fromGXL-methods: Methods for GXL manipulations in package graph
In pshannon-bioc/graph: graph: A package to handle graph data structures

Description Value Methods Note Author(s) Examples

GXL http://www.gupro.de/GXL is "an XML sublanguage designed to be a standard exchange format for graphs". This document describes tools in the graph package for importing GXL data to R and for writing graph data out as GXL.

`fromGXL`	currently returns a graphNEL when possible. This function is based on `xmlEventParse` with handlers defined in the function NELhandler. The dump() element of this handler should emit information on all children of nodes and edges; the asGraphNEL() element will return a `graphNEL` object with weights if child `<attr>` with name attribute "weights" is present for each edge element.
`toGXL`	for an input of class "graphNEL", returns an object of class c("XMLInternalDOM", "XMLOutputStream"); see the example for how to convert this to a text stream encoding XML
`dumpGXL`	returns an R list with all the node, edge, and named attribute information specified in the GXL stream
`validateGXL`	returns silently (invisibly returns the parsed tree) for a DTD-compliant stream, or is otherwise very noisy

fromGXL: con = connection: returns a graphNEL based on a parsing of the GXL stream on the connection
dumpGXL: con = connection: returns an R list based on a parsing of the GXL stream on the connection
validateGXL: con = connection: checks the GXL stream against its DTD
toGXL: object = graphNEL: creates an XMLInternalDOM representing the graph in GXL

At present, toGXL does not return a validating GXL stream because XML package does not properly handle the dtd and namespaces arguments to xmlTree. This is being repaired. To fix the stream, add <!DOCTYPE gxl SYSTEM "http://www.gupro.de/GXL/gxl-1.0.1.dtd"> as second record in the output.

Some structures in a graphNEL and some tags in GXL may not be handled at this time.

Vince Carey <stvjc@channing.harvard.edu>

sf <- file(system.file("GXL/simpleExample.gxl", package="graph"))
show(fromGXL(sf))
print(dumpGXL(sf))
close(sf)
#validateGXL(sf)
# bad <- file(system.file("GXL/c2.gxl", package="graph"))
# here's how you can check if the GXL is well-formed, if
# you have a libxml2-based version of R XML package
#
# try( validateGXL(bad) )
#
gR <- graphNEL(nodes=letters[1:4], edgeL=list(
 a=list(edges=4), b=list(edges=3), c=list(edges=c(2,1)), d=list(edges=1)),
 edgemode="directed")
#
# following requires that you are using XML bound with recent libxml2
#
#an <- as.numeric
#if (an(libxmlVersion()$major)>=2 && an(libxmlVersion()$minor)>=4)
## since toGXL returns an XML object, we need to attach the XML
## package.
library("XML")
cat(saveXML(toGXL(gR)$value()))
wtd <- file(system.file("GXL/kmstEx.gxl", package="graph"))
wtdg <- fromGXL(wtd)
close(wtd)
print(edgeWeights(wtdg))