Examples with DoubleParameter net.sf.mzmine.parameters.parametertypes.DoubleParameter used on opensource projects

Example 6 with DoubleParameter

use of net.sf.mzmine.parameters.parametertypes.DoubleParameter in project mzmine2 by mzmine.

the class UserParameterOpenHandler_2_3 method startElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String,
 *      java.lang.String, org.xml.sax.Attributes)
 */
public void startElement(String namespaceURI, String lName, String qName, Attributes attrs) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <PARAMETERS>
    if (qName.equals(UserParameterElementName_2_3.PARAMETERS.getElementName())) {
        String count = attrs.getValue(UserParameterElementName_2_3.COUNT.getElementName());
        totalParams = Integer.parseInt(count);
    }
    // <PARAMETER>
    if (qName.equals(UserParameterElementName_2_3.PARAMETER.getElementName())) {
        String name = attrs.getValue(UserParameterElementName_2_3.NAME.getElementName());
        String type = attrs.getValue(UserParameterElementName_2_3.TYPE.getElementName());
        if (type.equals(DoubleParameter.class.getSimpleName())) {
            currentParameter = new DoubleParameter(name, null);
        } else if (type.equals(StringParameter.class.getSimpleName())) {
            currentParameter = new StringParameter(name, null);
        } else if (type.equals(ComboParameter.class.getSimpleName())) {
            currentParameter = new ComboParameter<String>(name, null, new String[0]);
        } else {
            throw new SAXException("Unknown parameter type: " + type);
        }
        logger.finest("Loading parameter " + name);
        currentOptions.clear();
        currentValues.clear();
    }
    // <VALUE>
    if (qName.equals(UserParameterElementName_2_3.VALUE.getElementName())) {
        currentDataFileID = attrs.getValue(UserParameterElementName_2_3.DATA_FILE.getElementName());
    }
}

Example 7 with DoubleParameter

use of net.sf.mzmine.parameters.parametertypes.DoubleParameter in project mzmine2 by mzmine.

the class UserParameterOpenHandler_2_5 method endElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
 *      java.lang.String)
 */
@SuppressWarnings("unchecked")
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <OPTION>
    if (qName.equals(UserParameterElementName_2_5.OPTION.getElementName())) {
        String optionValue = getTextOfElement();
        currentOptions.add(optionValue);
    }
    // <VALUE>
    if (qName.equals(UserParameterElementName_2_5.VALUE.getElementName())) {
        RawDataFile currentDataFile = dataFilesIDMap.get(currentDataFileID);
        String valueString = getTextOfElement();
        Object value;
        if (currentParameter instanceof DoubleParameter) {
            value = new Double(valueString);
        } else
            value = valueString;
        currentValues.put(currentDataFile, value);
    }
    // <PARAMETER>
    if (qName.equals(UserParameterElementName_2_5.PARAMETER.getElementName())) {
        if (currentParameter instanceof ComboParameter) {
            String[] newChoices = currentOptions.toArray(new String[0]);
            ((ComboParameter<String>) currentParameter).setChoices(newChoices);
        }
        newProject.addParameter(currentParameter);
        for (RawDataFile dataFile : currentValues.keySet()) {
            Object value = currentValues.get(dataFile);
            newProject.setParameterValue(currentParameter, dataFile, value);
        }
        parsedParams++;
    }
}

Example 8 with DoubleParameter

use of net.sf.mzmine.parameters.parametertypes.DoubleParameter in project mzmine2 by mzmine.

