示例#1
0
文件: Genes.java 项目: dgaston/FGB
 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;
 }
示例#2
0
文件: Genes.java 项目: dgaston/FGB
 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;
 }
示例#3
0
文件: Genes.java 项目: dgaston/FGB
 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;
 }
示例#4
0
文件: Genes.java 项目: dgaston/FGB
 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;
 }