def test_separate_props(self):
'''Test modifying the properties of node and alias that are separate, i.e. not shared.
As in, if the position of an alias is changed, that of the node should remain the same,
and vice versa.
'''
alias_pos = Vec2(100, 100)
alias_size = Vec2(50, 50)
nodei = api.add_node(self.neti, id='Hookie')
aliasi = api.add_alias(self.neti, nodei, position=alias_pos, size=alias_size)
new_pos = Vec2(33, 33)
new_size = Vec2(66, 66)
new_lockNode = True
api.update_node(self.neti, nodei, position=Vec2(33, 33), size=Vec2(66, 66), lock_node=True)
node = api.get_node_by_index(self.neti, nodei)
alias = api.get_node_by_index(self.neti, aliasi)
# alias remains the same
self.assertEqual(alias_pos, alias.position)
self.assertEqual(alias_size, alias.size)
self.assertEqual(False, alias.lock_node)
# node is updated
self.assertEqual(new_pos, node.position)
self.assertEqual(new_size, node.size)
self.assertEqual(new_lockNode, node.lock_node)
def copy_node(node_index, net_index):
'''
Creates a new node, translated 300 px down and to the right.
Parameters: node index
Returns: index of new node
'''
node = api.get_node_by_index(net_index, node_index)
try:
inx = api.add_node(net_index,
id='copy_{}'.format(node.id),
shape_index=node.shape_index,
size=Vec2(node.size[0] + 60, node.size[1]),
position=Vec2(node.position[0] + 300,
node.position[1] + 300))
except IDRepeatError:
# find a unique id
all_ids = []
ns = api.get_nodes(net_index)
for n in ns:
all_ids.append(n.id)
c = 1
new_id = 'copy_{}_{}'.format(node.id, c)
while new_id in all_ids:
c += 1
new_id = 'copy_{}_{}'.format(node.id, c)
inx = api.add_node(net_index,
id=new_id,
shape_index=node.shape_index,
size=Vec2(node.size[0] + 60, node.size[1]),
position=Vec2(node.position[0] + 300,
node.position[1] + 300))
return inx
def find_center(self, num_nodes, nodes):
"""
Takes in the number of nodes and list of node indices and
computes the optimal centerpoint for the circle
Parameters: num_nodes(int) - number of nodes,
node_indices(list) - list of nodes indices
Returns: center(tuple)
"""
# Max dimension of the node size
max_dim = 0 # will consider this the diameter of a circle node
for i in nodes:
# Get node
node = api.get_node_by_index(0, i)
for dim in node.size:
if dim > max_dim:
max_dim = dim
# Approximate circumference estimate
spacing = max_dim / 4
circum_estimate = num_nodes * (max_dim + spacing)
# Computing radius
r = circum_estimate / (2 * np.pi) + max_dim
center = (r, r)
return center
def test_set_prop(self):
api.add_node(0, 'foo')
api.set_node_shape_property(0, 0, 0, 'fill_color',
api.Color(66, 66, 66))
foo = api.get_node_by_index(0, 0)
primitive = foo.shape.items[0]
primitive, _transform = foo.shape.items[0]
self.assert_(isinstance(primitive, RectanglePrim))
self.assert_(hasattr(primitive, 'fill_color'))
self.assertEqual(getattr(primitive, 'fill_color'),
api.Color(66, 66, 66))
def test_default_shape(self):
'''Make sure the default shape is a single rectangle primitive'''
api.add_node(0, 'foo')
foo = api.get_node_by_index(0, 0)
self.assertEqual(0, foo.shape_index)
self.assertTrue(isinstance(foo.shape, CompositeShape))
self.assertEqual(1, len(foo.shape.items))
primitive, transform = foo.shape.items[0]
self.assertTrue(isinstance(primitive, RectanglePrim))
self.assertEqual(transform.scale, Vec2(1, 1))
self.assertEqual(transform.translation, Vec2(0, 0))
def get_new_position(self, node_index, r, theta):
"""
Takes in the node index and outputs the new position for that node
Parameters: r(double), theta(double in radians)
Returns: (x,y) cartesian coordinate tuple
"""
node = api.get_node_by_index(0, node_index)
size = node.size # (width, height)
# accounting for slight offset, converting to cartesian
nodeCenter = self.cart(r - size[0], theta)
# accounting for node position being specified by top left corner
x = r + nodeCenter[0] - size[0] / 2
y = r + nodeCenter[1] + size[1] / 2
return Vec2(x, y)
def Show(self, evt):
"""
Handler for the "Export" button.
