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);
}
/**
* 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();
}
}
}
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);
}
/** 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;
}
private void handleShowFirstExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
ExonDTO exonDTO = searchService.findFirstExon();
request.set("exon_id", exonDTO.getId());
this.handleShowExon(request);
}