/**
* Create a visualization of the mapping showing what columns the file had and what isatab fields
* each of these columns have been mapped to
*
* @param sequence - sequence of assay processing.
* @param nameOfFileBeingMapped - name to save the mapping visualization as.
* @param mapping - Mappings for each isatab file to the incoming column name(s) and any literals.
* @return JLayeredPane containing the GUI to display the mapping visualization.
*/
private JLayeredPane createMappingVisualization(
final int sequence,
final String nameOfFileBeingMapped,
Map<MappingField, List<String>> mapping) {
JPanel visContainer = new JPanel();
visContainer.setLayout(new BoxLayout(visContainer, BoxLayout.PAGE_AXIS));
visContainer.setSize(
new Dimension((int) (menuPanels.getWidth() * 0.80), (int) (menuPanels.getHeight() * 0.90)));
Tree t = null;
GenerateMappingView gmv = new GenerateMappingView(nameOfFileBeingMapped, mapping);
File treeFile = gmv.generateView();
try {
t = (Tree) new TreeMLReader().readGraph(treeFile);
} catch (Exception e) {
e.printStackTrace();
}
// create a new treemap
final TreeView tview =
new TreeView(
t,
new Dimension(
(int) (menuPanels.getWidth() * 0.80), (int) (menuPanels.getHeight() * 0.90)));
tview.setBackground(UIHelper.BG_COLOR);
tview.setForeground(UIHelper.GREY_COLOR);
visContainer.add(tview);
JLabel help_section = new JLabel(mappingVisualisationHelp);
visContainer.add(help_section);
ImageIcon crumb = ((sequence - 1) == -1) ? breadcrumb4 : breadcrumb6;
final JLayeredPane finalPanel =
getGeneralLayout(mappingOverviewHeader, crumb, "", visContainer, 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);
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
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) {
nextButton.setIcon(next);
Thread performMappingProcess =
new Thread(
new Runnable() {
public void run() {
try {
if (sequence <= assaysToBeDefined.size() - 1) {
AssaySelection aso = assaysToBeDefined.get(sequence);
String nextMeasurement = aso.getMeasurement();
String nextTechnology = aso.getTechnology();
setCurrentPage(
createMappings(
sequence,
getTableReferenceObject(nextTechnology, nextMeasurement),
fileColumns,
nameOfFileBeingMapped,
reader));
} else {
setCurrentPage(createSaveMappings());
}
} catch (BiffException e) {
setCurrentPage(lastPage);
log.error(e.getMessage());
} catch (IOException e) {
setCurrentPage(lastPage);
log.error(e.getMessage());
} catch (NoAvailableLoaderException e) {
setCurrentPage(lastPage);
log.error(e.getMessage());
}
}
});
lastPage = currentPage;
setCurrentPage(workingProgressScreen);
performMappingProcess.start();
}
};
assignListenerToLabel(nextButton, listeners[1]);
return finalPanel;
}
/**
* 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;
}