Get the network on canvas and change it to an SBML string.
"""
isReversible = True
netIn = 0
numNodes = api.node_count(netIn)
numReactions = api.reaction_count(netIn)
if numNodes == 0 or numReactions == 0:
wx.MessageBox(
"Please import a network with at least one reaction on canvas",
"Message", wx.OK | wx.ICON_INFORMATION)
else:
allNodes = api.get_nodes(netIn)
allReactions = api.get_reactions(netIn)
allcompartments = api.get_compartments(netIn)
numCompartments = len(allcompartments)
#######################################
# Creates an SBMLNamespaces object with the given SBML level, version
# package name, package version.
#
# (NOTE) By default, the name of package (i.e. "layout") will be used
# if the argument for the prefix is missing or empty. Thus the argument
# for the prefix can be added as follows:
#
# SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT")
#
sbmlns = SBMLNamespaces(3, 1, "layout", 1)
# create the document
document = SBMLDocument(sbmlns)
# set the "required" attribute of layout package to "true"
document.setPkgRequired("layout", False)
# create the Model
model = document.createModel()
model.setId("Model_layout")
document.setModel(model)
# create the Compartment and species
comp_id_list = []
for i in range(numCompartments):
comp_id_list.append(allcompartments[i].id)
if numCompartments != 0:
if "_compartment_default_" not in comp_id_list:
compartment = model.createCompartment()
comp_id = "_compartment_default_"
compartment.setId(comp_id)
compartment.setConstant(True)
for i in range(numCompartments):
compartment = model.createCompartment()
comp_id = allcompartments[i].id
compartment.setId(comp_id)
compartment.setConstant(True)
for i in range(numNodes):
original_index = allNodes[i].original_index
if original_index == -1:
spec_id = allNodes[i].id
species = model.createSpecies()
species.setId(spec_id)
comp_idx = allNodes[i].comp_idx
if comp_idx != -1:
comp_id = allcompartments[comp_idx].id
species.setCompartment(comp_id)
else:
species.setCompartment("_compartment_default_")
species.setInitialConcentration(1.0)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
if allNodes[i].floating_node == False:
species.setBoundaryCondition(True)
species.setConstant(True)
else: #set default compartment
compartment = model.createCompartment()
comp_id = "_compartment_default_"
compartment.setId(comp_id)
compartment.setConstant(True)
for i in range(numNodes):
original_index = allNodes[i].original_index
if original_index == -1:
spec_id = allNodes[i].id
species = model.createSpecies()
species.setId(spec_id)
species.setCompartment(comp_id)
species.setInitialConcentration(1.0)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
if allNodes[i].floating_node == False:
species.setBoundaryCondition(True)
species.setConstant(True)
# create reactions:
for i in range(numReactions):
reaction_id = allReactions[i].id
rct = [] # id list of the rcts
prd = []
rct_num = len(allReactions[i].sources)
prd_num = len(allReactions[i].targets)
for j in range(rct_num):
rct.append(
get_node_by_index(netIn,
allReactions[i].sources[j]).id)
for j in range(prd_num):
prd.append(
get_node_by_index(netIn,
allReactions[i].targets[j]).id)
kinetic_law = ''
parameter_list = []
kinetic_law = kinetic_law + 'E' + str(i) + '*(k' + str(i)
parameter_list.append('E' + str(i))
parameter_list.append('k' + str(i))
for j in range(rct_num):
kinetic_law = kinetic_law + '*' + rct[j]
reaction = model.createReaction()
reaction.setId(allReactions[i].id)
reaction.setReversible(False)
reaction.setFast(False)
if isReversible:
reaction.setReversible(True)
kinetic_law = kinetic_law + ' - k' + str(i) + 'r'
parameter_list.append('k' + str(i) + 'r')
for j in range(prd_num):
kinetic_law = kinetic_law + '*' + prd[j]
kinetic_law = kinetic_law + ')'
for j in range(len(parameter_list)):
parameters = model.createParameter()
parameters.setId(parameter_list[j])
parameters.setValue(0.1)
parameters.setConstant(True)
kinetics = reaction.createKineticLaw()
kinetics.setFormula(kinetic_law)
for j in range(rct_num):
reference = reaction.createReactant()
reference.setSpecies(rct[j])
ref_id = "SpecRef_" + reaction_id + "_rct" + str(j)
reference.setId(ref_id)
reference.setStoichiometry(1.)
