com.hp.hpl.guess
Class Graph

java.lang.Object
  edu.uci.ics.jung.utils.UserDataDelegate
      edu.uci.ics.jung.graph.impl.AbstractArchetypeGraph
          edu.uci.ics.jung.graph.impl.AbstractSparseGraph
              edu.uci.ics.jung.graph.impl.SparseGraph
                  com.hp.hpl.guess.Graph

All Implemented Interfaces:

ArchetypeGraph, Cloneable, Graph, NumberEdgeValue, UserDataContainer

Direct Known Subclasses:

StateGraph

public class Graph

extends SparseGraph

implements NumberEdgeValue

Nested Class Summary

Nested classes inherited from class edu.uci.ics.jung.utils.UserDataContainer

UserDataContainer.CopyAction

Field Summary

Fields inherited from interface edu.uci.ics.jung.graph.Graph

DIRECTED_EDGE, NOT_PARALLEL_EDGE, SIMPLE_EDGE, UNDIRECTED_EDGE

Fields inherited from interface edu.uci.ics.jung.graph.ArchetypeGraph

SUBSET_MANAGER

Constructor Summary

Graph(FrameListener display, InterpreterAbstraction interp)
create a new graph.

Graph(FrameListener display, InterpreterAbstraction interp, boolean multiedge)
create a new graph.

