private TableReferenceObject getTableReferenceObject(String technology, String endpoint) {
if (endpoint.equalsIgnoreCase("[sample]")) {
return ConfigurationManager.selectTROForUserSelection(MappingObject.STUDY_SAMPLE);
} else {
technology =
technology.equalsIgnoreCase(AssaySelectionUI.NO_TECHNOLOGY_TEXT) ? "" : technology;
return ConfigurationManager.selectTROForUserSelection(endpoint, technology);
}
}
/**
* Create JPanel asking users to select the assay used in each file (iteratively)
*
* @param fileToMap - file to be mapped.
* @return JPanel containing elements allowing confirmation of assay type
*/
private JLayeredPane createAssayUsedPanel(final String fileToMap) {
Map<String, List<String>> measToAllowedTechnologies =
ConfigurationManager.getAllowedTechnologiesPerEndpoint();
final AssaySelectionUI assaySelection = new AssaySelectionUI(measToAllowedTechnologies);
assaySelection.createGUI();
if (preExistingMapping != null) {
assaySelection.addAssaysToDefine(preExistingMapping.getPreviousAssaySelections());
}
final JLayeredPane finalPanel =
getGeneralLayout(
selectAssaysUsedHeader, breadcrumb2, fileBeingMapped, assaySelection, getHeight());
// by having an array of MouseListeners, we can pass this to a History object which allows the
// functionality specific
// to buttons on certain pages to be transported.
final MouseListener[] listeners = new MouseListener[2];
listeners[0] =
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
backButton.setIcon(backOver);
}
public void mouseExited(MouseEvent mouseEvent) {
backButton.setIcon(back);
}
public void mousePressed(MouseEvent mouseEvent) {
backButton.setIcon(back);
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
HistoryComponent hc = previousPage.pop();
assignListenerToLabel(backButton, hc.getListeners()[0]);
assignListenerToLabel(nextButton, hc.getListeners()[1]);
setCurrentPage(hc.getDisplayComponent());
}
});
}
};
assignListenerToLabel(backButton, listeners[0]);
listeners[1] =
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
nextButton.setIcon(nextOver);
}
public void mouseExited(MouseEvent mouseEvent) {
nextButton.setIcon(next);
}
public void mousePressed(MouseEvent mouseEvent) {
nextButton.setIcon(next);
previousPage.push(new HistoryComponent(finalPanel, listeners));
assaysToBeDefined = assaySelection.getAssaysToDefine();
assaySelections = new HashMap<String, AssaySelection>();
Thread loadFileProcess =
new Thread(
new Runnable() {
public void run() {
// attempt to load the supplied fileToMap/directory...
Loader l = new Loader();
String fileName = null;
try {
Map<String, String[]> fileColumnMap = l.loadFile(new File(fileToMap));
fileColumns = null;
for (String file : fileColumnMap.keySet()) {
fileColumns = fileColumnMap.get(file);
fileBeingMapped = file.substring(file.lastIndexOf(File.separator) + 1);
fileName = file;
break;
}
status.setText("");
reader = l.getReaderToUse();
if (reader == FileLoader.SHEET_READER) {
fileName = fileToMap;
}
// we will always start off with defining the study sample file!
// it will be in the create mappings listeners where we
// will iterate around the assays to be defined.
setCurrentPage(
createMappings(
-1,
getTableReferenceObject("", "[Sample]"),
fileColumns,
fileName,
reader));
} catch (NoAvailableLoaderException e) {
setCurrentPage(lastPage);
showErrorPanel();
log.error("No loader available for file format!");
} catch (MultipleExtensionsException e) {
setCurrentPage(lastPage);
showErrorPanel();
log.error(
"There are files with different extensions in the selected folder! This is not allowed.");
} catch (BiffException e) {
setCurrentPage(lastPage);
showErrorPanel();
log.error(e.getMessage());
} catch (IOException e) {
setCurrentPage(lastPage);
showErrorPanel();
log.error(e.getMessage());
}
}
});
lastPage = currentPage;
setCurrentPage(workingProgressScreen);
loadFileProcess.start();
}
};
assignListenerToLabel(nextButton, listeners[1]);
return finalPanel;
}