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

Example 16 with ParameterSetupDialog

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

the class GnpsGcExportAndSubmitParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    String message = "<html><strong>Export/Submit to GNPS-GC:</strong>" + "<p>The GNPS Export module was designed for the <strong>GC</strong> workflow on GNPS <a href=\"http://gnps.ucsd.edu\">http://gnps.ucsd.edu</a>.<br>" + "See the <a href=\"https://ccms-ucsd.github.io/GNPSDocumentation/gc-ms-documentation/\"><strong>GNPS-GC-MS documentation here</strong></a> and <strong>please cite</strong>:<br>" + "<ul>" + "<li>the preprint <strong>GC-MS</strong> on GNPS: Aksenov et al.: <a href=\"https://www.biorxiv.org/content/10.1101/812404v1\">bioRxiv 812404 (2019)</a>.</li>" + "<li>the <strong>GNPS</strong> paper: Wang et al.:<a href=\"https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html\">Nature Biotechnology 34.8 (2016): 828-837</a></li>" + "<li>and the <strong>MZmine</strong> paper: Pluskal et al.: <a href=\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395\">BMC Bioinformatics, 11, 395 (2010)</a></li>" + "</ul></p>";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

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

Example 17 with ParameterSetupDialog

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

the class GnpsGcSubmitParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this);
    // add button to create Kovats file
    FileNameComponent pn = (FileNameComponent) ((OptionalParameterComponent) dialog.getComponentForParameter(KOVATS_FILE)).getEmbeddedComponent();
    JButton btn = new JButton("Create");
    pn.add(btn);
    btn.addActionListener(e -> openKovatsDialog(pn));
    dialog.updateMinimumSize();
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : FileNameComponent(net.sf.mzmine.parameters.parametertypes.filenames.FileNameComponent) JButton(javax.swing.JButton) ParameterSetupDialog(net.sf.mzmine.parameters.dialogs.ParameterSetupDialog)

Example 18 with ParameterSetupDialog

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

the class SiriusParameters method showSetupDialog.

/**
 * Disclaimer message about boecker-labs
 */
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    String message = "<html>SIRIUS Module Disclaimer:" + "<br>    - Identification task consists of two parts:" + "<br>      1) Sirius Identification job, the timer you specify above controls the execution of this job. " + "<br>      2) FingerId Identification job, it is executed after Sirius Identification Job and uses its results. It makes web requests to boecker-labs server (FingerId web-api). " + "<br>    - If you use the SIRIUS Identification module, cite <a href=\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395\">MZmine2 paper</a> and the following articles: " + "<br>     <a href=\"http://www.pnas.org/content/112/41/12580.abstract\">Dührkop et al., Proc Natl Acad Sci USA 112(41):12580-12585</a> " + "and <a href=\"https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0116-8\">Boecker et al., Journal of Cheminformatics (2016) 8:5</a>" + "<br>    - 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>" + "<br>    - 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>.";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

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

Example 19 with ParameterSetupDialog

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

the class GnpsFbmnExportAndSubmitParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    String message = "<html><strong>About the GNPS Export/Submit Module:</strong>" + "<p>The GNPS Export module was designed for the <strong>Feature-Based Molecular Networking</strong> (FBMN) workflow on GNPS <a href=\"http://gnps.ucsd.edu\">http://gnps.ucsd.edu</a>.<br>" + "See the <a href=\"https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/\"><strong>FBMN documentation here</strong></a> (or a youtube <a href=\"https://www.youtube.com/watch?v=vFcGG7T_44E&list=PL4L2Xw5k8ITzd9hx5XIP94vFPxj1sSafB&index=4&t=146s\">playlist here</a>) and <strong>please cite</strong>:<br>" + "<ul>" + "<li>our preprint on <strong>FBMN</strong>: Nothias et al.: <a href=\"https://www.biorxiv.org/content/10.1101/812404v1\">bioRxiv 812404 (2019)</a>.</li>" + "<li>the <strong>GNPS</strong> paper: Wang et al.:<a href=\"https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html\">Nature Biotechnology 34.8 (2016): 828-837</a></li>" + "<li>and the <strong>MZmine</strong> paper: Pluskal et al.: <a href=\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395\">BMC Bioinformatics, 11, 395 (2010)</a></li>" + "</ul></p>";
    ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

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

Example 20 with ParameterSetupDialog

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

the class KovatsIndexExtractionParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    if ((getParameters() == null) || (getParameters().length == 0))
        return ExitCode.OK;
    // at least one raw data file in project
    RawDataFile[] raw = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
    if (raw == null || raw.length <= 0) {
        DialogLoggerUtil.showMessageDialogForTime(MZmineCore.getDesktop().getMainWindow(), "No RAW data files", "Cannot use Kovats extraction without raw data files in this project", 3500);
        return ExitCode.ERROR;
    }
    // set choices of kovats to min max
    int min = getParameter(minKovats).getValue();
    int max = getParameter(maxKovats).getValue();
    getParameter(kovats).setChoices(KovatsIndex.getRange(min, max));
    ParameterSetupDialog dialog = new KovatsIndexExtractionDialog(parent, this);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Also used : RawDataFile(net.sf.mzmine.datamodel.RawDataFile) 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