Method Summary

void	add(PySequence seq) add nodes and edges from the graph
DirectedEdge	addDirectedEdge(Node source, Node dest) user's API for adding a new directed edge to the graph and database
DirectedEdge	addDirectedEdgeWID(Node source, Node dest, int id) user's API for adding a new directed edge to the graph and database
Edge	addEdge(Edge e) used to load edges from the database into the graph
UndirectedEdge	addEdge(Node node1, Node node2) user's API shortcut for adding a new undirected edge.
Field	addEdgeField(String fieldName, int sqlType, Object defaultValue)
Edge	addEdgeNoCheck(Edge e) use this if you know the storage object already contains the edge.
Node	addNode(Node n) used to load nodes from the database into the graph
Node	addNode(String name) user's API for adding a new node to the graph and database
Field	addNodeField(String fieldName, int sqlType, Object defaultValue)
UndirectedEdge	addUndirectedEdge(Node node1, Node node2)
UndirectedEdge	addUndirectedEdgeWID(Node node1, Node node2, int id)
Set	biComponentClusters() do Bi-Component Clustering
void	binPackLayout() packs all nodes
void	binPackLayout(boolean rescale) packs all nodes
void	centerAfterLayout(boolean state) should we center after doing a layout disable this to control it yourself
void	circleLayout() places all nodes in a circle
void	circleLayout(Field f, Node c) places all nodes in a circle with node c in the middle and its neighbors around that center with a radius proportional to field f (all nodes that are not neighbors of c will be left as is)
void	circleLayout(Field f, Node c, double xorigin, double yorigin) places all nodes in a circle with node c in the middle and its neighbors around that center with a radius proportional to field f (all nodes that are not neighbors of c will be left as is)
static Set	clusters(Graph graph, GraphClusterer clusterer) meta clustering algorithm, takes a clustering algorithm and a graph and returns a set of sets
void	colorize(Field f)
void	colorize(Field f, Color start, Color end)
void	colorize(Field f, Color start, Color middle, Color end)
void	colorize(Field f, String start, String end)
void	colorize(Field f, String start, String middle, String end)
Set	complement(GraphElement t) returns all nodes/edges in the graph that are NOT the argument node/edge
Set	complement(PySequence seq) returns the complement (e.g.
void	computeAbstractRanker(AbstractRanker centrality, String guessKey, ArchetypeGraph ag) computes the ranking for nodes or edges and deposits the results based on guessKey
void	computeBetweennessCentrality()
void	computeDegreeDistributionRank()
void	computeDegrees()
void	computeHITS()
void	computePageRank()
void	computeRandomWalkBetweenness()
void	dagLayout() DAG
double	density()
Set	edgeBetweennessClusters(int numEdgesToRemove) do Edge betweenness clustering
Set	exactFlowCommunity(int cohesion) doesn't do anything right now
void	exportGDF(String filename)
void	frLayout() Fruchterman-Rheingold, puts nodes in 1000 x 1000 square
void	frLayout(int width, int height) Fruchterman-Rheingold into a width x height grid
void	gemLayout() GEM Layout
Edge	getEdgeByID(Integer id) lookup a edge by id
EdgeSchema	getEdgeSchema()
long	getLastModTime() get the time of last modification
Node	getNodeByName(String name) lookup a node by name
Set	getNodes()
NodeSchema	getNodeSchema()
Number	getNumber(ArchetypeEdge e) for NumberEdgeValue interface, returns the weight of the given edge.
double	getPageRankBias()
Collection	groupAndSortBy(Field field)
Collection	groupAndSortBy(PySequence seq, Field field)
Collection	groupAndSortEdgesBy(String field)
Collection	groupAndSortNodesBy(String field)
Collection	groupBy(Field field)
Collection	groupBy(PySequence seq, Field field)
Collection	groupEdgesBy(String field)
Collection	groupNodesBy(String field)
void	hideDisconnected()
void	isomLayout() ISOM Layout, asks every 30 seconds if you want to continue
void	isomLayout(int max) ISOM Layout for max steps
void	jfrLayout() the JUNG Fructerman-Rheingold Layout
void	jkkLayout1() the JUNG Kamada-Kawai (regular)
void	jkkLayout2() the JUNG Kamada-Kawai (int)
void	jSpringLayout() the JUNG Spring Layout (seems a little broken).
void	jSpringLayout(int max) run the JUNG spring layout for max iterations
void	kkLayout() Kamada-Kawai, puts nodes in 1000 x 1000 square
void	kkLayout(int width, int height) Kamada-Kawai into a width x height grid
void	layout(Layout lay) basic layout command, runs until completes or 30 seconds depending on if the layout is iterative
void	layout(Layout lay, int mi) runs the layout for some number of iterations (mi).
void	makeBarabasiAlbertRandom(int vert, int edges, int evolve)
void	makeEppsteinRandom(int nodes, int edges, int r)
void	makeErdosRenyiRandom(int nodes, double p)
void	makeFromDL(String filename)
void	makeFromGDF(String filename)
void	makeFromGenerator(GraphGenerator gg)
void	makeFromGML(String filename)
void	makeFromPajek(String filename)
void	makeKleinbergRandom(int nodes, double clust)
void	makeLattice1DRandom(int nodes, boolean tor)
void	makeLattice2DRandom(int nodes, boolean tor)
void	makeSimpleDirectedRandom(int nodes, int edges)
void	makeSimpleRandom(int nodes, int edges)
void	mdsLayout() Multidimensional scaling layout based on edge weight
void	morph(int state, long duration)
void	morph(String state, long duration)
void	moveLayout(double newX, double newY)
void	moveLayout(int newX, int newY) moves the nodes to a new origin
void	physicsLayout() physics layout, asks every 30 seconds if you want to keep running
void	physicsLayout(boolean gather, int max) physics layout
void	physicsLayout(int max) run physics layout for max steps
void	radialLayout(Node center) places all nodes in a growing radius around center
void	radialLayout(Node center, PySequence seq)
void	randomLayout() randomly places nodes in a 1000 x 1000 grid
void	randomLayout(int width, int height) randomly places nodes in a width x height grid
void	readjustEdges() moves edges so they don't overlap
Set	remove(PySequence seq) remove nodes and edges from the graph
void	removeComplete(PySequence seq) remove nodes and edges completely from the system (all states)
Set	removeDisconnected()
Set	removeEdge(Edge e) remove an edge from the graph
void	removeEdgeComplete(Edge e) removes an edge completely.
Set	removeNode(Node n) remove a node from the graph
void	removeNodeComplete(Node n) removes a node completely (node, and all edges connected to it, will likely be unrecoverable).
Set	removeSelfLoops()
void	rescaleLayout(double percent) rescales the layout to %percent
void	rescaleLayout(double xpercent, double ypercent) rescales the layout to %xpercent X %ypercent
void	rescaleLayout(int width, int height) rescales nodes to fit into width x height
void	resetLastMod() resets the last mod so we don't have to update fields
void	resizeLinear(Field f, double start, double end)
void	resizeRandom(Field f, double start, double end)
void	setIdToEdge(Edge e) put the edge into the table, will not work if the id = -1.
void	setNumber(ArchetypeEdge edge, Number number) needed for NumberEdgeValue interface
void	setPageRankBias(double bias)
void	setRankerWeightField(Field f)
Collection	sortBy(Field field)
Collection	sortBy(PySequence seq, Field field)
void	springLayout() spring layout, runs for 30 seconds and asks if you want to continue
void	springLayout(int max) spring layout for max iterations
void	sugiyamaLayout() Sugiyama
void	sugiyamaLayout(boolean bends) Sugiyama
void	sugiyamaLayout2() Sugiyama
static Color	toColor(Object object)
static double	toDouble(Object object)
void	translateLayout(double newX, double newY)
void	translateLayout(int newX, int newY) moves the nodes to a new origin
Set	weakComponentClusters() do weak component clustering
void	weightedKKLayout() the JUNG Kamada-Kawai (regular)
void	weightedSpringLayout(int min, int max) spring layout, runs for 30 seconds and asks if you want to continue
void	weightedSpringLayout(int minL, int maxL, int max) spring layout for max iterations

