public Graph search(IFas fas, List<Node> nodes) {
long beginTime = System.currentTimeMillis();
logger.log("info", "Starting FCI algorithm.");
logger.log("info", "Independence test = " + getIndependenceTest() + ".");
setMaxPathLength(maxPathLength);
this.graph = new EdgeListGraph(nodes);
long start1 = System.currentTimeMillis();
fas.setKnowledge(getKnowledge());
fas.setDepth(depth);
fas.setVerbose(verbose);
// fas.setFci(true);
graph = fas.search();
graph.reorientAllWith(Endpoint.CIRCLE);
this.sepsets = fas.getSepsets();
long stop1 = System.currentTimeMillis();
long start2 = System.currentTimeMillis();
// The original FCI, with or without JiJi Zhang's orientation rules
fciOrientbk(getKnowledge(), graph, variables);
ruleR0_RFCI(getRTuples()); // RFCI Algorithm 4.4
doFinalOrientation();
long endTime = System.currentTimeMillis();
this.elapsedTime = endTime - beginTime;
logger.log("graph", "Returning graph: " + graph);
long stop2 = System.currentTimeMillis();
logger.log("info", "Elapsed time adjacency search = " + (stop1 - start1) / 1000L + "s");
logger.log("info", "Elapsed time orientation search = " + (stop2 - start2) / 1000L + "s");
return graph;
}
