public MappingChoice(
String[] columnsToBeMappedTo, boolean lastInList, ISAField preExistingMapping) {
this(columnsToBeMappedTo, lastInList, preExistingMapping, MappingEntryGUI.getInitialData());
}
/**
* Create JPanel allowing users to map a column to an ISATAB column in the sample or assay files.
*
* @param sequence - which sequence we are currently in with respect to defining the mappings. -1
* = defining sample file.
* @param tableReference - TableReferenceObject to be used for the definition.
* @param columnsToBeMappedTo - array of strings representing header value to be mapped to.
* @param fileName - name of file being mapped
* @param readerToUse - type of reader to use, @see FileLoader.CSV_READER_TXT,
* FileLoader.CSV_READER_CSV or FileLoader.SHEET_READER
* @return JPanel containing the GUI to allow for mappings!
*/
private JLayeredPane createMappings(
final int sequence,
final TableReferenceObject tableReference,
final String[] columnsToBeMappedTo,
final String fileName,
final int readerToUse)
throws BiffException, IOException, NoAvailableLoaderException {
fixedMappings = sequence == -1 ? new HashMap<String, MappedElement>() : fixedMappings;
final MappingEntryGUI mappingTableGUI =
new MappingEntryGUI(
tableReference,
columnsToBeMappedTo,
fileName,
readerToUse,
preExistingMapping,
fixedMappings);
mappingTableGUI.performPreliminaryLoading();
mappingTableGUI.createGUI();
mappingTableGUI.setSize(
new Dimension((int) (menuPanels.getWidth() * 0.80), (int) (menuPanels.getHeight() * 0.90)));
mappingTableGUI.setBorder(null);
ImageIcon crumb = sequence == -1 ? breadcrumb3 : breadcrumb5;
final JLayeredPane finalPanel =
getGeneralLayout(
performMappingHeader,
crumb,
getDescriptiveStringForFile(fileBeingMapped, sequence),
mappingTableGUI,
getHeight());
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);
HistoryComponent hc = previousPage.pop();
setCurrentPage(hc.getDisplayComponent());
assignListenerToLabel(backButton, hc.getListeners()[0]);
assignListenerToLabel(nextButton, hc.getListeners()[1]);
}
};
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) {
// call mapping function!
Thread mappingThread =
new Thread(
new Runnable() {
public void run() {
final MappingLogic mu =
new MappingLogic(
mappingTableGUI.getTreeInfo(),
tableReference,
readerToUse,
mapToBlankFields);
TableReferenceObject populatedTRO = mu.doMapping(fileName, readerToUse);
// whenever we create the mappings now, we now add the mappings in a Map
// which
// point to the populated TROs for each of the assays to be defined and the
// study
// sample file to be defined!
if (sequence == -1) {
fixedMappings.put(
"Sample Name", mappingTableGUI.getMappingNodeForField("Sample Name"));
definitions.put(MappingObject.STUDY_SAMPLE, populatedTRO);
} else {
assaySelections.put(
populatedTRO.getTableName(), assaysToBeDefined.get(sequence));
definitions.put(populatedTRO.getTableName(), populatedTRO);
}
// at this point, we want to populate a Map relating field names
// with ISAFieldMappings for output at a later stage in XML format.
mappingsToSave.putAll(mappingTableGUI.createMappingRefs());
nextButton.setIcon(next);
previousPage.push(new HistoryComponent(finalPanel, listeners));
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
setCurrentPage(
createMappingVisualization(
sequence + 1, fileName, mu.getVisMapping()));
}
});
}
});
setCurrentPage(workingProgressScreen);
mappingThread.start();
}
};
assignListenerToLabel(nextButton, listeners[1]);
return finalPanel;
}