Examples with UserParameter net.sf.mzmine.parameters.UserParameter used on opensource projects

Example 6 with UserParameter

use of net.sf.mzmine.parameters.UserParameter in project mzmine2 by mzmine.

the class ProjectParametersImporter method importParameters.

public boolean importParameters() {
    // Let user choose a CSV file for importing
    File parameterFile = chooseFile();
    if (parameterFile == null) {
        logger.info("Parameter importing cancelled.");
        return false;
    }
    // Read and interpret parameters
    UserParameter<?, ?>[] parameters = processParameters(parameterFile);
    if (parameters == null)
        return false;
    // TODO: Show a dialog for selecting which parameters to import and edit
    // their types
    // Read values of parameters and store them in the project
    processParameterValues(parameterFile, parameters);
    return true;
}

Example 7 with UserParameter

use of net.sf.mzmine.parameters.UserParameter in project mzmine2 by mzmine.

the class ProjectParametersImporter method processParameters.

private UserParameter<?, ?>[] processParameters(File parameterFile) {
    ArrayList<UserParameter<?, ?>> parameters = new ArrayList<UserParameter<?, ?>>();
    // Open reader
    BufferedReader parameterFileReader;
    try {
        parameterFileReader = new BufferedReader(new FileReader(parameterFile));
        // Read column headers which are used as parameter names
        String firstRow = parameterFileReader.readLine();
        StringTokenizer st = new StringTokenizer(firstRow, ",");
        // Assume first column contains file names
        st.nextToken();
        ArrayList<String> parameterNames = new ArrayList<String>();
        Hashtable<String, ArrayList<String>> parameterValues = new Hashtable<String, ArrayList<String>>();
        while (st.hasMoreTokens()) {
            String paramName = st.nextToken();
            if (parameterValues.containsKey(paramName)) {
                logger.severe("Did not import parameters because of a non-unique parameter name: " + paramName);
                desktop.displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Could not open file " + parameterFile);
                parameterFileReader.close();
                return null;
            }
            parameterNames.add(paramName);
            parameterValues.put(paramName, new ArrayList<String>());
        }
        // Read rest of the rows which contain file name in the first column
        // and parameter values in the rest of the columns
        String nextRow = parameterFileReader.readLine();
        int rowNumber = 2;
        while (nextRow != null) {
            st = new StringTokenizer(nextRow, ",");
            // Skip first column (File name)
            if (st.hasMoreTokens())
                st.nextToken();
            Iterator<String> parameterNameIterator = parameterNames.iterator();
            while (st.hasMoreTokens()) {
                if (st.hasMoreTokens() ^ parameterNameIterator.hasNext()) {
                    logger.severe("Incorrect number of parameter values on row " + rowNumber);
                    desktop.displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Incorrect number of parameter values on row " + rowNumber);
                    parameterFileReader.close();
                    return null;
                }
                parameterValues.get(parameterNameIterator.next()).add(st.nextToken());
            }
            nextRow = parameterFileReader.readLine();
            rowNumber++;
        }
        // Decide parameter types (all numeric => Double, all unique string
        // => String, at least one duplicate string => Object with possible
        // values
        Iterator<String> parameterNameIterator = parameterNames.iterator();
        while (parameterNameIterator.hasNext()) {
            String name = parameterNameIterator.next();
            ArrayList<String> vals = parameterValues.get(name);
            // Test for all numeric
            Iterator<String> valIterator = vals.iterator();
            boolean isAllNumeric = true;
            while (valIterator.hasNext()) {
                try {
                    Double.valueOf(valIterator.next());
                } catch (NumberFormatException ex) {
                    isAllNumeric = false;
                    break;
                }
            }
            if (isAllNumeric) {
                parameters.add(new DoubleParameter(name, null));
                continue;
            }
            // Test for "set of values"
            ArrayList<String> uniqueValues = new ArrayList<String>();
            valIterator = vals.iterator();
            while (valIterator.hasNext()) {
                String val = valIterator.next();
                if (!uniqueValues.contains(val))
                    uniqueValues.add(val);
            }
            if (uniqueValues.size() < vals.size()) {
                parameters.add(new ComboParameter<String>(name, null, uniqueValues.toArray(new String[0])));
                continue;
            }
            // Otherwise it is a free text parameter
            parameters.add(new StringParameter(name, null));
        }
        // Close reader
        parameterFileReader.close();
    } catch (IOException ex) {
        logger.severe("Could not read file " + parameterFile);
        desktop.displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Could not open file " + parameterFile);
        return null;
    }
    return parameters.toArray(new UserParameter[0]);
}

Example 8 with UserParameter

use of net.sf.mzmine.parameters.UserParameter in project mzmine2 by mzmine.

