/**
* Make the view menu
*
* @param viewMenu view menu
* @return The view menu
*/
public JMenu makeViewMenu(JMenu viewMenu) {
showAlignmentPointsMI = new JCheckBoxMenuItem("Show Alignment Points", true);
viewMenu.add(showAlignmentPointsMI);
showAlignmentPointsMI.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ae) {
repaint();
}
});
viewMenu.addSeparator();
super.makeViewMenu(viewMenu);
viewMenu.addSeparator();
viewMenu.add(makeMenuItem("Black background", CMD_BLACKBG));
viewMenu.add(makeMenuItem("White background", CMD_WHITEBG));
return viewMenu;
}
/**
* Show the saved results on the server.
*
* @param mysettings jemboss settings
* @param frameName title name for frame
*/
public ShowSavedResults(final JembossParams mysettings, final JFrame f) {
this("Saved results list" + (Jemboss.withSoap ? " on server" : ""));
try {
final ResultList reslist = new ResultList(mysettings);
JMenu resFileMenu = new JMenu("File");
resMenu.add(resFileMenu);
final JCheckBoxMenuItem listByProgram = new JCheckBoxMenuItem("List by program");
listByProgram.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
listByProgramName();
}
});
resFileMenu.add(listByProgram);
JCheckBoxMenuItem listByDate = new JCheckBoxMenuItem("List by date", true);
listByDate.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
listByDateRun(reslist, false);
}
});
resFileMenu.add(listByDate);
ButtonGroup group = new ButtonGroup();
group.add(listByProgram);
group.add(listByDate);
JButton refresh = new JButton(rfii);
refresh.setMargin(new Insets(0, 1, 0, 1));
refresh.setToolTipText("Refresh");
resMenu.add(refresh);
refresh.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
try {
setCursor(cbusy);
ResultList newlist = new ResultList(mysettings);
setCursor(cdone);
if (newlist.getStatus().equals("0")) {
reslist.updateRes(newlist.hash());
datasets.removeAllElements();
StringTokenizer tok = new StringTokenizer((String) reslist.get("list"), "\n");
while (tok.hasMoreTokens()) datasets.addElement(convertToPretty(tok.nextToken()));
if (listByProgram.isSelected()) listByProgramName();
else listByDateRun(reslist, false);
} else {
JOptionPane.showMessageDialog(
null, newlist.getStatusMsg(), "Soap Error", JOptionPane.ERROR_MESSAGE);
}
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
}
});
resFileMenu.addSeparator();
JMenuItem resFileMenuExit = new JMenuItem("Close");
resFileMenuExit.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, ActionEvent.CTRL_MASK));
resFileMenuExit.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
dispose();
}
});
resFileMenu.add(resFileMenuExit);
setJMenuBar(resMenu);
// this is the list of saved results
listByDateRun(reslist, true);
final JList st = new JList(datasets);
st.setCellRenderer(new TabListCellRenderer());
st.addListSelectionListener(
new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
if (e.getValueIsAdjusting()) return;
JList theList = (JList) e.getSource();
if (theList.isSelectionEmpty()) {
System.out.println("Empty selection");
} else {
int index = theList.getSelectedIndex();
String thisdata = convertToOriginal(datasets.elementAt(index));
aboutRes.setText((String) reslist.get(thisdata));
aboutRes.setCaretPosition(0);
}
}
});
st.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
try {
setCursor(cbusy);
String project = convertToOriginal(st.getSelectedValue());
ResultList thisres = new ResultList(mysettings, project, "show_saved_results");
new ShowResultSet(thisres.hash(), project, mysettings);
setCursor(cdone);
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
}
}
});
sp.add(st);
// display retrieves all files and shows them in a window
JPanel resButtonPanel = new JPanel();
JButton showResButton = new JButton("Display");
showResButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String sel = convertToOriginal(st.getSelectedValue());
if (sel != null) {
try {
setCursor(cbusy);
ResultList thisres = new ResultList(mysettings, sel, "show_saved_results");
if (thisres.hash().size() == 0)
JOptionPane.showMessageDialog(
sp,
"This application launch '" + sel + "' didn't produce any result files.");
else new ShowResultSet(thisres.hash(), sel, mysettings);
setCursor(cdone);
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
} else {
statusField.setText("Nothing selected to be displayed.");
}
}
});
// add a users note for that project
JButton addNoteButton = new JButton("Edit Notes");
addNoteButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
String sel = convertToOriginal(st.getSelectedValue());
if (sel != null) {
try {
setCursor(cbusy);
ResultList thisres =
new ResultList(mysettings, sel, "Notes", "show_saved_results");
new ShowResultSet(thisres.hash(), sel, mysettings);
setCursor(cdone);
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
} else {
statusField.setText("Selected a project!");
}
}
});
// delete removes the file on the server & edits the list
JButton delResButton = new JButton("Delete");
delResButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
Object sel[] = st.getSelectedValues();
if (sel != null) {
String selList = new String("");
JTextPane delList = new JTextPane();
FontMetrics fm = delList.getFontMetrics(delList.getFont());
int maxWidth = 0;
for (int i = 0; i < sel.length; i++) {
if (i == sel.length - 1) selList = selList.concat((String) sel[i]);
else selList = selList.concat(sel[i] + "\n");
int width = fm.stringWidth((String) sel[i]);
if (width > maxWidth) maxWidth = width;
}
int ok = JOptionPane.OK_OPTION;
if (sel.length > 1) {
JScrollPane scrollDel = new JScrollPane(delList);
delList.setText(selList);
delList.setEditable(false);
delList.setCaretPosition(0);
Dimension d1 = delList.getPreferredSize();
int maxHeight = (int) d1.getHeight() + 5;
if (maxHeight > 350) maxHeight = 350;
else if (maxHeight < 50) maxHeight = 50;
scrollDel.setPreferredSize(new Dimension(maxWidth + 30, maxHeight));
ok =
JOptionPane.showConfirmDialog(
null, scrollDel, "Confirm Deletion", JOptionPane.YES_NO_OPTION);
}
if (ok == JOptionPane.OK_OPTION) {
try // ask the server to delete these results
{
setCursor(cbusy);
selList = convertToOriginal(selList);
new ResultList(mysettings, selList, "delete_saved_results");
setCursor(cdone);
// amend the list
for (int i = 0; i < sel.length; i++) datasets.removeElement(sel[i]);
statusField.setText("Deleted " + sel.length + " result(s)");
aboutRes.setText("");
st.setSelectedIndex(-1);
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
}
} else {
statusField.setText("Nothing selected for deletion.");
}
}
});
resButtonPanel.add(delResButton);
resButtonPanel.add(addNoteButton);
resButtonPanel.add(showResButton);
resButtonStatus.add(resButtonPanel, BorderLayout.CENTER);
resButtonStatus.add(statusField, BorderLayout.SOUTH);
Container c = getContentPane();
c.add(ss, BorderLayout.WEST);
c.add(aboutScroll, BorderLayout.CENTER);
c.add(resButtonStatus, BorderLayout.SOUTH);
pack();
setVisible(true);
} catch (JembossSoapException eae) {
AuthPopup ap = new AuthPopup(mysettings, f);
ap.setBottomPanel();
ap.setSize(380, 170);
ap.pack();
ap.setVisible(true);
}
}
/** Create the UI for this editor */
void makeUI() {
JPanel mainPanel = new JPanel(new BorderLayout());
mainPanel.setBorder(new LineBorder(Color.blue));
getContentPane().add(mainPanel, BorderLayout.CENTER);
// the map and associated toolbar
npEditControl = new NPController();
mapEditPanel = npEditControl.getNavigatedPanel(); // here's where the map will be drawn
mapEditPanel.setPreferredSize(new Dimension(250, 250));
