/*package*/ PointsStyleFrame(PointsView[] ptv, boolean isLine) {
_ptv = ptv;
_panel = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
JRadioButton line = new JRadioButton("Line");
line.setSelected(isLine);
line.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {}
});
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = 0;
_panel.add(line, c);
JRadioButton marks = new JRadioButton("Marks");
marks.setSelected(!isLine);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 1;
c.gridy = 0;
_panel.add(marks, c);
JComboBox lineStyles = new JComboBox(PointsView.Line.values());
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = 1;
_panel.add(lineStyles, c);
JComboBox markStyles = new JComboBox(PointsView.Mark.values());
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 1;
c.gridy = 1;
_panel.add(markStyles, c);
// JLabel sizeLabel = new JLabel("Size:");
// c.fill = GridBagConstraints.HORIZONTAL;
// c.anchor = GridBagConstraints.CENTER;
// c.weightx = 10;
// c.gridx = 0;
// c.gridy = 2;
// _panel.add(sizeLabel,c);
JComboBox size = new JComboBox(_sizes);
size.setEditable(true);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 1;
c.gridy = 2;
_panel.add(size, c);
JComboBox colors = new JComboBox(Colors.values());
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 1;
c.gridy = 3;
_panel.add(colors, c);
add(_panel);
pack();
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setVisible(true);
}
public static int numColors() {
return Colors.values().length;
}
@Koan
public void basicEnumsAccess() {
Colors[] colorArray = Colors.values();
assertEquals(colorArray[2], Colors.Green);
}
public static final Color resolveIndex(int i) {
return Colors.values()[i % Colors.length].getColor();
}
public enum Colors {
// 240°
BLUE {
@Override
public Color getColor() {
return Color.BLUE;
}
},
// 120°
GREEN {
@Override
public Color getColor() {
return Color.GREEN;
}
},
// 0°
RED {
@Override
public Color getColor() {
return Color.RED;
}
},
// 180°
CYAN {
@Override
public Color getColor() {
return Color.CYAN;
}
},
// 47°
ORANGE {
@Override
public Color getColor() {
return Color.ORANGE;
}
},
// 180°
TEAL {
@Override
public Color getColor() {
return new Color(0, 128, 128);
}
},
// 60°
YELLOW {
@Override
public Color getColor() {
return Color.YELLOW;
}
},
// 300°
MAGENTA {
@Override
public Color getColor() {
return Color.MAGENTA;
}
},
// 0°
PINK {
@Override
public Color getColor() {
return Color.PINK;
}
},
// 0°
BLACK {
@Override
public Color getColor() {
return Color.BLACK;
}
},
NAVY {
@Override
public Color getColor() {
return new Color(0, 0, 128);
}
},
// 0°
GRAY {
@Override
public Color getColor() {
return Color.GRAY;
}
},
// 0°
LIGHT_GRAY {
@Override
public Color getColor() {
return Color.LIGHT_GRAY;
}
},
DARK_GRAY {
@Override
public Color getColor() {
return Color.DARK_GRAY;
}
},
FUCHSIA {
@Override
public Color getColor() {
return new Color(255, 0, 255);
}
},
// Netscape alias for cyan
AQUA {
@Override
public Color getColor() {
return Color.CYAN;
}
},
LIME {
@Override
public Color getColor() {
return new Color(204, 255, 0);
}
},
MAROON {
@Override
public Color getColor() {
return new Color(128, 0, 0);
}
},
OLIVE {
@Override
public Color getColor() {
return new Color(128, 128, 0);
}
},
PURPLE {
@Override
public Color getColor() {
return new Color(128, 0, 128);
}
},
SILVER {
@Override
public Color getColor() {
return new Color(192, 192, 192);
}
},
WHITE {
@Override
public Color getColor() {
return Color.WHITE;
}
};
public abstract Color getColor();
public static final int length = Colors.values().length;
public static final Color resolveIndex(int i) {
return Colors.values()[i % Colors.length].getColor();
}
};
/** @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent) */
public void actionPerformed(ActionEvent event) {
String command = event.getActionCommand();
if (command.equals("SHOW_SPECTRUM")) {
CursorPosition pos = getCursorPosition();
if (pos != null) {
SpectraVisualizerModule.showNewSpectrumWindow(pos.getDataFile(), pos.getScanNumber());
}
}
if (command.equals("SETUP_AXES")) {
AxesSetupDialog dialog = new AxesSetupDialog(this, IDAPlot.getXYPlot());
dialog.setVisible(true);
}
if (command.equals("SHOW_DATA_POINTS")) {
IDAPlot.switchDataPointsVisible();
}
if (command.equals("SWITCH_TOOLTIPS")) {
if (tooltipMode) {
IDAPlot.showPeaksTooltips(false);
toolBar.setTooltipButton(false);
tooltipMode = false;
} else {
IDAPlot.showPeaksTooltips(true);
toolBar.setTooltipButton(true);
tooltipMode = true;
}
}
if (command.equals("FIND_SPECTRA")) {
// Parameters
final DoubleParameter inputMZ =
new DoubleParameter("Ion m/z", "m/z value of ion to search for.");
final MZToleranceParameter inputMZTolerance = new MZToleranceParameter();
final DoubleParameter inputIntensity =
new DoubleParameter(
"Min. ion intensity",
"Only ions with intensities above this value will be searched for.");
final BooleanParameter inputNL =
new BooleanParameter(
"Neutral Loss",
"If selected, the ion to be searched for will be a neutral loss ion.\nIn this case, only ions above the min. intensity will be examined.",
false);
final ComboParameter<Colors> inputColors =
new ComboParameter<Colors>(
"Color", "The color which the data points will be marked with.", Colors.values());
Parameter<?>[] parameters = new Parameter<?>[5];
parameters[0] = inputMZ;
parameters[1] = inputMZTolerance;
parameters[2] = inputIntensity;
parameters[3] = inputNL;
parameters[4] = inputColors;
final ParameterSet parametersSearch = new SimpleParameterSet(parameters);
ExitCode exitCode = parametersSearch.showSetupDialog(this, true);
if (exitCode != ExitCode.OK) return;
double searchMZ = parametersSearch.getParameter(inputMZ).getValue();
MZTolerance searchMZTolerance = parametersSearch.getParameter(inputMZTolerance).getValue();
double minIntensity = parametersSearch.getParameter(inputIntensity).getValue();
boolean neutralLoss = parametersSearch.getParameter(inputNL).getValue();
Color highligtColor = Color.red;
;
if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.green)) {
highligtColor = Color.green;
}
if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.blue)) {
highligtColor = Color.blue;
}
// Find and highlight spectra with specific ion
dataset.highlightSpectra(
searchMZ, searchMZTolerance, minIntensity, neutralLoss, highligtColor);
// Add legend entry
LegendItemCollection chartLegend = IDAPlot.getXYPlot().getLegendItems();
chartLegend.add(
new LegendItem(
"Ion: " + searchMZ,
"",
"MS/MS spectra which contain the "
+ searchMZ
+ " ion\nTolerance: "
+ searchMZTolerance.toString()
+ "\nMin intensity: "
+ minIntensity,
"",
new Ellipse2D.Double(0, 0, 7, 7),
highligtColor));
IDAPlot.getXYPlot().setFixedLegendItems(chartLegend);
}
}
