nodeColorStyle <- function(nodes, colors, style_name)
{
  # 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", style_name)

  # 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.", nodes, "=", colors, sep="")
  mapping <- paste("nodes.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", 
    "nodeColoring", props, "nodes")
  
  # 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.
  
  style
}

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", 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

#vmm <- .jcall("cytoscape/Cytoscape", "Lcytoscape/visual/VisualMappingManager;", 
#    "getVisualMappingManager")
#oldStyle <- .jcall(vmm, "Lcytoscape/visual/VisualStyle;", "getVisualStyle")

animation <- .jnew("edu/iastate/cytoscape/animation/SimpleAnimation")
sapply(comps, function(comp) {
  #frame <- .jnew("edu/iastate/cytoscape/animation/SimpleFrame", 
  #  nodeColorStyle(comp, "255,0,0", "boost scc"), 3)
  rules <- paste("node canonicalName =", comp, "-> fill color = 255,0,0", collapse=";")
  #style <- .jnew("cytoscape/visual/VisualStyle", oldStyle, "scc frame")
  #sapply(rules, function(rule) .jcall("edu/iastate/cytoscape/mapping/MappingRuleParser",
  #  "V", "mergeRule", rule, style))
  frame <- .jnew("edu/iastate/cytoscape/animation/SimpleFrame", rules, 0.5)
  #animation$addFrame(frame)
  .jcall(animation, "V", "addFrame", .jcast(frame, "edu/iastate/cytoscape/animation/Frame"))
})

.jcall("Animator", "V", "playAnimation", 
  .jcast(animation, "edu/iastate/cytoscape/animation/Animation"))