require(rmetnet)
require(RBGL)
#.jinit("/home/daisy/research/cytoscape-v2.3/cytoscape.jar")

# ok, now get the network
cy_network <- .jcall("cytoscape/Cytoscape", "Lcytoscape/CyNetwork;", "getCurrentNetwork")
print("got a cy network")
# and create our graph object
network <- new("graphCytoscape", network = cy_network)
print("got a network")
# now pass to RBGL to find strongly connected components
comps <- strongComp(network)
print("analyzed")
comps <- comps[sapply(comps, length)>1] # get rid of all the singletons

# convert those components to visual mapping

# First, get the visual mapping manager and its catalog

vmm <- .jcall("cytoscape/Cytoscape", "Lcytoscape/visual/VisualMappingManager;", 
  "getVisualMappingManager")
catalog <- .jcall(vmm, "Lcytoscape/visual/CalculatorCatalog;", "getCalculatorCatalog")

# Create a new visual style from the currently active one

oldStyle <- .jcall(vmm, "Lcytoscape/visual/VisualStyle;", "getVisualStyle")
style <- .jnew("cytoscape/visual/VisualStyle", oldStyle)
.jcall(style, "S", "setName", "Boost SCC")

# Create a mapping from "canonicalName" to color, according to cluster
# We build a Java properties object describing the mapping
type <- paste("type", "DiscreteMapping", sep="=")
attr <- paste("controller", "canonicalName", sep="=")
# red for the clusters, white for the rest
colors <- paste("map.", unlist(comps), "=255,0,0",sep="")
mapping <- paste("cluster.mapping", c(type, attr, colors), sep=".", collapse="\n")
props <- .jnew("java/util/Properties")
.jcall(props, , "load", .jcast(.jnew("java/io/StringBufferInputStream", mapping), 
  "java/io/InputStream"))

# Place the mapping inside a node color calculator
fillColor <- .jnew("cytoscape/visual/calculators/GenericNodeColorCalculator", 
  "clusterColoring", props, "cluster")
  
# That calculator needs to be in a node apperance calculator set on the style
nodeAppearance <- .jcall(style, "Lcytoscape/visual/NodeAppearanceCalculator;", 
  "getNodeAppearanceCalculator")
.jcall(nodeAppearance, , "setNodeFillColorCalculator", 
  .jcast(fillColor, "cytoscape/visual/calculators/NodeColorCalculator"))
#.jcall(style, "Lcytoscape/visual/NodeAppearanceCalculator;", 
#  "setNodeAppearanceCalculator", nodeAppearance)

# Finally, add the visual style to a calculator and set it to active
.jcall(catalog, , "addVisualStyle", style)
.jcall(vmm, "Lcytoscape/visual/VisualStyle;", "setVisualStyle", style)
.jcall(vmm, , "applyNodeAppearances")

# Make the network visual update

# Don't know how to do this yet - probably need to get the Swing component 
# and repaint it.