private JPanel createCompressionRateChoiceUI() {
JPanel compressionOptionContainer = new JPanel(new BorderLayout());
selectedCompression =
UIHelper.createLabel("", UIHelper.VER_12_PLAIN, UIHelper.DARK_GREEN_COLOR, JLabel.CENTER);
OptionGroup<String> compressionOptions =
new OptionGroup<String>(OptionGroup.HORIZONTAL_ALIGNMENT, true, 90);
compressionOptions.addOptionItem(
"<html><strong>fast</strong> speed & <strong>low</strong> compression</html>",
true,
fastLowCompressionSelected,
fastLowCompressionNotSelected,
true,
false);
compressionOptions.addOptionItem(
"<html><strong>medium</strong> speed & <strong>medium</strong> compression</html>",
false,
medCompressionSelected,
medCompressionNotSelected,
true,
false);
compressionOptions.addOptionItem(
"<html><strong>slow</strong> speed & <strong>high</strong> compression</html>",
false,
slowHighCompressionSelected,
slowHighCompressionNotSelected,
true,
false);
compressionOptionContainer.add(new JLabel(chooseCompression, JLabel.LEFT), BorderLayout.NORTH);
compressionOptionContainer.add(compressionOptions, BorderLayout.CENTER);
compressionOptions.addPropertyChangeListener(
"optionSelectionChange",
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
selectedCompression.setText(
((OptionItem<String>) propertyChangeEvent.getNewValue()).getUserObject());
}
});
compressionOptionContainer.add(selectedCompression, BorderLayout.SOUTH);
selectedCompression.setText(compressionOptions.getSelectedItem());
return compressionOptionContainer;
}
/**
* Create the JPanel to allow users to save the mappings created to be used in a proceeding
* mapping activity!
*
* @return JLayeredPane containing the gui to allow a user to save the mapping file!
*/
private JLayeredPane createSaveMappings() {
JPanel saveMappingFilesCont = new JPanel();
saveMappingFilesCont.setSize(new Dimension(400, 300));
saveMappingFilesCont.setLayout(new BoxLayout(saveMappingFilesCont, BoxLayout.PAGE_AXIS));
saveMappingFilesCont.add(
UIHelper.wrapComponentInPanel(new JLabel(saveMappingHelp, SwingConstants.CENTER)));
saveMappingFilesCont.add(Box.createVerticalStrut(10));
saveMappingFilesCont.add(
UIHelper.wrapComponentInPanel(
UIHelper.createLabel(
""
+ "<html>"
+ "Please be aware, the mappings saved are saved on a field by field basis. "
+ "This means that regardless of what assay you selected to do this/these mappings,"
+ " common fields amongst all assays automatically inherit the mapping information. This has a number"
+ " of benefits and a number of negative points. "
+ "<br/>"
+ "<p>The <strong>main benefit</strong> being that common field mappings are transportable regardless of assay types.<p>"
+ "<p>The <strong>main problem</strong> is that because fields are saved on a field name basis, duplicate fields like"
+ " <strong>Protocol REF</strong> columns are not saved. This mechanism for saving will be changed in the next release!</p>"
+ "<br/>"
+ "<br/>"
+ "<br/>"
+ "</html>",
UIHelper.VER_11_PLAIN,
UIHelper.GREY_COLOR)));
// create selector for mapping files
JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle("Choose where and what to save the file as...");
chooser.setApproveButtonText("Select file");
chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
JPanel selectMappingPanel = new JPanel();
selectMappingPanel.setLayout(new BoxLayout(selectMappingPanel, BoxLayout.PAGE_AXIS));
selectMappingPanel.setOpaque(false);
// need a jcheckbox to ask users if they wish to use a mapping
JPanel useMappingContainer = new JPanel(new BorderLayout());
useMappingContainer.setOpaque(false);
final JPanel savedMappingsPanel = new JPanel();
savedMappingsPanel.setLayout(new BoxLayout(savedMappingsPanel, BoxLayout.PAGE_AXIS));
savedMappingsPanel.setOpaque(false);
savedMappingsPanel.setVisible(false);
final JLabel saveStatusInfo =
UIHelper.createLabel("", UIHelper.VER_11_BOLD, UIHelper.GREY_COLOR);
final FileSelectionPanel savedMappingsFile =
new FileSelectionPanel(
"<html>select <strong>where</strong> to save file and <strong>it's name</strong>: </html>",
chooser,
FileSelectionPanel.SAVE);
final JCheckBox useMapping = new JCheckBox("save mapping?");
UIHelper.renderComponent(useMapping, UIHelper.VER_11_BOLD, UIHelper.GREY_COLOR, false);
useMapping.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
savedMappingsPanel.setVisible(useMapping.isSelected());
saveStatusInfo.setText("");
}
});
useMappingContainer.add(useMapping, BorderLayout.WEST);
