BiMap<V,​java.lang.String> getVertexIDs()
        Returns:
        a bidirectional map relating vertices and IDs.

      • getEdgeIDs

        public com.google.common.collect.BiMap<E,​java.lang.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 java.util.Map<java.lang.String,​GraphMLMetadata<G>> getGraphMetadata()
        Returns:
        a map from graph type name to type metadata

      • getVertexMetadata

        public java.util.Map<java.lang.String,​GraphMLMetadata<V>> getVertexMetadata()
        Returns:
        a map from vertex type name to type metadata

      • getEdgeMetadata

        public java.util.Map<java.lang.String,​GraphMLMetadata<E>> getEdgeMetadata()
        Returns:
        a map from edge type name to type metadata

      • getGraphDescriptions

        public java.util.Map<G,​java.lang.String> getGraphDescriptions()
        Returns:
        a map from graphs to graph descriptions

      • getVertexDescriptions

        public java.util.Map<V,​java.lang.String> getVertexDescriptions()
        Returns:
        a map from vertices to vertex descriptions

      • getEdgeDescriptions

        public java.util.Map<E,​java.lang.String> getEdgeDescriptions()
        Returns:
        a map from edges to edge descriptions