sl.writeSBMLFile("ftest_layout_override.xml")
# This will write if allowed, and when it is read back in, it displays as
# a single blob of garbage because everything is plotted with the same centers
# sl.writeSBMLFile("test_layout_override.xml")
# slr = SBMLlayout("test_layout_override.xml", autoComputeLayout=False)
slr = SBMLlayout(str(model_file), autoComputeLayout=False)
slr._describeModel()
slr.drawNetwork()
assert slr.getNodeTextAnchor("MKK_P") == "center"
# bottom means top in this situation
assert slr.getNodeVTextAnchor("MAPK") == "bottom"
assert slr.getNodeFontSize("MKK") == 11
assert slr.getNodeEdgeColor("MKKK") == "#969696"
assert slr.getNodeFillColor("MAPK_P") == "#c9e0fb"
assert slr.getReactionEdgeColor("J1") == [('MKKK_P', 'SUBSTRATE', '#ff9900'),
('MKKK', 'PRODUCT', '#ff9900')]
assert slr.getReactionFillColor("J2") == [('MKK', 'SUBSTRATE', '#ff9900'),
('MKK_P', 'PRODUCT', '#ff9900'),
('MKKK_P', 'ACTIVATOR', '#ff9900')]
sl.setNodeFillColor("X0", "yellow")
sl.setNodeEdgeWidth("all", 2)
sl.setNodeEdgeWidth("X1", 5)
sl.setNodeEdgeWidth(["A", "B", "C"], 3)
sl.setReactionCurveWidth("_J0", 3)
sl.setReactionColor("all", "purple")
sl.setReactionColor("_J0", "green")
# KeyError in setter
#sl.setReactionColor("_J", "green")
# ValueError in matplotlib
#sl.setReactionColor("_J1", "greene")
print("reaction edge: ", sl.getReactionEdgeColor("_J0"))
print("reaction fill: ", sl.getReactionFillColor("_J0"))
sl.drawNetwork()
sl.showLayoutAlgorithmOptions()
#sl.setLayoutAlgorithm_grav(20)
sl.setLayoutAlgorithmOptions(k=40, grav=20)
#sl.setLayoutAlgorithmOptions(mag=1)
sl.showLayoutAlgorithmOptions()
sl.regenerateLayout()
assert sl.getNodeVTextAnchor("pyruvate") == "bottom"
assert sl.getNodeVTextAnchor("ADP") == "bottom"
assert sl.getNodeFillColor("NAD") == "#7fff55"
assert sl.getNodeFillColor("NADH") == "#d4ffaa"
assert sl.getNodeFillColor("ATP") == "#ff7faa"
assert sl.getNodeFillColor("ADP") == "#ffd4d4"
assert sl.getNodeEdgeColor("glycerate_3_phosphate") == "#969696"
sl.writeSBMLFile("glycolysis_original.xml")
slr = SBMLlayout("glycolysis_original.xml")
slr.drawNetwork()
assert slr.getNumberOfNodes() == 23
assert slr.getNumberOfReactions() == 11
assert slr.getReactionCurveWidth("J9") == [('ATP', 'SUBSTRATE', 2.0),
('ADP', 'PRODUCT', 2.0)]
assert slr.getReactionEdgeColor("J10") == [('External_acetaldehyde',
'SUBSTRATE', '#ff9900'),
('Sink', 'PRODUCT', '#ff9900')]
assert slr.getReactionFillColor("J0") == [('External_glucose', 'SUBSTRATE',
'#ff9900'),
('Glucose', 'PRODUCT', '#ff9900')]
sl.setNodeFillColor("A", "pink")
sl.setNodeEdgeColor("all", "green")
sl.setNodeEdgeWidth(["D", "X1", "C"], 3)
sl.setNodeFontWeight(["X0", "A", "B", "C", "D", "X1"], "bold")
sl.setNodeTextAnchor("X0", "right")
sl.setNodeTextAnchor("A", "left")
sl.setNodeVTextAnchor("B", "center")
sl.drawNetwork()
print("_J0 width: ", sl.getReactionCurveWidth("_J0"))
print("_J1 edge color: ", sl.getReactionEdgeColor("_J1"))
print("_J1 fill color: ", sl.getReactionFillColor("_J1"))
print("_J3 edge color: ", sl.getReactionEdgeColor("_J3"))
print("_J3 fill color: ", sl.getReactionFillColor("_J3"))
print("_J4 edge color: ", sl.getReactionEdgeColor("_J4"))
print("_J4 fill color: ", sl.getReactionFillColor("_J4"))
print("A: fill color: ", sl.getNodeFillColor("A"))
print("B: edge color: ", sl.getNodeEdgeColor("B"))
print("C: edge width: ", sl.getNodeEdgeWidth("C"))
print("X0: text anchor: ", sl.getNodeTextAnchor("X0"))
print("A: text anchor: ", sl.getNodeTextAnchor("A"))
print("B: vtext anchor: ", sl.getNodeVTextAnchor("B"))
