libXpertMass Developer Documentation
  • libXpertMassGui
  • IsotopicClusterShaperDlg

    • Contents

    IsotopicClusterShaperDlg Class

    class MsXpS::libXpertMassGui::IsotopicClusterShaperDlg

    The IsotopicClusterShaperDlg class provides a graphical user interface for the full peak shaping process. More...

    Header: #include <IsotopicClusterShaperDlg.hpp>

    Public Functions

    IsotopicClusterShaperDlg(QWidget *program_window_p, const QString &applicationName, const QString &description)
    IsotopicClusterShaperDlg(QWidget *program_window_p, const QString &applicationName, const QString &description, pappso::TraceCstSPtr isotopic_cluster_sp, int normalizing_intensity = std::numeric_limits<double>::min())
    virtual ~IsotopicClusterShaperDlg()
    void setColorByteArray(QByteArray color_byte_array)
    void setIsotopiCluster(pappso::TraceCstSPtr isotopic_cluster_sp)
    void setMassSpectrumTitle(const QString &title)

    Public Slots

    void traceColorPushButtonClicked()

    Protected Functions

    void closeEvent(int *event)
    void colorizePushButton(int *push_button_p, QByteArray color_byte_array)
    QString craftMassSpectrumName()
    std::size_t fillInThePeakShapers()
    void message(const QString &message, int timeout = 3000)
    void readSettings(const QString &config_settings_file_path)
    void setupDialog()
    void writeSettings(const QString &config_settings_file_path)

    Protected Variables

    QString m_applicationName
    QByteArray m_colorByteArray
    libXpertMass::MassPeakShaperConfig m_config
    QString m_description
    QString m_fileName
    pappso::Trace m_finalTrace
    pappso::Trace m_isotopicCluster
    pappso::MapTrace m_mapTrace
    pappso::MzIntegrationParams m_mzIntegrationParams
    int m_normalizingIntensity
    QList<libXpertMass::MassPeakShaperSPtr> m_peakShapers
    double m_referencePeakMz
    MassPeakShaperConfigWidget *mp_massPeakShaperConfigWidget
    QWidget *mp_programWindow
    Ui::IsotopicClusterShaperDlg *mp_ui
    std::shared_ptr<QTimer> msp_msgTimer

    Detailed Description

    Each peak centroid in the isotopic cluster is shaped independently and all the obtained shapes are combined into a single mass spectrum.

    Member Function Documentation

    IsotopicClusterShaperDlg::IsotopicClusterShaperDlg(QWidget *program_window_p, const QString &applicationName, const QString &description)

    Constructs a IsotopicClusterShaperDlg instance.

    IsotopicClusterShaperDlg::IsotopicClusterShaperDlg(QWidget *program_window_p, const QString &applicationName, const QString &description, pappso::TraceCstSPtr isotopic_cluster_sp, int normalizing_intensity = std::numeric_limits<double>::min())

    Constructs a IsotopicClusterShaperDlg instance.

    [virtual noexcept] IsotopicClusterShaperDlg::~IsotopicClusterShaperDlg()

    Destructs this IsotopicClusterShaperDlg instance.

    [protected] void IsotopicClusterShaperDlg::closeEvent(int *event)

    Upon closing of the dialog window (unused event), writes the settings to the application configuration file.

    [protected] void IsotopicClusterShaperDlg::colorizePushButton(int *push_button_p, QByteArray color_byte_array)

    Colorizes the push_button_p push button with the color encoded in color_byte_array.

    [protected] QString IsotopicClusterShaperDlg::craftMassSpectrumName()

    Returns a string with the mass spectrum name.

    The mass spectrum is the result of the isotopic cluster shaping process.

    [protected] std::size_t IsotopicClusterShaperDlg::fillInThePeakShapers()

    Creates all the peak shapers required to process all the peak centroids in the isotopic cluster.

    [protected] void IsotopicClusterShaperDlg::message(const QString &message, int timeout = 3000)

    Set message to the message line edit widget with timeout.

