public void initSiRNA() {
siRNA s = new siRNA("p53.fasta");
List list = s.siRNA();
vertical.setBackground(new java.awt.Color(255, 215, 0));
vertical.setSize(this.scrollPane1.getWidth(), this.scrollPane1.getHeight());
s1.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
s2.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
//
// Modify the text color
s1.setForeground(Color.black);
s2.setForeground(Color.black);
s1.setFont(new java.awt.Font("Arial Black", 0, 18));
s2.setFont(new java.awt.Font("Arial Black", 0, 18));
// Modify the background color
// s1.setBackground(new Color(255, 192, 16));
// s2.setBackground(new Color(255, 192, 16));
//
t1 = new JTextArea();
t2 = new JTextArea();
// t1.setLineWrap(true);
// t2.setLineWrap(true);
t1.setText(list.get(0).toString());
t2.setText(list.get(1).toString());
vertical.add(s1);
vertical.add(t1);
vertical.add(s2);
vertical.add(t2);
scrollPane1.add(vertical);
}
private void jButton1ActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_jButton1ActionPerformed
OpenFastaFile f = new OpenFastaFile("", "");
try { // f.showSaveDataDialog();
FilePath = f.showOpenDataDialog();
} catch (IOException ex) {
// Logger.getLogger(Browser.class.getName()).log(Level.SEVERE, null, ex);
}
if (FilePath.isEmpty()) {
return;
}
Box vertical = Box.createVerticalBox();
vertical.setSize(this.scrollPane1.getWidth(), this.scrollPane1.getHeight());
siRNA s = new siRNA(new File(FilePath));
siRnaInputArea.setText(s.getGene());
if (s.isValid()) {
List list = s.siRNA();
t1.setText(list.get(0).toString());
t2.setText(list.get(1).toString());
s1.setForeground(Color.black);
s2.setForeground(Color.black);
}
} // GEN-LAST:event_jButton1ActionPerformed
/**
* 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;
}