Examples with ParameterSetupDialog - net.sf.mzmine.parameters.dialogs.ParameterSetupDialog

Example 11 with ParameterSetupDialog

use of net.sf.mzmine.parameters.dialogs.ParameterSetupDialog in project mzmine2 by mzmine.

the class ChromatogramBuilderParameters method showSetupDialog.

public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    String message = "<html><b>Note:</b> starting with MZmine 2.39, this module is considered deprecated <br>" + "and will be removed in future MZmine versions. Please use the <b>ADAP Chromatogram Builder</b>,<br>" + "which is much faster and generates better results.<br>" + "Contact the developers if you have any questions or concerns.</html>";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Example 12 with ParameterSetupDialog

use of net.sf.mzmine.parameters.dialogs.ParameterSetupDialog in project mzmine2 by mzmine.

the class PeakFilterParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    // Update the parameter choices
    UserParameter<?, ?>[] newChoices = MZmineCore.getProjectManager().getCurrentProject().getParameters();
    String[] choices;
    if (newChoices == null || newChoices.length == 0) {
        choices = new String[1];
        choices[0] = "No parameters defined";
    } else {
        choices = new String[newChoices.length + 1];
        choices[0] = "Ignore groups";
        for (int i = 0; i < newChoices.length; i++) {
            choices[i + 1] = "Filtering by " + newChoices[i].getName();
        }
    }
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : UserParameter(net.sf.mzmine.parameters.UserParameter) ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Example 13 with ParameterSetupDialog

use of net.sf.mzmine.parameters.dialogs.ParameterSetupDialog in project mzmine2 by mzmine.

the class SignificanceParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    // Update the parameter choices
    MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
    UserParameter[] newChoices = project.getParameters();
    getParameter(SignificanceParameters.selectionData).setChoices(newChoices);
    // Add a message
    String message = "<html>To view the results of ANOVA test, export the feature list to CSV file " + "and look for column ANOVA_P_VALUE. Click Help for details.</html>";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : UserParameter(net.sf.mzmine.parameters.UserParameter) MZmineProject(net.sf.mzmine.datamodel.MZmineProject) ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Example 14 with ParameterSetupDialog

use of net.sf.mzmine.parameters.dialogs.ParameterSetupDialog in project mzmine2 by mzmine.

the class SiriusExportParameters method showSetupDialog.

public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    String message = "<html>SIRIUS Module Disclaimer:" + "<ul>" + "<li>If you use the SIRIUS export module, cite <a href=\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395\">MZmine2 paper</a> and the following article:<br>" + "<a href=\"http://dx.doi.org/10.1038/s41592-019-0344-8\"> K. Dührkop, et al. “Sirius 4: a rapid tool for turning tandem mass spectra into metabolite structure information”, Nature Methods, 2019.</a>" + "<li>Sirius can be downloaded at the following address: <a href=\"https://bio.informatik.uni-jena.de/software/sirius/\">https://bio.informatik.uni-jena.de/software/sirius/</a>" + "<li>Sirius results can be mapped into <a href=\"http://gnps.ucsd.edu/\">GNPS</a> molecular networks. <a href=\"https://bix-lab.ucsd.edu/display/Public/Mass+spectrometry+data+pre-processing+for+GNPS\">See the documentation</a>." + "</ul>";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Example 15 with ParameterSetupDialog

use of net.sf.mzmine.parameters.dialogs.ParameterSetupDialog in project mzmine2 by mzmine.

the class LocalSpectralDBSearchParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    if ((getParameters() == null) || (getParameters().length == 0))
        return ExitCode.OK;
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this);
    int level = getParameter(msLevel).getValue() == null ? 2 : getParameter(msLevel).getValue();
    IntegerComponent msLevelComp = (IntegerComponent) dialog.getComponentForParameter(msLevel);
    JComponent mzTolPrecursor = dialog.getComponentForParameter(mzTolerancePrecursor);
    mzTolPrecursor.setEnabled(level > 1);
    msLevelComp.addDocumentListener(new DelayedDocumentListener(e -> {
        try {
            int level2 = Integer.parseInt(msLevelComp.getText());
            mzTolPrecursor.setEnabled(level2 > 1);
        } catch (Exception ex) {
            // do nothing user might be still typing
            mzTolPrecursor.setEnabled(false);
        }
    }));
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : JComponent(javax.swing.JComponent) BooleanParameter(net.sf.mzmine.parameters.parametertypes.BooleanParameter) MZmineCore(net.sf.mzmine.main.MZmineCore) Parameter(net.sf.mzmine.parameters.Parameter) MZToleranceParameter(net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter) Window(java.awt.Window) Collection(java.util.Collection) ModuleComboParameter(net.sf.mzmine.parameters.parametertypes.ModuleComboParameter) OptionalParameter(net.sf.mzmine.parameters.parametertypes.OptionalParameter) OptionalModuleParameter(net.sf.mzmine.parameters.parametertypes.submodules.OptionalModuleParameter) IntegerComponent(net.sf.mzmine.parameters.parametertypes.IntegerComponent) DelayedDocumentListener(net.sf.mzmine.framework.listener.DelayedDocumentListener) RTToleranceParameter(net.sf.mzmine.parameters.parametertypes.tolerances.RTToleranceParameter) MassListParameter(net.sf.mzmine.parameters.parametertypes.MassListParameter) FileNameParameter(net.sf.mzmine.parameters.parametertypes.filenames.FileNameParameter) MassListDeisotoperParameters(net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.isotopes.MassListDeisotoperParameters) IntegerParameter(net.sf.mzmine.parameters.parametertypes.IntegerParameter) PeakListsParameter(net.sf.mzmine.parameters.parametertypes.selectors.PeakListsParameter) SimpleParameterSet(net.sf.mzmine.parameters.impl.SimpleParameterSet) DoubleParameter(net.sf.mzmine.parameters.parametertypes.DoubleParameter) ExitCode(net.sf.mzmine.util.ExitCode) SpectralSimilarityFunction(net.sf.mzmine.util.scans.similarity.SpectralSimilarityFunction) ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog) IntegerComponent(net.sf.mzmine.parameters.parametertypes.IntegerComponent) JComponent(javax.swing.JComponent) DelayedDocumentListener(net.sf.mzmine.framework.listener.DelayedDocumentListener) ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Aggregations

ParameterSetupDialog (net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)24 RawDataFile (net.sf.mzmine.datamodel.RawDataFile)3 UserParameter (net.sf.mzmine.parameters.UserParameter)3 RawDataFilesParameter (net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter)3 Window (java.awt.Window)2 JComponent (javax.swing.JComponent)2 Parameter (net.sf.mzmine.parameters.Parameter)2 BooleanParameter (net.sf.mzmine.parameters.parametertypes.BooleanParameter)2 DoubleParameter (net.sf.mzmine.parameters.parametertypes.DoubleParameter)2 IntegerParameter (net.sf.mzmine.parameters.parametertypes.IntegerParameter)2 ModuleComboParameter (net.sf.mzmine.parameters.parametertypes.ModuleComboParameter)2 RawDataFilesComponent (net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesComponent)2 Collection (java.util.Collection)1 JButton (javax.swing.JButton)1 MZmineProject (net.sf.mzmine.datamodel.MZmineProject)1 Scan (net.sf.mzmine.datamodel.Scan)1 DelayedDocumentListener (net.sf.mzmine.framework.listener.DelayedDocumentListener)1 MZmineCore (net.sf.mzmine.main.MZmineCore)1 MZmineProcessingStep (net.sf.mzmine.modules.MZmineProcessingStep)1 MassListDeisotoperParameters (net.sf.mzmine.modules.visualization.spectra.simplespectra.datapointprocessing.isotopes.MassListDeisotoperParameters)1