    At the end of the time out the message is erased.

    [protected] void IsotopicClusterShaperDlg::readSettings(const QString &config_settings_file_path)

    Reads the settings of this dialog window from the application configuration file (config_settings_file_path).

    The configuration is read from the file to set back the dialog window in the same status.

    void IsotopicClusterShaperDlg::setColorByteArray(QByteArray color_byte_array)

    Sets the color_byte_array color.

    Colorizes the push button to provide a visual feedback of the color that was selected.

    void IsotopicClusterShaperDlg::setIsotopiCluster(pappso::TraceCstSPtr isotopic_cluster_sp)

    Sets the isotopic_cluster_sp isotopic cluster that is the starting material for the computations.

    void IsotopicClusterShaperDlg::setMassSpectrumTitle(const QString &title)

    Sets title as the mass spectrum title to the line edit widget.

    [protected] void IsotopicClusterShaperDlg::setupDialog()

    Sets up the dialog window.

    [slot] void IsotopicClusterShaperDlg::traceColorPushButtonClicked()

    Selects a color for the mass spectrum trace to be plotted.

    [protected] void IsotopicClusterShaperDlg::writeSettings(const QString &config_settings_file_path)

    Saves the settings of this dialog window to the application configuration file (config_settings_file_path).

    The saved configuration is read from the file to set back the dialog window in the same status.

    Member Variable Documentation

    QString IsotopicClusterShaperDlg::m_applicationName

    This variable holds the name of the application.

    QByteArray IsotopicClusterShaperDlg::m_colorByteArray

    This variable holds the byte array representation of the color with which the spectrum might be traced.

    libXpertMass::MassPeakShaperConfig IsotopicClusterShaperDlg::m_config

    This variable holds the peak shaping process configuration.

    QString IsotopicClusterShaperDlg::m_description

    This variable holds the description of this IsotopicClusterShaperDlg dialog window instance.

    QString IsotopicClusterShaperDlg::m_fileName

    This variable holds the name of the file to which results might be written.

    pappso::Trace IsotopicClusterShaperDlg::m_finalTrace

    This variable holds the finale pappso::Trace in which to store the final mass spectrum.

    pappso::Trace IsotopicClusterShaperDlg::m_isotopicCluster

    This variable holds the isotopic cluster in the form of a pappso::Trace instance.

    pappso::MapTrace IsotopicClusterShaperDlg::m_mapTrace

    This variable holds the map trace that is used to combine each individual peak shape into a single mass spectrum.

    pappso::MzIntegrationParams IsotopicClusterShaperDlg::m_mzIntegrationParams

    This variable holds the mass spectrum combination parameters (size of the bins, for example).

    int IsotopicClusterShaperDlg::m_normalizingIntensity

    This variable holds the intensity value that the most intense peak in the cluster should have.

    All the other peaks intensities are normalized against this value.

    QList<libXpertMass::MassPeakShaperSPtr> IsotopicClusterShaperDlg::m_peakShapers

    This variable holds the list of peak shapers used to shape the peak around each isotopic cluster peak centroid.

    Each peak centroid of the isotopic cluster will be handled by its own peak shaper instance.

    double IsotopicClusterShaperDlg::m_referencePeakMz

    This variable holds the m/z value that is used as the reference peak when convertring full with at half maximum values to and from resolving power values.

    MassPeakShaperConfigWidget *IsotopicClusterShaperDlg::mp_massPeakShaperConfigWidget

    This variable holds the widget where the mass peak shaping process configuration is done..

    QWidget *IsotopicClusterShaperDlg::mp_programWindow

    This variable holds the main program window.

    Ui::IsotopicClusterShaperDlg *IsotopicClusterShaperDlg::mp_ui

    This variable holds the graphical user interface definition.

    std::shared_ptr<QTimer> IsotopicClusterShaperDlg::msp_msgTimer

    This variable holds the timer used to erase messages output to the user.

    Filippo Rusconi