Methods inherited from class edu.uci.ics.jung.graph.impl.AbstractSparseGraph

addEdge, addVertex, getEdges, getVertices, isDirected, removeEdge, removeEdges, removeVertex, removeVertices

Methods inherited from class edu.uci.ics.jung.graph.impl.AbstractArchetypeGraph

addListener, copy, getEdgeConstraints, getVertexConstraints, newInstance, numEdges, numVertices, removeAllEdges, removeAllVertices, removeListener, toString

Methods inherited from class edu.uci.ics.jung.utils.UserDataDelegate

addUserDatum, clone, containsUserDatumKey, getUserDatum, getUserDatumCopyAction, getUserDatumKeyIterator, importUserData, removeUserDatum, setUserDataFactory, setUserDatum

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.uci.ics.jung.graph.ArchetypeGraph

addListener, copy, getEdgeConstraints, getVertexConstraints, newInstance, numEdges, numVertices, removeAllEdges, removeAllVertices, removeListener

Methods inherited from interface edu.uci.ics.jung.utils.UserDataContainer

addUserDatum, clone, containsUserDatumKey, getUserDatum, getUserDatumCopyAction, getUserDatumKeyIterator, importUserData, removeUserDatum, setUserDatum

Constructor Detail

Graph

public Graph(FrameListener display,
             InterpreterAbstraction interp)

create a new graph. Must be tied to a display object right now as well as an interpreter instance. Will probably relax that in the future

Parameters:

display - something we render to

interp - the interpreter

Graph

public Graph(FrameListener display,
             InterpreterAbstraction interp,
             boolean multiedge)

create a new graph. Must be tied to a display object right now as well as an interpreter instance. Will probably relax that in the future

Parameters:

display - something we render to

interp - the interpreter

Method Detail

getLastModTime

public long getLastModTime()

get the time of last modification

resetLastMod

public void resetLastMod()

resets the last mod so we don't have to update fields

getNodeByName

public Node getNodeByName(String name)

lookup a node by name

Parameters:

name - the node name

Returns:

the node object or null if not found

getEdgeByID

public Edge getEdgeByID(Integer id)

lookup a edge by id

Parameters:

id - the edge id

Returns:

the edge object or null if not found

setIdToEdge

public void setIdToEdge(Edge e)

put the edge into the table, will not work if the id = -1. Will overwrite previous entry

Parameters:

e - the edge

addNode

public Node addNode(Node n)

used to load nodes from the database into the graph

Parameters:

n - the node we're adding

Returns:

the added node (possibly a different object)

addNode

public Node addNode(String name)

user's API for adding a new node to the graph and database

Parameters:

name - the new node name

Returns:

a new node object

addEdge

public Edge addEdge(Edge e)

used to load edges from the database into the graph

Parameters:

e - the edge to add

Returns:

the created edge

addEdgeNoCheck

public Edge addEdgeNoCheck(Edge e)

use this if you know the storage object already contains the edge. Shortcut for speeding things up

addDirectedEdge

public DirectedEdge addDirectedEdge(Node source,
                                    Node dest)

user's API for adding a new directed edge to the graph and database

Parameters:

source - source node

dest - destinatin node

Returns:

