public static Element ranking_Genes(Document doc, IndividualStat is, int number) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
float[] scores = null;
Integer[] index;
if (number > Symbols.length) number = Symbols.length;
if (is != null) {
index = is.get_Order();
scores = is.get_GeneScores(Symbols.length - 1, 0);
for (int i = Symbols.length - 1; i >= Symbols.length - number; i--) {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[index[i]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index[i]]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index[i]] + 1));
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index[i]]));
XmlWriter.append_text_element(
doc,
gene,
Consts.XML_TAG_SCORE,
Float.toString(Math.round(scores[index[i]] * 10) / 10));
genes.appendChild(gene);
}
}
return genes;
}
public static Element overlap_Genes(
Document doc, String chr, int start, int end, IndividualStat is) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
if (ChrMap.containsKey(chr)) {
int[] range = binarySearchOverlap(ChrMap.get(chr), start, end);
if (range != null) {
float[] scores = null;
if (is != null) scores = is.get_GeneScores(range[1], range[0]);
for (int i = range[0]; i <= range[1]; i++) {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[i]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[i] + 1));
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[i]));
if (is != null)
XmlWriter.append_text_element(
doc,
gene,
Consts.XML_TAG_SCORE,
Float.toString(Math.round(scores[i - range[0]] * 10) / 10));
genes.appendChild(gene);
}
}
}
return genes;
}
