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;
}
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 find_Gene(Document doc, String prefix) {
prefix = prefix.toUpperCase();
if (prefix.matches("C[XY0-9]+ORF")) {
prefix = prefix.replaceFirst("ORF", "orf");
} else if (prefix.matches("C[XY0-9]+OR")) {
prefix = prefix.replaceFirst("OR", "or");
} else if (prefix.matches("^C[XY0-9]+O")) {
prefix = prefix.replaceFirst("O", "o");
}
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
int match = binarySearchPrefix(prefix);
if (match >= 0) {
for (int i = match; i < match + 5; i++) {
if (i >= Symbols_sorted.length || !Symbols_sorted[i].startsWith(prefix)) return genes;
else {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols_sorted[i]);
int index = SymbolMap.get(Symbols_sorted[i]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index] + 1));
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index]));
genes.appendChild(gene);
}
}
}
return genes;
}
public static Element gene_Info(Document doc, String symbol) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
if (SymbolMap.containsKey(symbol)) {
int index = SymbolMap.get(symbol);
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[index]);
genes.appendChild(gene);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index] + 1));
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index]));
if (!RefSeqs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_REFSEQ, RefSeqs[index]);
if (!UCSCs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_UCSC, UCSCs[index]);
if (!Ensembls[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_ENSEMBL, Ensembls[index]);
if (!Entrezs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_ENTREZ, Entrezs[index]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_HGNC, HGNCs[index]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_NAME, Names[index]);
}
return genes;
}