a new DirectedEdge between source and dest

addDirectedEdgeWID

public DirectedEdge addDirectedEdgeWID(Node source,
                                       Node dest,
                                       int id)

user's API for adding a new directed edge to the graph and database

Parameters:

source - source node

dest - destinatin node

id - override the id creation from the storage factory

Returns:

a new DirectedEdge between source and dest

addUndirectedEdge

public UndirectedEdge addUndirectedEdge(Node node1,
                                        Node node2)

addUndirectedEdgeWID

public UndirectedEdge addUndirectedEdgeWID(Node node1,
                                           Node node2,
                                           int id)

addEdge

public UndirectedEdge addEdge(Node node1,
                              Node node2)

user's API shortcut for adding a new undirected edge.

removeNode

public Set removeNode(Node n)

remove a node from the graph

Parameters:

n - the node to remove

removeNodeComplete

public void removeNodeComplete(Node n)

removes a node completely (node, and all edges connected to it, will likely be unrecoverable). Removes from all states.

Parameters:

n - the node to remove

removeEdgeComplete

public void removeEdgeComplete(Edge e)

removes an edge completely. Removes from all states.

Parameters:

e - the node to remove

removeComplete

public void removeComplete(PySequence seq)

remove nodes and edges completely from the system (all states)

Parameters:

seq - the nodes + edges

removeEdge

public Set removeEdge(Edge e)

remove an edge from the graph

Parameters:

e - the edge to remove

remove

public Set remove(PySequence seq)

remove nodes and edges from the graph

Parameters:

seq - the nodes + edges

complement

public Set complement(PySequence seq)

returns the complement (e.g. all nodes/edges in the graph that are not in the set). If the set contains only nodes only nodes will be returned. Likewise for edges. If the set contains both, both nodes and edges will be returned.

Parameters:

seq - the nodes and/or edges

complement

public Set complement(GraphElement t)

returns all nodes/edges in the graph that are NOT the argument node/edge

add

public void add(PySequence seq)

add nodes and edges from the graph

Parameters:

seq - the nodes + edges

getNodes

public Set getNodes()

Returns:

all the nodes in the graph

toColor

public static Color toColor(Object object)

Returns:

figures out if you have a Color object, Python object, or a string object, automagically converts

toDouble

public static double toDouble(Object object)

Returns:

figures out if you have a Double object, Python object and automatically converts

readjustEdges

public void readjustEdges()

moves edges so they don't overlap

kkLayout

public void kkLayout()

Kamada-Kawai, puts nodes in 1000 x 1000 square

sugiyamaLayout

public void sugiyamaLayout()

Sugiyama

sugiyamaLayout

public void sugiyamaLayout(boolean bends)

Sugiyama

sugiyamaLayout2

public void sugiyamaLayout2()

Sugiyama

dagLayout

public void dagLayout()

DAG

frLayout

public void frLayout()

Fruchterman-Rheingold, puts nodes in 1000 x 1000 square

mdsLayout

public void mdsLayout()

Multidimensional scaling layout based on edge weight

moveLayout

public void moveLayout(int newX,
                       int newY)

moves the nodes to a new origin

Parameters:

newX -

newY -

moveLayout

public void moveLayout(double newX,
                       double newY)

translateLayout

public void translateLayout(int newX,
                            int newY)

moves the nodes to a new origin

Parameters:

newX -

newY -

translateLayout

public void translateLayout(double newX,
                            double newY)

rescaleLayout

public void rescaleLayout(int width,
                          int height)

rescales nodes to fit into width x height

Parameters:

width - the rescale width

height - the rescale height

rescaleLayout

public void rescaleLayout(double percent)

rescales the layout to %percent

Parameters:

percent - the percent to shrink/grow

rescaleLayout

public void rescaleLayout(double xpercent,
                          double ypercent)

rescales the layout to %xpercent X %ypercent

Parameters:

xpercent - the percent to shrink/grow

ypercent - the percent to shrink/grow

radialLayout

public void radialLayout(Node center)

places all nodes in a growing radius around center

Parameters:

center - the node to put in the center

radialLayout

public void radialLayout(Node center,
                         PySequence seq)

randomLayout

public void randomLayout()

randomly places nodes in a 1000 x 1000 grid

randomLayout

public void randomLayout(int width,
                         int height)

randomly places nodes in a width x height grid

Parameters:

width - width

height - height

jfrLayout

public void jfrLayout()

the JUNG Fructerman-Rheingold Layout

jkkLayout1

public void jkkLayout1()

the JUNG Kamada-Kawai (regular)

jkkLayout2

public void jkkLayout2()

the JUNG Kamada-Kawai (int)

weightedKKLayout

public void weightedKKLayout()

the JUNG Kamada-Kawai (regular)

frLayout

public void frLayout(int width,
                     int height)

