2.6.0/html/TOPPViewBase_8h_source.html

// --------------------------------------------------------------------------

//                   OpenMS -- Open-Source Mass Spectrometry

// --------------------------------------------------------------------------

// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,

// ETH Zurich, and Freie Universitaet Berlin 2002-2020.

//

// This software is released under a three-clause BSD license:

//  * Redistributions of source code must retain the above copyright

//    notice, this list of conditions and the following disclaimer.

//  * Redistributions in binary form must reproduce the above copyright

//    notice, this list of conditions and the following disclaimer in the

//    documentation and/or other materials provided with the distribution.

//  * Neither the name of any author or any participating institution

//    may be used to endorse or promote products derived from this software

//    without specific prior written permission.

// For a full list of authors, refer to the file AUTHORS.

// --------------------------------------------------------------------------

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING

// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,

// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,

// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;

// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,

// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR

// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF

// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

//

// --------------------------------------------------------------------------

// $Maintainer: Timo Sachsenberg$

// $Authors: Marc Sturm, Timo Sachsenberg $

// --------------------------------------------------------------------------


#pragma once


// OpenMS_GUI config

#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>


//OpenMS

#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/VISUAL/EnhancedTabBar.h>

#include <OpenMS/VISUAL/EnhancedWorkspace.h>

#include <OpenMS/SYSTEM/FileWatcher.h>

#include <OpenMS/VISUAL/FilterList.h>

#include <OpenMS/VISUAL/SpectraViewWidget.h>

#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>

#include <OpenMS/VISUAL/SpectrumCanvas.h>

#include <OpenMS/VISUAL/SpectrumWidget.h>

#include <OpenMS/VISUAL/TOPPViewSpectraViewBehavior.h>

#include <OpenMS/VISUAL/TOPPViewIdentificationViewBehavior.h>


//STL

#include <map>


//QT

#include <QtWidgets/QMainWindow>

#include <QtWidgets/QButtonGroup>

#include <QtWidgets/QActionGroup>

#include <QtCore/QStringList>

#include <QtCore/QProcess>


class QAction;

class QComboBox;

class QLabel;

class QLineEdit;

class QListWidget;

class QListWidgetItem;

class QTreeWidget;

class QTreeWidgetItem;

class QDockWidget;

class QToolButton;

class QCloseEvent;

class QTextEdit;

class QCheckBox;

class QSplashScreen;

class QToolButton;

class QWorkspace;


namespace OpenMS

{

  class Spectrum1DWidget;

  class Spectrum2DWidget;

  class Spectrum3DWidget;

  class ToolsDialog;

  class MultiGradientSelector;

  class FileWatcher;


  class OPENMS_GUI_DLLAPI TOPPViewBase :

    public QMainWindow,

    public DefaultParamHandler

  {

    Q_OBJECT


    friend class TestTOPPView;


public:


    //Feature map type

    typedef LayerData::FeatureMapType FeatureMapType;

    //Feature map managed type

    typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType;


    //Consensus feature map type

    typedef LayerData::ConsensusMapType ConsensusMapType;

    //Consensus  map managed type

    typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;


    //Peak map type

    typedef LayerData::ExperimentType ExperimentType;

    //Main managed data type (experiment)

    typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType;

    //Main on-disc managed data type (experiment)

    typedef LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType;

    typedef ExperimentType::SpectrumType SpectrumType;


    TOPPViewBase(QWidget* parent = nullptr);

    ~TOPPViewBase() override;


    void addDataFile(const String& filename, bool show_options, bool add_to_recent, String caption = "", UInt window_id = 0, Size spectrum_id = 0);


    void addData(FeatureMapSharedPtrType feature_map,

                 ConsensusMapSharedPtrType consensus_map,

                 std::vector<PeptideIdentification>& peptides,

                 ExperimentSharedPtrType peak_map,

                 ODExperimentSharedPtrType on_disc_peak_map,

                 LayerData::DataType data_type,

                 bool show_as_1d,

                 bool show_options,

                 bool as_new_window = true,

                 const String& filename = "",

                 const String& caption = "",

                 UInt window_id = 0,

                 Size spectrum_id = 0);


    void loadFiles(const StringList& list, QSplashScreen* splash_screen);


    void loadPreferences(String filename = "");


    void savePreferences();


    Param getSpectrumParameters(UInt dim);


    const LayerData* getCurrentLayer() const;


    //@name Accessors for the main gui components.

    //@brief The top level enhanced workspace and the EnhancedTabWidgets resing in the EnhancedTabBar.

    EnhancedWorkspace* getWorkspace();


    SpectrumWidget* getActiveSpectrumWidget() const;


    Spectrum1DWidget* getActive1DWidget() const;


    Spectrum2DWidget* getActive2DWidget() const;


    Spectrum3DWidget* getActive3DWidget() const;


    SpectrumCanvas* getActiveCanvas() const;


