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 void writeSelf(
String origTarget, GeneBranch currentParent, GeneBranch down, Writer writer1, Writer writer2)
throws IOException {
if (!down.isSelected()) return;
String edgeTag;
if (down.isLeaf() || travExp.getUpstream(down.gene).contains(currentParent)) {
edgeTag = SIFEnum.CONTROLS_EXPRESSION_OF.getTag();
} else edgeTag = SIFEnum.CONTROLS_STATE_CHANGE_OF.getTag();
writer1.write(currentParent.gene + "\t" + edgeTag + "\t" + down.gene + "\n");
writeWeights(origTarget, currentParent, down, edgeTag, writer2);
writeBranches(origTarget, down, writer1, writer2);
}