Пример #1
0
 private void handleShowPrevExon(Tuple request) {
   SearchService searchService = ServiceLocator.instance().getSearchService();
   ExonDTO exonDTO = searchService.findPrevExon(request.getInt("exon_id"));
   request.set("__action", "showExon");
   request.set("exon_id", exonDTO.getId());
   this.handleShowExon(request);
 }
Пример #2
0
  /**
   * Needed for hyperlink form switches...
   *
   * @param request
   * @throws DatabaseException
   */
  private void doXrefselect(Tuple request) throws DatabaseException {
    // also set the parent menu
    if (getParent() != null && getParent() instanceof MenuController) {
      // set the filter to select the xref-ed entity
      pager.resetFilters();
      getModel().setUserRules(new ArrayList<QueryRule>());
      QueryRule rule =
          new QueryRule(
              request.getString("attribute"),
              QueryRule.Operator.valueOf(request.getString("operator")),
              request.getString("value"));
      pager.addFilter(rule);

      // tell "my" menu to select me
      Tuple parentRequest = new SimpleTuple();
      String aChildName = getModel().getName();
      ScreenController<?> aParent = getParent();
      while (aParent != null) {
        if (aParent instanceof MenuModel) {
          parentRequest.set("select", aChildName);
          MenuController c = (MenuController) aParent;
          c.doSelect(parentRequest);
        }
        aChildName = aParent.getName();
        aParent = aParent.getParent();
      }
    }
  }
Пример #3
0
 private void handleShowNextMutation(Tuple request) {
   SearchService searchService = ServiceLocator.instance().getSearchService();
   MutationSummaryDTO mutationSummaryDTO =
       searchService.findNextMutation(request.getString("mid"));
   request.set("mid", mutationSummaryDTO.getIdentifier());
   this.handleShowMutation(request);
 }
Пример #4
0
 /** NOTE: Copied from InvestigationExcelReader */
 private void writeSheetToFile(Sheet sheet, File file) throws FileNotFoundException {
   List<String> headers = new ArrayList<String>();
   Cell[] headerCells = sheet.getRow(0); // assume headers are on first
   // line
   ArrayList<Integer> namelessHeaderLocations = new ArrayList<Integer>(); // allow
   // for
   // empty
   // columns,
   // also
   // column
   // order
   // does
   // not
   // matter
   for (int i = 0; i < headerCells.length; i++) {
     if (!headerCells[i].getContents().equals("")) {
       headers.add(headerCells[i].getContents());
     } else {
       headers.add("nameless" + i);
       namelessHeaderLocations.add(i);
     }
   }
   PrintWriter pw = new PrintWriter(file);
   CsvWriter cw = new CsvWriter(pw, headers);
   cw.setMissingValue("");
   cw.writeHeader();
   for (int rowIndex = 1; rowIndex < sheet.getRows(); rowIndex++) {
     Tuple t = new SimpleTuple();
     int colIndex = 0;
     for (Cell c : sheet.getRow(rowIndex)) {
       if (!namelessHeaderLocations.contains(colIndex)) {
         t.set(headers.get(colIndex), c.getContents());
       }
       colIndex++;
     }
     cw.writeRow(t);
   }
   cw.close();
 }
 private boolean writeSheetToFile(Sheet sheet, File file) throws FileNotFoundException {
   List<String> headers = new ArrayList<String>();
   Cell[] headerCells = sheet.getRow(0); // assume headers are on first line
   if (headerCells.length == 0) {
     return false;
   }
   ArrayList<Integer> namelessHeaderLocations =
       new ArrayList<Integer>(); // allow for empty columns, also column order does not matter
   for (int i = 0; i < headerCells.length; i++) {
     if (!headerCells[i].getContents().equals("")) {
       headers.add(headerCells[i].getContents());
     } else {
       headers.add("nameless" + i);
       namelessHeaderLocations.add(i);
     }
   }
   PrintWriter pw = new PrintWriter(file);
   CsvWriter cw = new CsvWriter(pw, headers);
   cw.setMissingValue("");
   cw.writeHeader();
   for (int rowIndex = 1; rowIndex < sheet.getRows(); rowIndex++) {
     Tuple t = new SimpleTuple();
     int colIndex = 0;
     for (Cell c : sheet.getRow(rowIndex)) {
       if (!namelessHeaderLocations.contains(colIndex)
           && colIndex < headers.size()
           && c.getContents() != null) {
         t.set(headers.get(colIndex), c.getContents());
       }
       colIndex++;
     }
     cw.writeRow(t);
   }
   cw.close();
   return true;
 }
Пример #6
0
 private void handleShowFirstExon(Tuple request) {
   SearchService searchService = ServiceLocator.instance().getSearchService();
   ExonDTO exonDTO = searchService.findFirstExon();
   request.set("exon_id", exonDTO.getId());
   this.handleShowExon(request);
 }