private Set<Vertex> computeMinVertexCover(Set<Vertex> side1, Set<Vertex> side2) {
Set<Vertex> konigSet = new HashSet<Vertex>();
Set<Vertex> unmatched = new TreeSet<Vertex>(side1);
unmatched.removeAll(matches);
// System.out.println("Matches: " + matches);
// System.out.println("side 1 unmatched set: " + unmatched);
for (Vertex v : unmatched) {
konigDFS(konigSet, v, false);
}
// System.out.println("Konig set: " + konigSet);
Set<Vertex> result = new HashSet<Vertex>(side2);
result.retainAll(konigSet);
// System.out.println("side 2 intersect konigSet: " + result);
Set<Vertex> side1notInKonigSet = new HashSet<Vertex>(side1);
side1notInKonigSet.removeAll(konigSet);
// System.out.println("side 1 not in Konig set: " + side1notInKonigSet);
result.addAll(side1notInKonigSet);
return result;
}
public static double repairAccuracy(Set<RepairedCell> truth, Set<RepairedCell> found) {
if (found.size() != 0) {
Set<RepairedCell> tAndF = new HashSet<RepairedCell>();
tAndF.addAll(truth);
tAndF.retainAll(found);
double precision = tAndF.size() * 1.0 / found.size(),
recall = tAndF.size() * 1.0 / truth.size();
if (debug)
System.out.println("repair precision = " + precision + ", repair recall = " + recall);
return 2 * precision * recall / (precision + recall);
}
return 0;
}
private void writeWeights(
String orig, GeneBranch from, GeneBranch to, String edgeType, Writer writer)
throws IOException {
Set<String> dwstr = to.getAllGenes();
dwstr.retainAll(downstream.get(orig));
assert !dwstr.isEmpty();
double cumPval = calcPVal(orig, dwstr);
boolean upreg = calcChangeDirection(orig, to.gene);
String key = from.gene + " " + edgeType + " " + to.gene;
writer.write("edge\t" + key + "\tcolor\t" + val2Color(cumPval, 0) + "\n");
writer.write("edge\t" + key + "\twidth\t2\n");
if (affectedDw.get(orig).contains(to.gene)) {
double pval = calcPVal(orig, Collections.singleton(to.gene));
writer.write("node\t" + to.gene + "\tcolor\t" + val2Color(pval, upreg ? 1 : -1) + "\n");
} else {
writer.write("node\t" + to.gene + "\tcolor\t255 255 255\n");
}
}