public Graph search(IFas fas, List<Node> nodes) { this.logger.log("info", "Starting PC algorithm"); this.logger.log("info", "Independence test = " + getIndependenceTest() + "."); // this.logger.log("info", "Variables " + independenceTest.getVariables()); long startTime = System.currentTimeMillis(); if (getIndependenceTest() == null) { throw new NullPointerException(); } List<Node> allNodes = getIndependenceTest().getVariables(); if (!allNodes.containsAll(nodes)) { throw new IllegalArgumentException( "All of the given nodes must " + "be in the domain of the independence test provided."); } fas.setKnowledge(getKnowledge()); fas.setDepth(getDepth()); fas.setVerbose(verbose); graph = fas.search(); sepsets = fas.getSepsets(); this.numIndependenceTests = fas.getNumIndependenceTests(); this.numFalseDependenceJudgements = fas.getNumFalseDependenceJudgments(); this.numDependenceJudgements = fas.getNumDependenceJudgments(); // enumerateTriples(); SearchGraphUtils.pcOrientbk(knowledge, graph, nodes); SearchGraphUtils.orientCollidersUsingSepsets(this.sepsets, knowledge, graph, verbose); MeekRules rules = new MeekRules(); rules.setAggressivelyPreventCycles(this.aggressivelyPreventCycles); rules.setKnowledge(knowledge); rules.setUndirectUnforcedEdges(false); rules.orientImplied(graph); this.logger.log("graph", "\nReturning this graph: " + graph); this.elapsedTime = System.currentTimeMillis() - startTime; this.logger.log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s"); this.logger.log("info", "Finishing PC Algorithm."); this.logger.flush(); return graph; }