selectMappingPanel.add(useMappingContainer);
// add button to save mappings
final JLabel saveMappingsButton = new JLabel(saveMappingsButtonIcon);
saveMappingsButton.setVerticalAlignment(JLabel.BOTTOM);
saveMappingsButton.addMouseListener(
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
saveMappingsButton.setIcon(saveMappingsButtonIconOver);
}
public void mouseExited(MouseEvent mouseEvent) {
saveMappingsButton.setIcon(saveMappingsButtonIcon);
}
public void mousePressed(MouseEvent mouseEvent) {
// save the mapping
MappingXMLCreator mappingCreator = new MappingXMLCreator();
try {
if (useMapping.isSelected()) {
if (!savedMappingsFile.getSelectedFilePath().equals("")) {
nextButton.setEnabled(false);
backButton.setEnabled(false);
mappingCreator.createXMLFile(
savedMappingsFile.getSelectedFilePath(), mappingsToSave, assaysToBeDefined);
saveStatusInfo.setText("mappings saved successfully...");
} else {
saveStatusInfo.setText("please select a file...");
}
}
} catch (FileNotFoundException e) {
e.printStackTrace();
saveStatusInfo.setText("mappings not saved..." + e.getMessage());
} finally {
nextButton.setEnabled(true);
backButton.setEnabled(true);
}
}
});
final JLayeredPane finalPanel =
getGeneralLayout(saveMappingsHeader, breadcrumb7, "", saveMappingFilesCont, 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);
saveStatusInfo.setText("");
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 performMappingLogic =
new Thread(
new Runnable() {
public void run() {
investigation =
MappingLogic.createInvestigation(
definitions, assaySelections, dataEntryEnvironment);
// now we need to construct the investigation from the defined table
// reference objects and the
ApplicationManager.assignDataEntryToISASection(
investigation,
new InvestigationDataEntry(investigation, dataEntryEnvironment));
investigation.setConfigurationCreateWith(
ApplicationManager.getCurrentApplicationInstance()
.getLoadedConfiguration());
investigation.setLastConfigurationUsed(
ApplicationManager.getCurrentApplicationInstance()
.getLoadedConfiguration());
dataEntryEnvironment.createGUIFromInvestigation(investigation);
previousPage.push(new HistoryComponent(finalPanel, listeners));
ApplicationManager.getCurrentApplicationInstance().hideGlassPane();
ApplicationManager.getCurrentApplicationInstance()
.setCurDataEntryPanel(dataEntryEnvironment);
ApplicationManager.getCurrentApplicationInstance()
.setCurrentPage(dataEntryEnvironment);
}
});
setCurrentPage(workingProgressScreen);
performMappingLogic.start();
}
};
JPanel saveMappingsSection = new JPanel();
saveMappingsSection.setLayout(new BoxLayout(saveMappingsSection, BoxLayout.LINE_AXIS));
saveMappingsSection.add(savedMappingsFile);
saveMappingsSection.add(Box.createHorizontalStrut(10));
JPanel saveButtonContainer = new JPanel(new BorderLayout());
saveButtonContainer.add(saveMappingsButton, BorderLayout.SOUTH);
saveMappingsSection.add(UIHelper.wrapComponentInPanel(saveButtonContainer));
savedMappingsPanel.add(saveMappingsSection);
selectMappingPanel.add(savedMappingsPanel);
saveMappingFilesCont.add(selectMappingPanel);
saveMappingFilesCont.add(UIHelper.wrapComponentInPanel(saveStatusInfo));
assignListenerToLabel(nextButton, listeners[1]);
return finalPanel;
}
/**
* Create JPanel asking users to select the file or directory containing files to be mapped and an
* existing mapping file if they have one.
*
* @return JPanel containing elements!
*/
private JLayeredPane createSelectFilesPanel() {
// create overall panel
final JPanel selectFilesContainer = new JPanel();
selectFilesContainer.setSize(new Dimension(400, 100));
selectFilesContainer.setLayout(new BoxLayout(selectFilesContainer, BoxLayout.PAGE_AXIS));
// create selector for mapping files
final FileSelectionPanel fileToMapFSP =
new FileSelectionPanel(
"<html>please select file(s) to be mapped (txt, csv or xls (Excel). Please ensure "
+ "that this file has <b>no empty columns</b> and if possible, please remove any special characters, e.g. μ</html>",
fileChooser);
selectFilesContainer.add(fileToMapFSP);
JPanel selectMappingPanel = new JPanel();
selectMappingPanel.setLayout(new BoxLayout(selectMappingPanel, BoxLayout.PAGE_AXIS));
selectMappingPanel.setOpaque(false);
// need a jcheckbox to ask users if they wish to use a mapping
JPanel useMappingContainer = new JPanel(new BorderLayout());
useMappingContainer.setOpaque(false);
// need a file selection panel to select the file.