mapEditPanel.setSelectRegionMode(true);
JToolBar navToolbar = mapEditPanel.getNavToolBar();
navToolbar.setFloatable(false);
JToolBar moveToolbar = mapEditPanel.getMoveToolBar();
moveToolbar.setFloatable(false);
// toolbar.remove("setReference");
JPanel toolbar = new JPanel();
List localMaps = maps;
if (localMaps == null) {
localMaps = getDefaultMaps();
}
JMenu mapMenu = new JMenu("Maps");
JMenuBar menuHolder = new JMenuBar();
menuHolder.setBorder(null);
menuHolder.add(mapMenu);
toolbar.add(menuHolder);
for (int mapIdx = 0; mapIdx < localMaps.size(); mapIdx++) {
final MapData mapData = (MapData) localMaps.get(mapIdx);
final JCheckBoxMenuItem cbx =
new JCheckBoxMenuItem(mapData.getDescription(), mapData.getVisible());
if (mapData.getVisible()) {
toggleMap(mapData, true);
}
mapMenu.add(cbx);
cbx.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent event) {
toggleMap(mapData, cbx.isSelected());
}
});
}
GuiUtils.limitMenuSize(mapMenu, "Maps ", 20);
toolbar.add(navToolbar);
toolbar.add(moveToolbar);
JPanel mapSide = new JPanel();
mapSide.setLayout(new BorderLayout());
TitledBorder mapBorder =
new TitledBorder(
standardBorder, "Edit Projection", TitledBorder.ABOVE_TOP, TitledBorder.CENTER);
mapSide.setBorder(mapBorder);
mapSide.add(toolbar, BorderLayout.NORTH);
mapSide.add(mapEditPanel, BorderLayout.CENTER);
mainPanel.add(mapSide, BorderLayout.WEST);
// the projection parameters
// the Projection name
JLabel nameLabel = GuiUtils.rLabel("Name: ");
nameTF = new JTextField(20);
// the list of Projection classes is kept in a comboBox
typeLabel = GuiUtils.rLabel("Type: ");
projClassCB = new JComboBox();
// standard list of projection classes
List classNames = getDefaultProjections();
for (int i = 0; i < classNames.size(); i++) {
String className = (String) classNames.get(i);
try {
projClassCB.addItem(new ProjectionClass(className));
} catch (ClassNotFoundException ee) {
System.err.println("ProjectionManager failed on " + className + " " + ee);
} catch (IntrospectionException ee) {
System.err.println("ProjectionManager failed on " + className + " " + ee);
}
}
GuiUtils.tmpInsets = new Insets(4, 4, 4, 4);
JPanel topPanel =
GuiUtils.doLayout(
new Component[] {nameLabel, nameTF, typeLabel, projClassCB},
2,
GuiUtils.WT_N,
GuiUtils.WT_N);
// the Projection parameter area
paramPanel = new JPanel();
paramPanel.setLayout(new BorderLayout());
paramPanel.setBorder(
new TitledBorder(
standardBorder,
"Projection Parameters",
TitledBorder.ABOVE_TOP,
TitledBorder.CENTER));
// the bottom button panel
JPanel buttPanel = new JPanel();
JButton acceptButton = new JButton("Save");
JButton previewButton = new JButton("Preview");
JButton cancelButton = new JButton("Cancel");
buttPanel.add(acceptButton, null);
buttPanel.add(previewButton, null);
buttPanel.add(cancelButton, null);
JPanel mainBox = GuiUtils.topCenterBottom(topPanel, paramPanel, buttPanel);
mainPanel.add(mainBox, BorderLayout.CENTER);
pack();
// enable event listeners when we're done constructing the UI
projClassCB.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
ProjectionClass selectClass = (ProjectionClass) projClassCB.getSelectedItem();
setProjection(selectClass.makeDefaultProjection());
}
});
acceptButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
accept();
}
});
previewButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
ProjectionClass projClass = findProjectionClass(editProjection);
if (null != projClass) {
setProjFromDialog(projClass, editProjection);
setProjection(editProjection);
}
}
});
cancelButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent evt) {
NewProjectionDialog.this.setVisible(false);
}
});
}
/**
* Set up the menu bar.
*
* @return The JMenuBar we set up.