reference.setConstant(False)
for j in range(prd_num):
reference = reaction.createProduct()
reference.setSpecies(prd[j])
ref_id = "SpecRef_" + reaction_id + "_prd" + str(j)
reference.setId(ref_id)
reference.setStoichiometry(1.)
reference.setConstant(False)
# create the Layout
#
# set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
#
layoutns = LayoutPkgNamespaces(3, 1, 1)
renderns = RenderPkgNamespaces(3, 1, 1)
#
# Get a LayoutModelPlugin object plugged in the model object.
#
# The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
# thus the value needs to be casted for the corresponding derived class.
#
mplugin = model.getPlugin("layout")
# rPlugin = model.getPlugin("render")
# if rPlugin is None:
# print("there is no render outside layout.")
# lolPlugin = mplugin.getListOfLayouts().getPlugin("render")
# if lolPlugin is None:
# print("there is no render info inside layout.")
if mplugin is None:
# print(
# "[Fatal Error] Layout Extension Level " + layoutns.getLevel() + " Version " + layoutns.getVersion() + " package version " + layoutns.getPackageVersion() + " is not registered.")
# sys.exit(1)
wx.MessageBox("There is no layout information.", "Message",
wx.OK | wx.ICON_INFORMATION)
#
# Creates a Layout object via LayoutModelPlugin object.
#
layout = mplugin.createLayout()
layout.setId("Layout_1")
layout.setDimensions(Dimensions(layoutns, 800.0, 800.0))
# random network (40+800x, 40+800y)
#create the CompartmentGlyph and SpeciesGlyphs
if numCompartments != 0:
# if "_compartment_default_" not in comp_id_list:
# comp_id= "_compartment_default_"
# compartmentGlyph = layout.createCompartmentGlyph()
# compG_id = "CompG_" + comp_id
# compartmentGlyph.setId(compG_id)
# compartmentGlyph.setCompartmentId(comp_id)
# bb_id = "bb_" + comp_id
# pos_x = 10
# pos_y = 10
# width = 3900
# height = 2400
# compartmentGlyph.setBoundingBox(BoundingBox(layoutns, bb_id, pos_x, pos_y, width, height))
for i in range(numCompartments):
comp_id = allcompartments[i].id
if comp_id != "_compartment_default_":
compartmentGlyph = layout.createCompartmentGlyph()
compG_id = "CompG_" + comp_id
compartmentGlyph.setId(compG_id)
compartmentGlyph.setCompartmentId(comp_id)
bb_id = "bb_" + comp_id
pos_x = allcompartments[i].position.x
pos_y = allcompartments[i].position.y
width = allcompartments[i].size.x
height = allcompartments[i].size.y
compartmentGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
for i in range(numNodes):
spec_id = allNodes[i].id
spec_index = allNodes[i].index
spec_shapeIdx = allNodes[i].shape_index
speciesGlyph = layout.createSpeciesGlyph()
specG_id = "SpecG_" + spec_id + '_idx_' + str(spec_index)
speciesGlyph.setId(specG_id)
speciesGlyph.setSpeciesId(spec_id)
bb_id = "bb_" + spec_id + '_idx_' + str(spec_index)
pos_x = allNodes[i].position.x
pos_y = allNodes[i].position.y
width = allNodes[i].size.x
height = allNodes[i].size.y
speciesGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph = layout.createTextGlyph()
textG_id = "TextG_" + spec_id + '_idx_' + str(spec_index)
textGlyph.setId(textG_id)
bb_id = "bb_spec_text_" + spec_id + '_idx_' + str(
spec_index)