Fruchterman-Rheingold into a width x height grid

Parameters:

width -

height -

kkLayout

public void kkLayout(int width,
                     int height)

Kamada-Kawai into a width x height grid

Parameters:

width -

height -

physicsLayout

public void physicsLayout(boolean gather,
                          int max)

physics layout

Parameters:

gather - merges connected nodes first (not very useful)

max - loops max times

physicsLayout

public void physicsLayout()

physics layout, asks every 30 seconds if you want to keep running

physicsLayout

public void physicsLayout(int max)

run physics layout for max steps

Parameters:

max - the number of steps

jSpringLayout

public void jSpringLayout()

the JUNG Spring Layout (seems a little broken). Asks every 30 seconds if you want to keep running

jSpringLayout

public void jSpringLayout(int max)

run the JUNG spring layout for max iterations

Parameters:

max - the number of iterations

circleLayout

public void circleLayout()

places all nodes in a circle

binPackLayout

public void binPackLayout()

packs all nodes

binPackLayout

public void binPackLayout(boolean rescale)

packs all nodes

circleLayout

public void circleLayout(Field f,
                         Node c)

places all nodes in a circle with node c in the middle and its neighbors around that center with a radius proportional to field f (all nodes that are not neighbors of c will be left as is)

Parameters:

f - the field to use to calc the radius

c - the node to put in the center

circleLayout

public void circleLayout(Field f,
                         Node c,
                         double xorigin,
                         double yorigin)

places all nodes in a circle with node c in the middle and its neighbors around that center with a radius proportional to field f (all nodes that are not neighbors of c will be left as is)

Parameters:

f - the field to use to calc the radius

c - the node to put in the center

xorigin - the x location for the center node

yorigin - the y location for the center node

springLayout

public void springLayout()

spring layout, runs for 30 seconds and asks if you want to continue

springLayout

public void springLayout(int max)

spring layout for max iterations

Parameters:

max - number of iterations

weightedSpringLayout

public void weightedSpringLayout(int min,
                                 int max)

spring layout, runs for 30 seconds and asks if you want to continue

weightedSpringLayout

public void weightedSpringLayout(int minL,
                                 int maxL,
                                 int max)

spring layout for max iterations

Parameters:

max - number of iterations

gemLayout

public void gemLayout()

GEM Layout

isomLayout

public void isomLayout()

ISOM Layout, asks every 30 seconds if you want to continue

isomLayout

public void isomLayout(int max)

ISOM Layout for max steps

Parameters:

max - the number of iterations

layout

public void layout(Layout lay)

basic layout command, runs until completes or 30 seconds depending on if the layout is iterative

Parameters:

lay - the layout to run

centerAfterLayout

public void centerAfterLayout(boolean state)

should we center after doing a layout disable this to control it yourself

layout

public void layout(Layout lay,
                   int mi)

runs the layout for some number of iterations (mi). If mi == Integer.MAX_VALUE this will run until the layout completes or if it is iterative it will ask every 30 seconds if you want to continue

Parameters:

lay - the layout to run

mi - the maximum iterations

biComponentClusters

public Set biComponentClusters()

do Bi-Component Clustering

Returns:

a set of sets

edgeBetweennessClusters

public Set edgeBetweennessClusters(int numEdgesToRemove)

do Edge betweenness clustering

Parameters:

numEdgesToRemove - edges to remove

Returns:

a set of sets

weakComponentClusters

public Set weakComponentClusters()

do weak component clustering

Returns:

a set of sets

exactFlowCommunity

public Set exactFlowCommunity(int cohesion)

doesn't do anything right now

clusters

public static Set clusters(Graph graph,
                           GraphClusterer clusterer)

meta clustering algorithm, takes a clustering algorithm and a graph and returns a set of sets

Parameters:

graph - the graph to analyze

clusterer - the clustering algorithm to use

Returns:

a set of sets

setNumber

public void setNumber(ArchetypeEdge edge,
                      Number number)

needed for NumberEdgeValue interface

Specified by:

setNumber in interface NumberEdgeValue

getNumber

public Number getNumber(ArchetypeEdge e)

for NumberEdgeValue interface, returns the weight of the given edge.