the class UserParameterOpenHandler_2_5 method startElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String,
 *      java.lang.String, org.xml.sax.Attributes)
 */
public void startElement(String namespaceURI, String lName, String qName, Attributes attrs) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <PARAMETERS>
    if (qName.equals(UserParameterElementName_2_5.PARAMETERS.getElementName())) {
        String count = attrs.getValue(UserParameterElementName_2_5.COUNT.getElementName());
        totalParams = Integer.parseInt(count);
    }
    // <PARAMETER>
    if (qName.equals(UserParameterElementName_2_5.PARAMETER.getElementName())) {
        String name = attrs.getValue(UserParameterElementName_2_5.NAME.getElementName());
        String type = attrs.getValue(UserParameterElementName_2_5.TYPE.getElementName());
        if (type.equals(DoubleParameter.class.getSimpleName())) {
            currentParameter = new DoubleParameter(name, null);
        } else if (type.equals(StringParameter.class.getSimpleName())) {
            currentParameter = new StringParameter(name, null);
        } else if (type.equals(ComboParameter.class.getSimpleName())) {
            currentParameter = new ComboParameter<String>(name, null, new String[0]);
        } else {
            throw new SAXException("Unknown parameter type: " + type);
        }
        logger.finest("Loading parameter " + name);
        currentOptions.clear();
        currentValues.clear();
    }
    // <VALUE>
    if (qName.equals(UserParameterElementName_2_5.VALUE.getElementName())) {
        currentDataFileID = attrs.getValue(UserParameterElementName_2_5.DATA_FILE.getElementName());
    }
}

Example 9 with DoubleParameter

use of net.sf.mzmine.parameters.parametertypes.DoubleParameter in project mzmine2 by mzmine.

the class MsMsVisualizerWindow method actionPerformed.

/**
 * @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);
    }
}

Example 10 with DoubleParameter

use of net.sf.mzmine.parameters.parametertypes.DoubleParameter in project mzmine2 by mzmine.

the class AddProjectParameterDialog method actionPerformed.

public void actionPerformed(ActionEvent actionEvent) {
    Object src = actionEvent.getSource();
    Desktop desktop = MZmineCore.getDesktop();
    if (src == buttonAddParameter) {
        if (fieldName.getText().length() == 0) {
            desktop.displayErrorMessage(this, "Give a name for the parameter first.");
            return;
        }
        String paramName = fieldName.getText();
        UserParameter<?, ?> parameter = null;
        if (radiobuttonNumerical.isSelected()) {
            parameter = new DoubleParameter(paramName, null);
        }
        if (radiobuttonFreeText.isSelected()) {
            parameter = new StringParameter(paramName, null);
        }
        if (radiobuttonCategorical.isSelected()) {
            String[] possibleValues = new String[categories.size()];
            if (possibleValues.length == 0) {
                desktop.displayErrorMessage(this, "Give at least a single parameter value.");
                return;
            }
            for (int valueIndex = 0; valueIndex < categories.size(); valueIndex++) possibleValues[valueIndex] = (String) categories.get(valueIndex);
            parameter = new ComboParameter<String>(paramName, null, possibleValues);
        }
        mainDialog.addParameter(parameter);
        dispose();
    }
    if (src == buttonCancel) {
        dispose();
    }
    if ((src == radiobuttonNumerical) || (src == radiobuttonCategorical) || (src == radiobuttonFreeText)) {
        if (radiobuttonCategorical.isSelected()) {
            switchCategoricalFields(true);
        } else {
            switchCategoricalFields(false);
        }
    }
    if (src == buttonAddCategory) {
        String inputValue = JOptionPane.showInputDialog("Please input a new value");
        if ((inputValue == null) || (inputValue.trim().length() == 0))
            return;
        if (((DefaultListModel<String>) listCategories.getModel()).contains(inputValue)) {
            desktop.displayErrorMessage(this, "Value already exists.");
            return;
        }
        ((DefaultListModel<String>) listCategories.getModel()).addElement(inputValue);
    }
    if (src == buttonRemoveCategory) {
        int[] selectedIndices = listCategories.getSelectedIndices();
        if ((selectedIndices == null) || (selectedIndices.length == 0)) {
            desktop.displayErrorMessage(this, "Select at least one value first.");
            return;
        }
        for (int selectedIndex : selectedIndices) {
            ((DefaultListModel<String>) listCategories.getModel()).removeElementAt(selectedIndex);
        }
    }
}