if spec_shapeIdx == 6: #rough by eyes
pos_x_text = pos_x + 50
pos_y_text = pos_y + 30
else:
pos_x_text = pos_x
pos_y_text = pos_y
textGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x_text, pos_y_text,
width, height))
textGlyph.setOriginOfTextId(specG_id)
textGlyph.setGraphicalObjectId(specG_id)
else: #there is no compartment
comp_id = "_compartment_default_"
compartmentGlyph = layout.createCompartmentGlyph()
compG_id = "CompG_" + comp_id
compartmentGlyph.setId(compG_id)
compartmentGlyph.setCompartmentId(comp_id)
bb_id = "bb_" + comp_id
pos_x = 10
pos_y = 10
width = 3900
height = 2400
compartmentGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width, height))
for i in range(numNodes):
spec_id = allNodes[i].id
spec_index = allNodes[i].index
spec_shapeIdx = allNodes[i].shape_index
speciesGlyph = layout.createSpeciesGlyph()
specG_id = "SpecG_" + spec_id + '_idx_' + str(spec_index)
speciesGlyph.setId(specG_id)
speciesGlyph.setSpeciesId(spec_id)
bb_id = "bb_" + spec_id + '_idx_' + str(spec_index)
pos_x = allNodes[i].position.x
pos_y = allNodes[i].position.y
width = allNodes[i].size.x
height = allNodes[i].size.y
speciesGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph = layout.createTextGlyph()
textG_id = "TextG_" + spec_id + '_idx_' + str(spec_index)
textGlyph.setId(textG_id)
if spec_shapeIdx == 6: #rough by eyes
pos_x_text = pos_x + 50
pos_y_text = pos_y + 30
else:
pos_x_text = pos_x
pos_y_text = pos_y
bb_id = "bb_spec_text_" + spec_id + '_idx_' + str(
spec_index)
textGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x_text, pos_y_text,
width, height))
textGlyph.setOriginOfTextId(specG_id)
textGlyph.setGraphicalObjectId(specG_id)
# create the ReactionGlyphs and SpeciesReferenceGlyphs
for i in range(numReactions):
reaction_id = allReactions[i].id
reactionGlyph = layout.createReactionGlyph()
reactionG_id = "RectionG_" + reaction_id
reactionGlyph.setId(reactionG_id)
reactionGlyph.setReactionId(reaction_id)
reactionCurve = reactionGlyph.getCurve()
ls = reactionCurve.createLineSegment()
centroid = api.compute_centroid(0, allReactions[i].sources,
allReactions[i].targets)
ls.setStart(Point(layoutns, centroid.x, centroid.y))
ls.setEnd(Point(layoutns, centroid.x, centroid.y))
rct = [] # id list of the rcts
prd = []
rct_index = []
prd_index = []
rct_num = len(allReactions[i].sources)
prd_num = len(allReactions[i].targets)
for j in range(rct_num):
rct.append(
get_node_by_index(netIn,
allReactions[i].sources[j]).id)
rct_index.append(
get_node_by_index(netIn,
allReactions[i].sources[j]).index)
for j in range(prd_num):
prd.append(
get_node_by_index(netIn,
allReactions[i].targets[j]).id)
prd_index.append(
get_node_by_index(netIn,
allReactions[i].targets[j]).index)
for j in range(rct_num):
ref_id = "SpecRef_" + reaction_id + "_rct" + str(j)
speciesReferenceGlyph = reactionGlyph.createSpeciesReferenceGlyph(
)
specsRefG_id = "SpecRefG_" + reaction_id + "_rct" + str(j)
specG_id = "SpecG_" + rct[j] + '_idx_' + str(rct_index[j])
speciesReferenceGlyph.setId(specsRefG_id)
speciesReferenceGlyph.setSpeciesGlyphId(specG_id)
speciesReferenceGlyph.setSpeciesReferenceId(ref_id)
