Java Model.getRuleCount方法代码示例

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
private void parseRuleSBOL(Model sbmlModel, HashMap<String, AssemblyNode2> idToNode) {
	for (int i = 0; i < sbmlModel.getRuleCount(); i++) {
		Rule sbmlRule = sbmlModel.getRule(i);
		// Creates assembly node for rule
		if (sbmlRule.isAssignment() || sbmlRule.isRate()) {
			AssemblyNode2 ruleNode = constructNode(sbmlRule);
			if (ruleNode.getURIs().size() > 0)
				containsSBOL = true;
			// Connects assembly nodes for input species, reaction rates, and parameters to node for rule
			parseMath(sbmlRule, ruleNode, idToNode);
			// Connects assembly node for rule to node for its output species or parameter
			String output = SBMLutilities.getVariable(sbmlRule);
			if (output != null && idToNode.containsKey(output)) {
				AssemblyNode2 outputNode = idToNode.get(output);
				constructEdge(ruleNode, outputNode);
			}
			if (sbmlRule.getExtensionPackages().containsKey(CompConstants.namespaceURI))
				parsePortMappings(sbmlRule, ruleNode, idToNode);
		}
	}
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
/**
 * Determines if a variable is already in an initial assignment, assignment
 * rule, or rate rule
 */
public static boolean keepVarAssignRule(BioModel bioModel, String selected, String id) {
	if (!selected.equals(id)) {
		Model model = bioModel.getSBMLDocument().getModel();
		for (int i = 0; i < model.getInitialAssignmentCount(); i++) {
			InitialAssignment init = model.getInitialAssignment(i);
			if (init.getVariable().equals(id))
				return false;
		}
		for (int i = 0; i < model.getEventCount(); i++) {
			Event event = model.getEvent(i);
			for (int j = 0; j < event.getEventAssignmentCount(); j++) {
				if (id.equals(event.getListOfEventAssignments().get(j).getVariable())) {
					return false;
				}
			}
		}
		for (int i = 0; i < model.getRuleCount(); i++) {
			Rule rule = model.getRule(i);
			if (rule.isAssignment() && SBMLutilities.getVariable(rule).equals(id))
				return false;
			if (rule.isRate() && SBMLutilities.getVariable(rule).equals(id))
				return false;
		}
	}
	return true;
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
public static void expandFunctionDefinitions(SBMLDocument doc)
{
	Model model = doc.getModel();
	for (int i = 0; i < model.getInitialAssignmentCount(); i++)
	{
		InitialAssignment ia = model.getListOfInitialAssignments().get(i);
		if (ia.isSetMath())
		{
			ia.setMath(inlineFormula(model, ia.getMath()));
		}
	}
	for (int i = 0; i < model.getRuleCount(); i++)
	{
		Rule r = model.getRule(i);
		if (r.isSetMath())
		{
			r.setMath(inlineFormula(model, r.getMath()));
		}
	}
	for (int i = 0; i < model.getConstraintCount(); i++)
	{
		Constraint c = model.getConstraint(i);
		if (c.isSetMath())
		{
			c.setMath(inlineFormula(model, c.getMath()));
		}
	}
	for (int i = 0; i < model.getEventCount(); i++)
	{
		Event e = model.getEvent(i);
		if (e.getDelay() != null && e.getDelay().isSetMath())
		{
			e.getDelay().setMath(inlineFormula(model, e.getDelay().getMath()));
		}
		if (e.getTrigger() != null && e.getTrigger().isSetMath())
		{
			e.getTrigger().setMath(inlineFormula(model, e.getTrigger().getMath()));
		}
		if (e.getPriority() != null && e.getPriority().isSetMath())
		{
			e.getPriority().setMath(inlineFormula(model, e.getPriority().getMath()));
		}
		for (int j = 0; j < e.getEventAssignmentCount(); j++)
		{
			EventAssignment ea = e.getListOfEventAssignments().get(j);
			if (ea.isSetMath())
			{
				ea.setMath(inlineFormula(model, ea.getMath()));
			}
		}
	}
}