Nothing
library (RUnit)
source ('unitTests/test_cytoscape.R')
if (!exists ('cy')) {
write ('creating global variable "cy" -- an instance of CytoscapeConnection', stderr ())
cy = CytoscapeConnection ()
}
#------------------------------------------------------------------------------------------------------------------------
reload.rcytoscape = function ()
{
if (length (grep ('RCytoscape', names (sessionInfo()$otherPkgs))) > 0)
detach (package:RCytoscape)
library (RCytoscape)
} # reload.rcytoscape
#------------------------------------------------------------------------------------------------------------------------
getVizMapList = function (cw)
{
return (xml.rpc (cw@uri, 'Cytoscape.getVisualStyleNames'))
} # getVizMapList
#------------------------------------------------------------------------------------------------------------------------
current.vizmap = function (cw)
{
return (xml.rpc (cw@uri, 'Cytoscape.getCurrentVisualStyle'))
} # vizmap.names
#------------------------------------------------------------------------------------------------------------------------
set.vizmap = function (cw, style.name)
{
invisible (xml.rpc (cw@uri, 'Cytoscape.setVisualStyle', style.name))
} # set.vizmap
#------------------------------------------------------------------------------------------------------------------------
copy.vizmap = function (cw, from.name, to.name)
{
invisible (xml.rpc (cw@uri, 'Cytoscape.copyVisualStyle', from.name, to.name))
} # copy.vizmap
#------------------------------------------------------------------------------------------------------------------------
set.nodeShape = function (cw)
{
node.shapes = c ('triangle', 'rect', 'ellipse')
node.shapes = c ('diamond', 'triangle', 'rect')
node.shapes = c ('ellipse', 'trapezoid', 'triangle')
attribute.values = c ('kinase', 'glycoprotein', 'transcription factor')
window.id = cw@window.id
style.name = 'default'
style.name = 'newViz'
xml.rpc (cw@uri, "Cytoscape.setNodeShapeRule", window.id, style.name, 'type', 'ellipse', attribute.values, node.shapes, .convert=TRUE)
}
#------------------------------------------------------------------------------------------------------------------------
# temporary (25 dec 2010)
parse.pos = function (position.strings)
{
tokens = strsplit (position.strings, ":")
result = list ()
for (token in tokens) {
name = token [1]
xy.tokens = strsplit (token [2], ",")
x = as.integer (xy.tokens[[1]][1])
y = as.integer (xy.tokens[[1]][2])
printf ('%s: %d, %d', name, x, y)
result [[name]] = list (x=x, y=y)
} # for token
return (result)
} # parse.pos
#------------------------------------------------------------------------------------------------------------------------
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