speciesReferenceGlyph.setRole(SPECIES_ROLE_SUBSTRATE)
speciesReferenceCurve = speciesReferenceGlyph.getCurve()
cb = speciesReferenceCurve.createCubicBezier()
#cb = speciesReferenceCurve.createLineSegment()
cb.setStart(Point(layoutns, centroid.x, centroid.y))
handles = api.default_handle_positions(
netIn, allReactions[i].index)
pos_x = handles[1 + j].x
pos_y = handles[1 + j].y
cb.setBasePoint1(Point(layoutns, pos_x, pos_y))
cb.setBasePoint2(Point(layoutns, pos_x, pos_y))
pos_x = get_node_by_index(
netIn, allReactions[i].sources[j]).position.x
pos_y = get_node_by_index(
netIn, allReactions[i].sources[j]).position.y
width = get_node_by_index(
netIn, allReactions[i].sources[j]).size.x
height = get_node_by_index(
netIn, allReactions[i].sources[j]).size.y
cb.setEnd(
Point(layoutns, pos_x + 0.5 * width,
pos_y - 0.5 * height))
for j in range(prd_num):
ref_id = "SpecRef_" + reaction_id + "_prd" + str(j)
speciesReferenceGlyph = reactionGlyph.createSpeciesReferenceGlyph(
)
specsRefG_id = "SpecRefG_" + reaction_id + "_prd" + str(j)
specG_id = "SpecG_" + prd[j] + '_idx_' + str(prd_index[j])
speciesReferenceGlyph.setId(specsRefG_id)
speciesReferenceGlyph.setSpeciesGlyphId(specG_id)
speciesReferenceGlyph.setSpeciesReferenceId(ref_id)
speciesReferenceGlyph.setRole(SPECIES_ROLE_PRODUCT)
speciesReferenceCurve = speciesReferenceGlyph.getCurve()
cb = speciesReferenceCurve.createCubicBezier()
#cb = speciesReferenceCurve.createLineSegment()
cb.setStart(Point(layoutns, centroid.x, centroid.y))
handles = api.default_handle_positions(
netIn, allReactions[i].index)
pos_x = handles[1 + j].x
pos_y = handles[1 + j].y
cb.setBasePoint1(Point(layoutns, pos_x, pos_y))
cb.setBasePoint2(Point(layoutns, pos_x, pos_y))
pos_x = get_node_by_index(
netIn, allReactions[i].targets[j]).position.x
pos_y = get_node_by_index(
netIn, allReactions[i].targets[j]).position.y
width = get_node_by_index(
netIn, allReactions[i].targets[j]).size.x
height = get_node_by_index(
netIn, allReactions[i].targets[j]).size.y
cb.setEnd(
Point(layoutns, pos_x + 0.5 * width,
pos_y - 0.5 * height))
sbmlStr_layout = writeSBMLToString(
document) #sbmlStr is w/o layout info
#self.SBMLText.SetValue(sbmlStr_layout)
doc = readSBMLFromString(sbmlStr_layout)
model_layout = doc.getModel()
mplugin = model_layout.getPlugin("layout")
# add render information to the first layout
layout = mplugin.getLayout(0)
rPlugin = layout.getPlugin("render")
uri = RenderExtension.getXmlnsL2() if doc.getLevel(
) == 2 else RenderExtension.getXmlnsL3V1V1()
# enable render package
doc.enablePackage(uri, "render", True)
doc.setPackageRequired("render", False)
rPlugin = layout.getPlugin("render")
rInfo = rPlugin.createLocalRenderInformation()
rInfo.setId("info")
rInfo.setName("Render Information")
rInfo.setProgramName("RenderInformation")
rInfo.setProgramVersion("1.0")
# add some colors
color = rInfo.createColorDefinition()
color.setId("black")
color.setColorValue("#000000")
if numCompartments != 0:
for i in range(len(allcompartments)):
temp_id = allcompartments[i].id
if temp_id != '_compartment_default':
fill_color = allcompartments[i].fill_color
border_color = allcompartments[i].border_color
