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"); } }
private int countShared(GeoPoint[] a, GeoPoint[] b) { Set<GeoPoint> points = new HashSet<GeoPoint>(Arrays.asList(a)); points.retainAll(Arrays.asList(b)); return points.size(); }