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); }