comp_border_width = allcompartments[i].border_width
fill_color_str = '#%02x%02x%02x' % (
fill_color.r, fill_color.g, fill_color.b)
border_color_str = '#%02x%02x%02x' % (
border_color.r, border_color.g, border_color.b)
# color = rInfo.createColorDefinition()
# color.setId("comp_fill_color" + str(i))
# color.setColorValue(fill_color_str)
# color = rInfo.createColorDefinition()
# color.setId("comp_border_color" + str(i))
# color.setColorValue(border_color_str)
# # add a list of styles
# style = rInfo.createStyle("compStyle" + str(i))
# style.getGroup().setFillColor("comp_fill_color" + str(i))
# style.getGroup().setStroke("comp_border_color" + str (i))
# style.getGroup().setStrokeWidth(comp_border_width)
# style.addType("COMPARTMENTGLYPH")
# rectangle = style.getGroup().createRectangle()
# rectangle.setCoordinatesAndSize(RelAbsVector(0,0),RelAbsVector(0,0),RelAbsVector(0,0),RelAbsVector(0,100),RelAbsVector(0,100))
color = rInfo.createColorDefinition()
color.setId("comp_fill_color")
color.setColorValue(fill_color_str)
color = rInfo.createColorDefinition()
color.setId("comp_border_color")
color.setColorValue(border_color_str)
# add a list of styles
style = rInfo.createStyle("compStyle")
style.getGroup().setFillColor("comp_fill_color")
style.getGroup().setStroke("comp_border_color")
style.getGroup().setStrokeWidth(comp_border_width)
style.addType("COMPARTMENTGLYPH")
rectangle = style.getGroup().createRectangle()
rectangle.setCoordinatesAndSize(RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 100),
RelAbsVector(0, 100))
else:
comp_border_width = 2.
#fill_color_str = '#9ea9ff'
#border_color_str = '#001dff'
#set default compartment with white color
fill_color_str = '#ffffff'
border_color_str = '#ffffff'
color = rInfo.createColorDefinition()
color.setId("comp_fill_color")
color.setColorValue(fill_color_str)
color = rInfo.createColorDefinition()
color.setId("comp_border_color")
color.setColorValue(border_color_str)
# add a list of styles
style = rInfo.createStyle("compStyle")
style.getGroup().setFillColor("comp_fill_color")
style.getGroup().setStroke("comp_border_color")
style.getGroup().setStrokeWidth(comp_border_width)
style.addType("COMPARTMENTGLYPH")
rectangle = style.getGroup().createRectangle()
rectangle.setCoordinatesAndSize(RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 100),
RelAbsVector(0, 100))
for i in range(len(allNodes)):
node = allNodes[i]
#print(node.shape)
try:
primitive, transform = node.shape.items[0]
spec_fill_color = primitive.fill_color
spec_border_color = primitive.border_color
spec_fill_color_str = '#%02x%02x%02x' % (spec_fill_color.r,
spec_fill_color.g,
spec_fill_color.b)
spec_border_color_str = '#%02x%02x%02x' % (
spec_border_color.r, spec_border_color.g,
spec_border_color.b)
spec_border_width = primitive.border_width
except: #text-only
#spec_fill_color_str = '#ffcc99'
#spec_border_color_str = '#ff6c09'
#set default species/node with white color
spec_fill_color_str = '#ffffff'
spec_border_color_str = '#ffffff'
#transparent color does not work
#spec_fill_color_str = '#000000'
#spec_border_color_str = '#000000'
spec_border_width = 2.