Specified by:

getNumber in interface NumberEdgeValue

computeAbstractRanker

public void computeAbstractRanker(AbstractRanker centrality,
                                  String guessKey,
                                  ArchetypeGraph ag)

computes the ranking for nodes or edges and deposits the results based on guessKey

Parameters:

centrality - the ranker

guessKey - the place to put the results

computeBetweennessCentrality

public void computeBetweennessCentrality()

setPageRankBias

public void setPageRankBias(double bias)

getPageRankBias

public double getPageRankBias()

setRankerWeightField

public void setRankerWeightField(Field f)

computePageRank

public void computePageRank()

computeDegreeDistributionRank

public void computeDegreeDistributionRank()

computeHITS

public void computeHITS()

computeRandomWalkBetweenness

public void computeRandomWalkBetweenness()

computeDegrees

public void computeDegrees()

addNodeField

public Field addNodeField(String fieldName,
                          int sqlType,
                          Object defaultValue)

addEdgeField

public Field addEdgeField(String fieldName,
                          int sqlType,
                          Object defaultValue)

getNodeSchema

public NodeSchema getNodeSchema()

getEdgeSchema

public EdgeSchema getEdgeSchema()

sortBy

public Collection sortBy(PySequence seq,
                         Field field)

sortBy

public Collection sortBy(Field field)

groupBy

public Collection groupBy(PySequence seq,
                          Field field)

groupBy

public Collection groupBy(Field field)

groupAndSortBy

public Collection groupAndSortBy(Field field)

groupAndSortBy

public Collection groupAndSortBy(PySequence seq,
                                 Field field)

groupAndSortNodesBy

public Collection groupAndSortNodesBy(String field)

groupNodesBy

public Collection groupNodesBy(String field)

groupAndSortEdgesBy

public Collection groupAndSortEdgesBy(String field)

groupEdgesBy

public Collection groupEdgesBy(String field)

makeBarabasiAlbertRandom

public void makeBarabasiAlbertRandom(int vert,
                                     int edges,
                                     int evolve)

makeSimpleRandom

public void makeSimpleRandom(int nodes,
                             int edges)

makeSimpleDirectedRandom

public void makeSimpleDirectedRandom(int nodes,
                                     int edges)

makeEppsteinRandom

public void makeEppsteinRandom(int nodes,
                               int edges,
                               int r)

makeErdosRenyiRandom

public void makeErdosRenyiRandom(int nodes,
                                 double p)

makeLattice1DRandom

public void makeLattice1DRandom(int nodes,
                                boolean tor)

makeLattice2DRandom

public void makeLattice2DRandom(int nodes,
                                boolean tor)

makeKleinbergRandom

public void makeKleinbergRandom(int nodes,
                                double clust)

makeFromGenerator

public void makeFromGenerator(GraphGenerator gg)

makeFromGML

public void makeFromGML(String filename)

makeFromPajek

public void makeFromPajek(String filename)

makeFromDL

public void makeFromDL(String filename)

makeFromGDF

public void makeFromGDF(String filename)
                 throws IOException

Throws:

IOException

exportGDF

public void exportGDF(String filename)

morph

public void morph(String state,
                  long duration)

morph

public void morph(int state,
                  long duration)

colorize

public void colorize(Field f)

colorize

public void colorize(Field f,
                     Color start,
                     Color end)

colorize

public void colorize(Field f,
                     String start,
                     String end)

colorize

public void colorize(Field f,
                     Color start,
                     Color middle,
                     Color end)

colorize

public void colorize(Field f,
                     String start,
                     String middle,
                     String end)

resizeRandom

public void resizeRandom(Field f,
                         double start,
                         double end)

resizeLinear

public void resizeLinear(Field f,
                         double start,
                         double end)

density

public double density()

removeSelfLoops

public Set removeSelfLoops()

removeDisconnected

public Set removeDisconnected()

hideDisconnected

public void hideDisconnected()