the class ProjectParametersSetupDialog method copyParameterValuesToRawDataFiles.

private void copyParameterValuesToRawDataFiles() {
    MZmineProject currentProject = MZmineCore.getProjectManager().getCurrentProject();
    // Remove all previous parameters from project
    UserParameter<?, ?>[] parameters = currentProject.getParameters();
    for (UserParameter<?, ?> parameter : parameters) {
        currentProject.removeParameter(parameter);
    }
    // Add new parameters
    parameters = parameterValues.keySet().toArray(new UserParameter[0]);
    for (UserParameter<?, ?> parameter : parameters) {
        currentProject.addParameter(parameter);
    }
    // Set values for new parameters
    for (int columnIndex = 0; columnIndex < parameterValues.keySet().size(); columnIndex++) {
        UserParameter<?, ?> parameter = tablemodelParameterValues.getParameter(columnIndex + 1);
        for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
            RawDataFile file = dataFiles[dataFileIndex];
            Object value = tablemodelParameterValues.getValueAt(dataFileIndex, columnIndex + 1);
            if (parameter instanceof DoubleParameter) {
                Double doubleValue = null;
                if (value instanceof Double)
                    doubleValue = (Double) value;
                if (value instanceof String)
                    doubleValue = Double.parseDouble((String) value);
                currentProject.setParameterValue(parameter, file, doubleValue);
            }
            if (parameter instanceof StringParameter) {
                if (value == null)
                    value = "";
                currentProject.setParameterValue(parameter, file, (String) value);
            }
            if (parameter instanceof ComboParameter) {
                if (value == null)
                    value = "";
                currentProject.setParameterValue(parameter, file, (String) value);
            }
        }
    }
}

Example 9 with UserParameter

use of net.sf.mzmine.parameters.UserParameter in project mzmine2 by mzmine.

the class ProjectParametersSetupDialog method copyParameterValuesFromRawDataFiles.

private void copyParameterValuesFromRawDataFiles() {
    MZmineProject currentProject = MZmineCore.getProjectManager().getCurrentProject();
    for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
        RawDataFile file = dataFiles[dataFileIndex];
        UserParameter<?, ?>[] parameters = currentProject.getParameters();
        // Loop through all parameters defined for this file
        for (UserParameter<?, ?> p : parameters) {
            // Check if this parameter has been seen before?
            Object[] values;
            if (!(parameterValues.containsKey(p))) {
                // No, initialize a new array of values for this parameter
                values = new Object[dataFiles.length];
                for (int i = 0; i < values.length; i++) values[i] = p.getValue();
                parameterValues.put(p, values);
            } else {
                values = parameterValues.get(p);
            }
            // Set value of this parameter for the current raw data file
            values[dataFileIndex] = currentProject.getParameterValue(p, file);
        }
    }
}

Example 10 with UserParameter

use of net.sf.mzmine.parameters.UserParameter in project mzmine2 by mzmine.

the class UserParameterSaveHandler method saveParameters.

/**
 * Function which creates an XML file with user parameters
 */
void saveParameters() throws SAXException, IOException, TransformerConfigurationException {
    logger.info("Saving user parameters");
    StreamResult streamResult = new StreamResult(finalStream);
    SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
    TransformerHandler hd = tf.newTransformerHandler();
    Transformer serializer = hd.getTransformer();
    serializer.setOutputProperty(OutputKeys.INDENT, "yes");
    serializer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
    hd.setResult(streamResult);
    hd.startDocument();
    UserParameter<?, ?>[] projectParameters = project.getParameters();
    AttributesImpl atts = new AttributesImpl();
    atts.addAttribute("", "", UserParameterElementName.COUNT.getElementName(), "CDATA", String.valueOf(projectParameters.length));
    hd.startElement("", "", UserParameterElementName.PARAMETERS.getElementName(), atts);
    atts.clear();
    // <PARAMETER>
    for (UserParameter<?, ?> parameter : project.getParameters()) {
        if (canceled)
            return;
        logger.finest("Saving user parameter " + parameter.getName());
        atts.addAttribute("", "", UserParameterElementName.NAME.getElementName(), "CDATA", parameter.getName());
        atts.addAttribute("", "", UserParameterElementName.TYPE.getElementName(), "CDATA", parameter.getClass().getSimpleName());
        hd.startElement("", "", UserParameterElementName.PARAMETER.getElementName(), atts);
        atts.clear();
        fillParameterElement(parameter, hd);
        hd.endElement("", "", UserParameterElementName.PARAMETER.getElementName());
        completedParameters++;
    }
    hd.endElement("", "", UserParameterElementName.PARAMETERS.getElementName());
    hd.endDocument();
}