*/
private JMenuBar setupMenuBar() {
JMenuBar menuBar = new JMenuBar();
/* File */
JMenu fileMenu = new JMenu("File");
menuBar.add(fileMenu);
/* File -> Open CSV */
JMenuItem miFileOpenCSV =
new JMenuItem(
new AbstractAction("Open CSV") {
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd =
new FileDialog(mainFrame, "Open Darwin CSV file ...", FileDialog.LOAD);
fd.setVisible(true);
File file;
if (fd.getDirectory() != null) {
file = new File(fd.getDirectory(), fd.getFile());
} else if (fd.getFile() != null) {
file = new File(fd.getFile());
} else {
return;
}
// Clear out old file.
loadFile(null);
// SwingWorker MAGIC!
new MainFrameWorker("loading file '" + file + "'", file) {
@Override
protected Object doInBackground() throws Exception {
System.err.println("Loading file: " + input);
loadFile((File) input, DarwinCSV.FILE_CSV_DELIMITED);
return null;
}
}.execute();
}
});
fileMenu.add(miFileOpenCSV);
/* File -> Open CSV without UI */
JMenuItem miFileOpenCSVnoUI =
new JMenuItem(
new AbstractAction("Open CSV without UI") {
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd =
new FileDialog(mainFrame, "Open Darwin CSV file ...", FileDialog.LOAD);
fd.setVisible(true);
File file;
if (fd.getDirectory() != null) {
file = new File(fd.getDirectory(), fd.getFile());
} else if (fd.getFile() != null) {
file = new File(fd.getFile());
} else {
return;
}
// Clear out old file
loadFile(null);
loadFile(file, DarwinCSV.FILE_CSV_DELIMITED);
}
});
fileMenu.add(miFileOpenCSVnoUI);
/* File -> Open tab-delimited */
JMenuItem miFileOpenTab =
new JMenuItem(
new AbstractAction("Open tab-delimited") {
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd =
new FileDialog(
mainFrame, "Open Darwin tab-delimited file ...", FileDialog.LOAD);
fd.setVisible(true);
File file;
if (fd.getDirectory() != null) {
file = new File(fd.getDirectory(), fd.getFile());
} else if (fd.getFile() != null) {
file = new File(fd.getFile());
} else {
return;
}
// Clear out old file
loadFile(null);
// SwingWorker MAGIC!
new MainFrameWorker("loading file '" + file + "'", file) {
@Override
protected Object doInBackground() throws Exception {
loadFile((File) input, DarwinCSV.FILE_TAB_DELIMITED);
return null;
}
}.execute();
}
});
fileMenu.add(miFileOpenTab);
/* File -> Save CSV */
JMenuItem miFileSave =
new JMenuItem(
new AbstractAction("Save as CSV") {
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd =
new FileDialog(mainFrame, "Save Darwin CSV file ...", FileDialog.SAVE);
fd.setVisible(true);
File file;
if (fd.getDirectory() != null) {
file = new File(fd.getDirectory(), fd.getFile());
} else if (fd.getFile() != null) {
file = new File(fd.getFile());
} else {
return;
}
// SwingWorker MAGIC!
new MainFrameWorker("saving CSV file '" + file + "'", file) {
@Override
protected Object doInBackground() throws Exception {
currentCSV.saveToFile((File) input, DarwinCSV.FILE_CSV_DELIMITED);
return null;
}
}.execute();
}
});
fileMenu.add(miFileSave);
/* File -> Exit */
JMenuItem miFileExit =
new JMenuItem(
new AbstractAction("Exit") {
@Override
public void actionPerformed(ActionEvent e) {
mainFrame.setVisible(false);
mainFrame.dispose();
}
});
fileMenu.add(miFileExit);
/* Match */
JMenu matchMenu = new JMenu("Match");
menuBar.add(matchMenu);
/* Match -> Against CSV */
JMenuItem miMatchCSV =
new JMenuItem(
new AbstractAction("Match against CSV") {
@Override
public void actionPerformed(ActionEvent e) {
FileDialog fd =
new FileDialog(
mainFrame, "Open Darwin CSV file for matching ...", FileDialog.LOAD);
fd.setVisible(true);
if (fd.getFile() == null) return;
File file = new File(fd.getFile());
if (fd.getDirectory() != null) {
file = new File(fd.getDirectory(), fd.getFile());
}
// Clear out old match against.