JFileChooser mappingFileChooser = new JFileChooser();
mappingFileChooser.setDialogTitle("Choose mapping file (XML)");
mappingFileChooser.setApproveButtonText("select file");
mappingFileChooser.setFont(UIHelper.VER_11_PLAIN);
mappingFileChooser.setFileFilter(new CustomizableFileFilter("xml"));
final FileSelectionPanel savedMappingsFile =
new FileSelectionPanel(
"<html>please select saved mapping file (xml): </html>", mappingFileChooser);
savedMappingsFile.setVisible(false);
final JCheckBox useMapping = new JCheckBox("use a previous mapping?");
UIHelper.renderComponent(useMapping, UIHelper.VER_11_BOLD, UIHelper.GREY_COLOR, false);
useMapping.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
savedMappingsFile.setVisible(useMapping.isSelected());
}
});
useMappingContainer.add(useMapping, BorderLayout.WEST);
selectMappingPanel.add(useMappingContainer);
selectMappingPanel.add(savedMappingsFile);
selectFilesContainer.add(selectMappingPanel);
final RoundedJTextField rowOffset = new RoundedJTextField(3);
rowOffset.setEnabled(false);
rowOffset.setSize(new Dimension(20, 20));
rowOffset.setText("1");
final JCheckBox overrideRowPosition = new JCheckBox("override row start position?");
UIHelper.renderComponent(overrideRowPosition, UIHelper.VER_11_BOLD, UIHelper.GREY_COLOR, false);
overrideRowPosition.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
rowOffset.setEnabled(overrideRowPosition.isSelected());
}
});
Box fileInputPanel = Box.createHorizontalBox();
fileInputPanel.setSize(new Dimension(100, 20));
fileInputPanel.add(overrideRowPosition);
fileInputPanel.add(Box.createHorizontalStrut(5));
fileInputPanel.add(rowOffset);
selectFilesContainer.add(fileInputPanel);
selectFilesContainer.add(selectMappingPanel);
final JCheckBox mapToBlankFieldsCheckbox = new JCheckBox("Do not remove blank fields?", false);
UIHelper.renderComponent(
mapToBlankFieldsCheckbox, UIHelper.VER_11_BOLD, UIHelper.GREY_COLOR, false);
mapToBlankFieldsCheckbox.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
mapToBlankFields = mapToBlankFieldsCheckbox.isSelected();
}
});
JPanel removeBlanksContainer = new JPanel(new BorderLayout());
removeBlanksContainer.setOpaque(false);
removeBlanksContainer.add(mapToBlankFieldsCheckbox, BorderLayout.WEST);
selectFilesContainer.add(removeBlanksContainer);
JPanel statusPanel = new JPanel(new GridLayout(1, 1));
statusPanel.setPreferredSize(new Dimension(400, 30));
final JLabel statusLab = UIHelper.createLabel("", UIHelper.VER_11_BOLD, UIHelper.RED_COLOR);
statusPanel.add(statusLab);
selectFilesContainer.add(statusPanel);
final JLayeredPane finalLayout =
getGeneralLayout(selectFilesHeader, breadcrumb1, "", selectFilesContainer, 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() {
ApplicationManager.getCurrentApplicationInstance().setCurrentPage(menuPanels);
ApplicationManager.getCurrentApplicationInstance()
.setGlassPanelContents(menuPanels.getCreateISAMenuGUI());
menuPanels.startAnimation();
}
});
}
};
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 loadFile =
new Thread(
new Runnable() {
public void run() {
ISAcreatorProperties.setProperty(
"isacreator.rowOffset",
rowOffset.isEnabled() ? rowOffset.getText() : "1");
if (useMapping.isSelected()) {
if (!savedMappingsFile.getSelectedFilePath().trim().equals("")) {
MappingXMLLoader loader =
new MappingXMLLoader(savedMappingsFile.getSelectedFilePath());
try {
preExistingMapping = loader.loadMappings();
} catch (XmlException e) {
log.error(e.getMessage());
statusLab.setText(
"<html>problem found in xml for saved mapping: "
+ e.getMessage()
+ " </html>");
setCurrentPage(lastPage);
return;
} catch (IOException e) {
log.error(e.getMessage());
statusLab.setText(
"<html>problem found when resolving file for saved mapping: "
+ e.getMessage()
+ " </html>");
setCurrentPage(lastPage);
return;
}
} else {
statusLab.setText(
"<html>please select a file containing previous mappings...</html>");
setCurrentPage(lastPage);
return;
}
} else {
log.info("Mapping is not selected");
statusLab.setText("");
}
if (fileToMapFSP.notEmpty()) {
previousPage.push(new HistoryComponent(finalLayout, listeners));
