Package edu.cmu.tetrad.graph

Class GraphSaveLoadUtils

java.lang.Object

edu.cmu.tetrad.graph.GraphSaveLoadUtils

public class GraphSaveLoadUtils
extends Object

Methods to load or save graphs.

Version:

$Id: $Id

Author:

josephramsey

Method Summary

Modifier and Type	Method	Description
static nu.xom.Element	convertToXml(Graph graph)	convertToXml.
static List<Triple>	getCollidersFromGraph(Node node, Graph graph)	getCollidersFromGraph.
static nu.xom.Element	getRootElement(File file)	getRootElement.
static HashMap<String,PointXy>	grabLayout(List<Node> nodes)	grabLayout.
static String	graphRMatrixTxt(Graph graph)	graphRMatrixTxt.
static String	graphToAmatCpag(Graph g)	Converts a given graph into an adjacency matrix in CPAG format.
static String	graphToAmatPag(Graph g)	Saves a PAG in the "amat.pag" format of PCALG.
static String	graphToDot(Graph graph)	Converts a graph to a Graphviz .dot file
static void	graphToDot(Graph graph, File file)	graphToDot.
static String	graphToLavaan(Graph g)	graphToLavaan.
static String	graphToPcalg(Graph g)	graphToPcalg.
static String	graphToXml(Graph graph)	graphToXml.
static Graph	loadGraph(File file)	loadGraph.
static Graph	loadGraphAmatCpdag(File file)	Loads a CPDAG in the "amat.cpdag" format of PCALG.
static Graph	loadGraphAmatPag(File file)	Loads a PAG in the "amat.pag" format of PCALG.
static Graph	loadGraphBNTPcMatrix(List<Node> vars, DataSet dataSet)	loadGraphBNTPcMatrix.
static Graph	loadGraphJson(File file)	loadGraphJson.
static String	loadGraphRMatrix(Graph graph)	loadGraphRMatrix.
static Graph	loadGraphRuben(File file)	loadGraphRuben.
static String	loadGraphTxt(Graph graph, boolean pagEdgeSpecializationMarked)	Converts a given graph to human-readable text format.
static Graph	loadGraphTxt(File file)	loadGraphTxt.
static Graph	loadRSpecial(File file)	loadRSpecial.
static Graph	parseGraphXml(nu.xom.Element graphElement, Map<String,Node> nodes)	parseGraphXml.
static Graph	readerToGraphJson(Reader reader)	readerToGraphJson.
static Graph	readerToGraphRuben(Reader reader)	readerToGraphRuben.
static Graph	readerToGraphTxt(Reader reader)	readerToGraphTxt.
static Graph	readerToGraphTxt(String graphString)	readerToGraphTxt.
static void	saveGraph(Graph graph, File file, boolean xml)	saveGraph.

Methods inherited from class java.lang.Object

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

Method Details

loadGraph

public static Graph loadGraph(File file)

loadGraph.

Parameters:

file - a File object

Returns:

a Graph object

loadGraphTxt

public static Graph loadGraphTxt(File file)

loadGraphTxt.

Parameters:

file - a File object

Returns:

a Graph object

loadGraphRuben

public static Graph loadGraphRuben(File file)

loadGraphRuben.

Parameters:

file - a File object

Returns:

a Graph object

loadGraphJson

public static Graph loadGraphJson(File file)

loadGraphJson.

Parameters:

file - a File object

Returns:

a Graph object

loadGraphBNTPcMatrix

public static Graph loadGraphBNTPcMatrix(List<Node> vars,
 DataSet dataSet)

loadGraphBNTPcMatrix.

Parameters:

vars - a List object

dataSet - a DataSet object

Returns:

a Graph object

graphRMatrixTxt

public static String graphRMatrixTxt(Graph graph)
                              throws IllegalArgumentException

graphRMatrixTxt.

Parameters:

graph - a Graph object

Returns:

a String object

Throws:

IllegalArgumentException - if any.

loadRSpecial

public static Graph loadRSpecial(File file)

loadRSpecial.

Parameters:

file - a File object

Returns:

a Graph object

loadGraphAmatCpdag

public static Graph loadGraphAmatCpdag(File file)

Loads a CPDAG in the "amat.cpdag" format of PCALG. We will assume here that the graph in R has been saved to disk using the write.table(mat, path) method. For the amat.cpdag format, for a matrix m, there are two cases where edges occur in the graph: (1) m[i][j] = 0 and m[j][i] = 1, in which case an edge i->j exists; or, (2) m[i][j] = 1 and m[j][i] = 1, in which case an undirected edge i--j exists. In all other cases, there is no edge between i and j.

Parameters:

file - a file in the "amat.cpdag" format of PCALG.