matchAgainst(null);
// SwingWorker MAGIC!
new MainFrameWorker("matching against file '" + file + "'", file) {
@Override
protected Object doInBackground() throws Exception {
matchAgainst(new DarwinCSV((File) input, DarwinCSV.FILE_CSV_DELIMITED));
return null;
}
}.execute();
}
});
matchMenu.add(miMatchCSV);
/* Match -> Against ITIS */
JMenuItem miMatchITIS =
new JMenuItem(
new AbstractAction("Match against ITIS") {
@Override
public void actionPerformed(ActionEvent e) {
DarwinCSV csv = DownloadITIS.getIt(mainFrame);
matchAgainst(csv);
table.repaint();
}
});
matchMenu.add(miMatchITIS);
/* TaxonID */
JMenu taxonIDMenu = new JMenu("TaxonIDs");
menuBar.add(taxonIDMenu);
/* TaxonID -> Treat TaxonIDs as ... */
JMenu treatTaxonIDsAs = new JMenu("Treat TaxonIDs as ...");
taxonIDMenu.add(treatTaxonIDsAs);
/* TaxonID -> Treat -> ITIS TSNs */
JCheckBoxMenuItem miITIS_TSNs =
new JCheckBoxMenuItem(
new AbstractAction("ITIS TSNs") {
@Override
public void actionPerformed(ActionEvent e) {
// Don't let the user unselect this.
((JCheckBoxMenuItem) e.getSource()).setSelected(true);
}
});
miITIS_TSNs.setSelected(true);
treatTaxonIDsAs.add(miITIS_TSNs);
/* TaxonID -> Create family column */
JMenuItem miTaxonID_createFamily =
new JMenuItem(
new AbstractAction("Create family column") {
@Override
public void actionPerformed(ActionEvent e) {
/*
if(currentCSV == null)
return;
if(currentMatch == null)
return;
int col = getJTable().getSelectedColumn();
if(col == -1)
return;
RowIndex rowIndex = currentCSV.getRowIndex();
String colName = rowIndex.getColumnName(col);
if(rowIndex.hasColumn(colName + "_family")) {
// TODO MessageBox
return;
}
if(Name.class.isAssignableFrom(currentCSV.getRowIndex().getColumnClass(col))) {
// A name class! Make a new column!
currentCSV.getRowIndex().setColumnClass(colName + "_family", String.class);
currentCSV.getRowIndex().createNewColumn(colName + "_family", col + 1, colName, new MapOperation() {
@Override
public Object mapTo(Object value) {
return "family";
}
});
// Repaint the table.
getJTable().repaint();
}
*/
}
});
taxonIDMenu.add(miTaxonID_createFamily);
/* Help */
JMenu helpMenu = new JMenu("Help");
menuBar.add(helpMenu);
/* Help -> Memory information */
JMenuItem miHelpMemory =
new JMenuItem(
new AbstractAction("Memory information") {
@Override
public void actionPerformed(ActionEvent e) {
System.gc();
MessageBox.messageBox(
mainFrame,
"Memory information",
"Maximum memory: "
+ Runtime.getRuntime().maxMemory() / (1024 * 1024)
+ " MB\n"
+ "Total memory: "
+ Runtime.getRuntime().totalMemory() / (1024 * 1024)
+ " MB\n"
+ "Used memory: "
+ (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())
/ (1024 * 1024)
+ " MB\n"
+ "Free memory: "
+ Runtime.getRuntime().freeMemory() / (1024 * 1024)
+ " MB\n"
+ "Available memory: "
+ (Runtime.getRuntime().maxMemory()
- Runtime.getRuntime().totalMemory()
+ Runtime.getRuntime().freeMemory())
/ (1024 * 1024)
+ " MB");
}
});
helpMenu.add(miHelpMemory);
return menuBar;
}
/**
* Should we draw the alignment points in the canvas
*
* @return Draw the alignment points in the canvas
*/
public boolean shouldShowAlignmentPoints() {
if (showAlignmentPointsMI != null) {
return showAlignmentPointsMI.isSelected();
}
return true;
}