statusLab.setText("");
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
setCurrentPage(
createAssayUsedPanel(fileToMapFSP.getSelectedFilePath()));
}
});
} else {
statusLab.setText(
"<html>please <strong>select</strong> a file to map!</html>");
setCurrentPage(lastPage);
}
}
});
if (fileToMapFSP.notEmpty()
&& fileToMapFSP.checkFileExtensionValid("xls", "csv", "txt")) {
statusLab.setText("");
lastPage = currentPage;
setCurrentPage(workingProgressScreen);
loadFile.start();
} else {
statusLab.setText(
"<html>please select a file with the extension <strong>.xls</strong>, <strong>.csv</strong> or <strong>.txt</strong>...</html>");
}
}
};
assignListenerToLabel(nextButton, listeners[1]);
return finalLayout;
}
/** Creates panel with function logo and some utilities */
private Container createTopPanel() {
JPanel topContainer = new JPanel(new BorderLayout());
Box logoContainer = Box.createHorizontalBox();
logoContainer.add(new JLabel(logo));
topContainer.add(logoContainer, BorderLayout.WEST);
Box toolBox = Box.createHorizontalBox();
toolBox.add(new JLabel(toolboxIcon));
final JLabel highlightGroups = new JLabel(highlightOffIcon);
highlightGroups.addMouseListener(
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
highlightGroups.setIcon(isHighlighted ? highlightOnOver : highlightOffOver);
}
public void mouseExited(MouseEvent mouseEvent) {
highlightGroups.setIcon(isHighlighted ? highlightOnIcon : highlightOffIcon);
}
public void mousePressed(MouseEvent mouseEvent) {
if (isHighlighted) {
transposedSpreadsheetSubform.changeTableRenderer(
transposedSpreadsheetSubform.getLockedTable(), null);
transposedSpreadsheetSubform.changeTableRenderer(
transposedSpreadsheetSubform.getScrollTable(), null);
} else {
transposedSpreadsheetSubform.changeTableRenderer(
transposedSpreadsheetSubform.getLockedTable(),
new CustomRowRenderer(
transposedSpreadsheetModel.getRowToColour(), UIHelper.VER_11_BOLD));
transposedSpreadsheetSubform.changeTableRenderer(
transposedSpreadsheetSubform.getScrollTable(),
new CustomRowRenderer(
transposedSpreadsheetModel.getRowToColour(), UIHelper.VER_11_PLAIN));
}
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
transposedSpreadsheetSubform.validate();
transposedSpreadsheetSubform.repaint();
highlightGroups.setIcon(isHighlighted ? highlightOnIcon : highlightOffIcon);
}
});
isHighlighted = !isHighlighted;
}
});
toolBox.add(highlightGroups);
final JLabel goToRecordButton = new JLabel(goToRecord);
goToRecordButton.addMouseListener(
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
goToRecordButton.setIcon(goToRecordOver);
}
public void mouseExited(MouseEvent mouseEvent) {
goToRecordButton.setIcon(goToRecord);
}
});
toolBox.add(goToRecordButton);
Box goToRecordEntryField = Box.createVerticalBox();
final JTextField field = new JTextField("row #");
UIHelper.renderComponent(field, UIHelper.VER_10_PLAIN, UIHelper.LIGHT_GREY_COLOR, false);
Dimension fieldSize = new Dimension(60, 16);
field.setPreferredSize(fieldSize);
field.setSize(fieldSize);
goToRecordEntryField.add(Box.createVerticalStrut(5));
goToRecordEntryField.add(field);
goToRecordEntryField.add(Box.createVerticalStrut(5));
final JLabel goButton = new JLabel(go);
goButton.addMouseListener(
new MouseAdapter() {
public void mouseEntered(MouseEvent mouseEvent) {
goButton.setIcon(goOver);
}
public void mouseExited(MouseEvent mouseEvent) {
goButton.setIcon(go);
}
public void mousePressed(MouseEvent mouseEvent) {
goToColumn(field);
}
});
Action locateColumn =
new AbstractAction() {
public void actionPerformed(ActionEvent e) {
goToColumn(field);
}
};
field.getInputMap().put(KeyStroke.getKeyStroke("ENTER"), "LOCATE_COLUMN");
field.getActionMap().put("LOCATE_COLUMN", locateColumn);
toolBox.add(goToRecordEntryField);
toolBox.add(goButton);
goToRecordEntryField.add(Box.createVerticalStrut(5));
topContainer.add(toolBox, BorderLayout.EAST);
information = UIHelper.createLabel("", UIHelper.VER_11_PLAIN, UIHelper.LIGHT_GREY_COLOR);
information.setHorizontalAlignment(SwingConstants.RIGHT);
topContainer.add(UIHelper.wrapComponentInPanel(information), BorderLayout.SOUTH);
return topContainer;
}