color = rInfo.createColorDefinition()
color.setId("spec_fill_color" + str(i))
color.setColorValue(spec_fill_color_str)
color = rInfo.createColorDefinition()
color.setId("spec_border_color" + str(i))
color.setColorValue(spec_border_color_str)
style = rInfo.createStyle("specStyle" + str(i))
style.getGroup().setFillColor("spec_fill_color" + str(i))
style.getGroup().setStroke("spec_border_color" + str(i))
style.getGroup().setStrokeWidth(spec_border_width)
style.addType("SPECIESGLYPH")
if node.shape_index == 1 or node.shape_index == 6: #ellipse/text-outside
ellipse = style.getGroup().createEllipse()
ellipse.setCenter2D(RelAbsVector(0, 50),
RelAbsVector(0, 50))
ellipse.setRadii(RelAbsVector(0, 50), RelAbsVector(0, 50))
elif node.shape_index == 2: #hexagon(6)
polygon = style.getGroup().createPolygon()
renderPoint1 = polygon.createPoint()
renderPoint1.setCoordinates(RelAbsVector(0, 100),
RelAbsVector(0, 50))
renderPoint2 = polygon.createPoint()
renderPoint2.setCoordinates(RelAbsVector(0, 75),
RelAbsVector(0, 7))
renderPoint3 = polygon.createPoint()
renderPoint3.setCoordinates(RelAbsVector(0, 25),
RelAbsVector(0, 7))
renderPoint4 = polygon.createPoint()
renderPoint4.setCoordinates(RelAbsVector(0, 0),
RelAbsVector(0, 50))
renderPoint5 = polygon.createPoint()
renderPoint5.setCoordinates(RelAbsVector(0, 25),
RelAbsVector(0, 86))
renderPoint6 = polygon.createPoint()
renderPoint6.setCoordinates(RelAbsVector(0, 75),
RelAbsVector(0, 86))
elif node.shape_index == 3: #line(2)
polygon = style.getGroup().createPolygon()
renderPoint1 = polygon.createPoint()
renderPoint1.setCoordinates(RelAbsVector(0, 0),
RelAbsVector(0, 50))
renderPoint2 = polygon.createPoint()
renderPoint2.setCoordinates(RelAbsVector(0, 100),
RelAbsVector(0, 50))
elif node.shape_index == 4: #triangle(3)
polygon = style.getGroup().createPolygon()
renderPoint1 = polygon.createPoint()
renderPoint1.setCoordinates(RelAbsVector(0, 100),
RelAbsVector(0, 50))
renderPoint2 = polygon.createPoint()
renderPoint2.setCoordinates(RelAbsVector(0, 25),
RelAbsVector(0, 7))
renderPoint3 = polygon.createPoint()
renderPoint3.setCoordinates(RelAbsVector(0, 25),
RelAbsVector(0, 86))
else: #rectangle shape_index = 0/text-only 5/demo-combo 7/others as default (rectangle)
rectangle = style.getGroup().createRectangle()
rectangle.setCoordinatesAndSize(RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 100),
RelAbsVector(0, 100))
style = rInfo.createStyle("textStyle")
style.getGroup().setStroke("black")
style.getGroup().setStrokeWidth(1.)
style.addType("TEXTGLYPH")
if numReactions != 0:
for i in range(len(allReactions)):
reaction_fill_color = allReactions[i].fill_color
reaction_fill_color_str = '#%02x%02x%02x' % (
reaction_fill_color.r, reaction_fill_color.g,
reaction_fill_color.b)
reaction_line_thickness = allReactions[i].line_thickness
color = rInfo.createColorDefinition()
color.setId("reaction_fill_color" + str(i))
color.setColorValue(reaction_fill_color_str)
style = rInfo.createStyle("reactionStyle" + str(i))
style.getGroup().setStroke("reaction_fill_color" + str(i))
style.getGroup().setStrokeWidth(reaction_line_thickness)
style.addType("REACTIONGLYPH SPECIESREFERENCEGLYPH")
sbmlStr_layout_render = writeSBMLToString(doc)
self.SBMLText.SetValue(sbmlStr_layout_render)