Returns:

a graph.

loadGraphAmatPag

public static Graph loadGraphAmatPag(File file)

Loads a PAG in the "amat.pag" format of PCALG. We will assume here that the graph in R has been saved to disk using the write.table(mat, path) method. For the amat.pag format, for a matrix m, endpoints are explicitly represented, as follows. 1 is a circle endpoint, 2 is an arrow endpoint, 3 is a tail endpoint, and 0 is a null endpoint (i.e., no edge). For an edge i->j, m[i][j] = 2 and m[j][i] = 3.

Parameters:

file - a file in the "amat.cpdag" format of PCALG.

Returns:

a graph.

loadGraphRMatrix

public static String loadGraphRMatrix(Graph graph)
                               throws IllegalArgumentException

loadGraphRMatrix.

Parameters:

graph - a Graph object

Returns:

a String object

Throws:

IllegalArgumentException - if any.

readerToGraphTxt

public static Graph readerToGraphTxt(String graphString)
                              throws IOException

readerToGraphTxt.

Parameters:

graphString - a String object

Returns:

a Graph object

Throws:

IOException - if any.

readerToGraphTxt

public static Graph readerToGraphTxt(Reader reader)
                              throws IOException

readerToGraphTxt.

Parameters:

reader - a Reader object

Returns:

a Graph object

Throws:

IOException - if any.

saveGraph

public static void saveGraph(Graph graph,
 File file,
 boolean xml)

saveGraph.

Parameters:

graph - The graph to be saved.

file - The file to save it in.

xml - True if to be saved in XML, false if in text.

readerToGraphRuben

public static Graph readerToGraphRuben(Reader reader)
                                throws IOException

readerToGraphRuben.

Parameters:

reader - a Reader object

Returns:

a Graph object

Throws:

IOException - if any.

readerToGraphJson

public static Graph readerToGraphJson(Reader reader)
                               throws IOException

readerToGraphJson.

Parameters:

reader - a Reader object

Returns:

a Graph object

Throws:

IOException - if any.

graphToDot

public static String graphToDot(Graph graph)

Converts a graph to a Graphviz .dot file

Parameters:

graph - a Graph object

Returns:

a String object

graphToDot

public static void graphToDot(Graph graph,
 File file)

graphToDot.

Parameters:

graph - a Graph object

file - a File object

convertToXml

public static nu.xom.Element convertToXml(Graph graph)

convertToXml.

Parameters:

graph - a Graph object

Returns:

an XML element representing the given graph. (Well, only a basic graph for now...)

graphToXml

public static String graphToXml(Graph graph)

graphToXml.

Parameters:

graph - a Graph object

Returns:

a String object

graphToLavaan

public static String graphToLavaan(Graph g)

graphToLavaan.

Parameters:

g - a Graph object

Returns:

a String object

graphToPcalg

public static String graphToPcalg(Graph g)

graphToPcalg.

Parameters:

g - a Graph object

Returns:

a String object

graphToAmatCpag

public static String graphToAmatCpag(Graph g)

Converts a given graph into an adjacency matrix in CPAG format.

Parameters:

g - the input graph to be converted

Returns:

the adjacency matrix representation of the graph in CPAG format

Throws:

IllegalArgumentException - if the graph is not a MPDAG (including CPDAG or DAG)

graphToAmatPag

public static String graphToAmatPag(Graph g)

Saves a PAG in the "amat.pag" format of PCALG. We will save it in the form that R would print the matrix to file using write.matrix(mat, path). For the amat.pag format, for a matrix m, endpoints are explicitly represented, as follows. 1 is a circle endpoint, 2 is an arrow endpoint, 3 is a tail endpoint, and 0 is a null endpoint (i.e., no edge)

Parameters:

g - a Graph object

Returns:

a String object

parseGraphXml

public static Graph parseGraphXml(nu.xom.Element graphElement,
 Map<String,Node> nodes)
                           throws nu.xom.ParsingException

parseGraphXml.

Parameters:

graphElement - a Element object

nodes - a Map object

Returns:

a Graph object

Throws:

nu.xom.ParsingException - if any.

getRootElement

public static nu.xom.Element getRootElement(File file)
                                     throws nu.xom.ParsingException,
IOException

getRootElement.

Parameters:

file - a File object

Returns:

a Element object

Throws:

nu.xom.ParsingException - if any.

IOException - if any.

grabLayout

public static HashMap<String,PointXy> grabLayout(List<Node> nodes)

grabLayout.

Parameters:

nodes - a List object

Returns:

a HashMap object

getCollidersFromGraph

public static List<Triple> getCollidersFromGraph(Node node,
 Graph graph)

getCollidersFromGraph.

Parameters:

node - a Node object

graph - a Graph object

Returns:

A list of triples of the form X*->Y<-*Z.

loadGraphTxt

public static String loadGraphTxt(Graph graph,
 boolean pagEdgeSpecializationMarked)

Converts a given graph to human-readable text format.

Parameters:

graph - the graph to be converted

pagEdgeSpecializationMarked - whether to add edge specialization markups to the graph before conversion

Returns:

the human-readable representation of the graph