    SpectraIdentificationViewWidget* getSpectraIdentificationViewWidget();


    void showSpectrumWidgetInWindow(SpectrumWidget* sw, const String& caption);


public slots:

    void updateCurrentPath();

    void openFileDialog(const String& initial_directory = "");

    void showGoToDialog();

    void preferencesDialog();

    void layerStatistics();

    void editMetadata();

    void layerActivated();

    void layerZoomChanged();

    void linkZoom();

    void layerDeactivated();

    void closeFile();


    void updateBarsAndMenus();

    void updateToolBar();

    void updateLayerBar();

    void updateViewBar();

    void viewChanged(int);

    void viewTabwidgetDoubleClicked(int);

    void updateFilterBar();

    void updateMenu();

    void updateTabBar(QMdiSubWindow* w);


    void showStatusMessage(std::string msg, OpenMS::UInt time);

    void showCursorStatus(double mz, double rt);

    void showCursorStatusInvert(double mz, double rt);

    void showTOPPDialog();

    void annotateWithID();

    void showSpectrumGenerationDialog();

    void showSpectrumAlignmentDialog();

    void showSpectrumAs1D(int index);

    void showSpectrumAs1D(std::vector<int> indices);

    void showCurrentPeaksAs2D();

    void showCurrentPeaksAs3D();

    void showCurrentPeaksAsIonMobility();

    void showCurrentPeaksAsDIA();

    void saveLayerAll();

    void saveLayerVisible();

    void toggleGridLines();

    void toggleAxisLegends();

    void toggleInterestingMZs();

    void showPreferences();

    void metadataFileDialog();


    void setDrawMode1D(int);

    void setIntensityMode(int);

    void changeLayerFlag(bool);

    void changeLabel(QAction*);

    void changeUnassigned(QAction*);

    void resetZoom();

    void toggleProjections();


    void loadFile(QString);


    void layerFilterVisibilityChange(bool);


protected slots:

    void layerSelectionChange(int);

    void layerContextMenu(const QPoint& pos);

    void logContextMenu(const QPoint& pos);

    void layerVisibilityChange(QListWidgetItem* item);

    void layerEdit(QListWidgetItem* /*item*/);


    void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus);

    void abortTOPPTool();

    void rerunTOPPTool();

    void showSpectrumBrowser();

    void showSpectrumMetaData(int spectrum_index);


    void closeByTab(int id);

    void enhancedWorkspaceWindowChanged(int id);

    void openRecentFile();

    void copyLayer(const QMimeData* data, QWidget* source, int id = -1);


    void updateProcessLog();


    void fileChanged_(const String&);

protected:

    void initializeDefaultParameters_();


    bool annotateMS1FromMassFingerprinting_(const FeatureMap& identifications);


    std::set<String> getFilenamesOfOpenFiles_();


    QStringList getFileList_(const String& path_overwrite = "");


    EnhancedTabBarWidgetInterface* window_(int id) const;


    QDockWidget* layer_dock_widget_;

    QDockWidget* views_dockwidget_;

    QDockWidget* filter_dock_widget_;


    SpectraViewWidget* spectra_view_widget_;

    SpectraIdentificationViewWidget* spectra_identification_view_widget_;


    QListWidget* layers_view_;


    FilterList* filter_list_;


    FileWatcher* watcher_ = nullptr;


    bool watcher_msgbox_ = false;


    bool zoom_together_ = false;


    QAction* linkZoom_action_;


    QTextEdit* log_;


    QToolBar* tool_bar_;


    // common intensity modes

    QButtonGroup* intensity_button_group_;


    // 1D specific stuff

    QToolBar* tool_bar_1d_;

    QButtonGroup* draw_group_1d_;


    // 2D specific stuff

    QToolBar* tool_bar_2d_peak_;

    QToolBar* tool_bar_2d_feat_;

    QToolBar* tool_bar_2d_cons_;

    QToolBar* tool_bar_2d_ident_;

    QAction* dm_precursors_2d_;

    QAction* dm_hull_2d_;

    QAction* dm_hulls_2d_;

    QToolButton* dm_label_2d_;

    QActionGroup* group_label_2d_;

    QToolButton* dm_unassigned_2d_;

    QActionGroup* group_unassigned_2d_;

    QAction* dm_elements_2d_;

    QAction* projections_2d_;

    QAction* dm_ident_2d_;


    EnhancedWorkspace ws_;  // not a pointer, but an actual object, so it gets destroyed before the DefaultParamhandler (on which it depends)

    EnhancedTabBar tab_bar_;


    QLabel* message_label_;

    QLabel* mz_label_;

    QLabel* rt_label_;


    void addRecentFile_(const String& filename);

    void updateRecentMenu_();

    QStringList recent_files_;

    std::vector<QAction*> recent_actions_;


    void runTOPPTool_();

    struct

    {

      Param param;

      String tool;

      String in;

      String out;

      String file_name;

      String layer_name;

      UInt window_id;

      Size spectrum_id;

      QProcess* process = nullptr;

      QTime timer;

      bool visible;

    } topp_;


    void checkPreferences_();


    void closeEvent(QCloseEvent* event) override;


    enum LogState

    {

      LS_NOTICE,

      LS_WARNING,

      LS_ERROR

    };

    void showLogMessage_(LogState state, const String& heading, const String& body);


    QMenu* add_2d_context_;


    void showTOPPDialog_(bool visible);


    String current_path_;


    QTabWidget* views_tabwidget_;


    TOPPViewIdentificationViewBehavior identificationview_behavior_;

    TOPPViewSpectraViewBehavior spectraview_behavior_;


public:

    static float estimateNoiseFromRandomMS1Scans(const ExperimentType& exp, UInt n_scans = 10);


    static bool hasPeptideIdentifications(const ExperimentType& map);


private:

    static const String CAPTION_3D_SUFFIX_;

  }; //class


} //namespace