public void initPopupMenu() {
super.initPopupMenu();
if (getPopupMenu() != null) {
JMenu otherDataSourcesMenu = new JMenu("Other Data Sources");
getPopupMenu().add(otherDataSourcesMenu);
JMenuItem mi;
mi = new JMenuItem("Show Level Lists");
ShowLevelListAction showLevelList = new ShowLevelListAction("Show Level List");
mi.setAction(showLevelList);
getPopupMenu().add(mi);
mi = new JMenuItem("Add Level Lists");
AddLevelListAction addLevelList = new AddLevelListAction("Add Level List");
mi.setAction(addLevelList);
getPopupMenu().add(mi);
mi = new JMenuItem("OMIM");
mi.setActionCommand("goto OMIM");
otherDataSourcesMenu.add(mi);
mi = new JMenuItem("PubMed");
mi.setActionCommand("goto PubMed");
otherDataSourcesMenu.add(mi);
mi = new JMenuItem("NCI Thesaurus");
mi.setActionCommand("goto NCI Thesaurus Advice");
otherDataSourcesMenu.add(mi);
otherDataSourcesMenu.setOpaque(true);
getPopupMenu().setOpaque(true);
getPopupMenu().setLightWeightPopupEnabled(true);
}
}
public void populateMenu(JMenu menu, int flags) {
if (flags == (Plugin.MENU_TOOLS | Plugin.MENU_MID)) {
Sketch sketch = editor.getSketch();
JMenuItem item = new JMenu("Program Bootloader");
item.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
run();
}
});
menu.add(item);
PropertyFile props = sketch.mergeAllProperties();
String blProgs = props.get("bootloader.upload");
if (blProgs == null) {
JMenuItem sub = new JMenuItem("No bootloader programmer defined!");
item.add(sub);
return;
}
String[] progs = blProgs.split("::");
for (String prog : progs) {
JMenuItem sub = new JMenuItem(sketch.parseString(props.get("upload." + prog + ".name")));
sub.setActionCommand(prog);
sub.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
doProgram(e.getActionCommand());
}
});
item.add(sub);
}
}
}
/**
* 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;
}