edgeAttributes = Cytoscape.getEdgeAttributes();
nodeIds = new ArrayList<Integer>();
edgeIds = new ArrayList<Integer>();
// Process the layouts (Generate full id set and all edges for elements)
LayoutManipulator layoutManipulator = new LayoutManipulator(document.getModel(), layout);
layoutManipulator.generateAllEdges();
layout = layoutManipulator.getLayout();
addSpeciesGlyphNodes();
addReactionGlyphNodes();
addModelEdges();
addQualitativeModelEdges();
}