private Paint withoutGraphTheory(BiologicalNodeAbstract v) { boolean medium_check = false; if (v instanceof Transition) { if (((Transition) v).isSimulationActive()) { return Color.red; } } if (psV.getPicked().isEmpty()) { if (psE.getPicked().isEmpty()) { if (v.isReference() || v.isHidden()) return Color.LIGHT_GRAY; else if (v.hasBrendaNode() || v.hasKEGGNode()) return Color.RED; else if (settings.isBackgroundColor()) return Color.WHITE; else // return Color.BLACK; return Color.DARK_GRAY; } else { Set<BiologicalEdgeAbstract> set = psE.getPicked(); BiologicalEdgeAbstract e; for (Iterator<BiologicalEdgeAbstract> it = set.iterator(); it.hasNext(); ) { e = it.next(); // Pair points = e.getEndpoints(); if (v == e.getFrom() || v == e.getTo()) medium_check = true; } if (medium_check) { if (settings.isBackgroundColor()) { return Color.WHITE; } else { // return Color.BLACK; return Color.DARK_GRAY; } } else { return Color.LIGHT_GRAY; } } } else { if (psV.isPicked(v)) if (settings.isBackgroundColor()) return Color.WHITE; else // return Color.BLACK; // return Color.DARK_GRAY; return Color.BLUE; else { BiologicalNodeAbstract w; Iterator<BiologicalNodeAbstract> iter = pw.getGraph().getJungGraph().getNeighbors(v).iterator(); while (iter.hasNext()) { w = iter.next(); if (psV.isPicked(w)) medium_check = true; } Set<BiologicalEdgeAbstract> set = psE.getPicked(); BiologicalEdgeAbstract bea; for (Iterator<BiologicalEdgeAbstract> it = set.iterator(); it.hasNext(); ) { bea = it.next(); if (v == bea.getFrom() || v == bea.getTo()) medium_check = true; } if (medium_check) if (settings.isBackgroundColor()) return Color.WHITE; else // return Color.BLACK; return Color.DARK_GRAY; else return Color.LIGHT_GRAY; } } }