TOPPViewBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// 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/RecentFilesMenu.h>
#include <OpenMS/VISUAL/PlotCanvas.h>
#include <OpenMS/VISUAL/PlotWidget.h>
#include <OpenMS/VISUAL/TOPPViewMenu.h>
#include <OpenMS/VISUAL/TVToolDiscovery.h>
#include <OpenMS/VISUAL/DIALOGS/TheoreticalSpectrumGenerationDialog.h>

//STL
#include <map>

//QT
#include <QtWidgets/QMainWindow>
#include <QtWidgets/QButtonGroup>
#include <QtWidgets/QActionGroup>
#include <QtCore/QStringList>
#include <QtCore/QProcess>
#include <QElapsedTimer>

class QAction;
class QComboBox;
class QLabel;
class QLineEdit;
class QListWidget;
class QListWidgetItem;
class QTreeWidget;
class QTreeWidgetItem;
class QDockWidget;
class QToolButton;
class QCloseEvent;
class QCheckBox;
class QSplashScreen;
class QToolButton;

namespace OpenMS
{
  class DataSelectionTabs;
  class FileWatcher;
  class LogWindow;
  class LayerListView;
  class MultiGradientSelector;
  class Plot1DWidget;
  class Plot2DWidget;
  class Plot3DWidget;
  class ToolsDialog;

  class OPENMS_GUI_DLLAPI TOPPViewBase :
    public QMainWindow,
    public DefaultParamHandler
  {
    Q_OBJECT

    friend class TestTOPPView;

public:

    //Feature map type
    typedef LayerDataBase::FeatureMapType FeatureMapType;
    //Feature map managed type
    typedef LayerDataBase::FeatureMapSharedPtrType FeatureMapSharedPtrType;

    //Consensus feature map type
    typedef LayerDataBase::ConsensusMapType ConsensusMapType;
    //Consensus  map managed type
    typedef LayerDataBase::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;

    //Peak map type
    typedef LayerDataBase::ExperimentType ExperimentType;
    //Main managed data type (experiment)
    typedef LayerDataBase::ExperimentSharedPtrType ExperimentSharedPtrType;
    //Main on-disc managed data type (experiment)
    typedef LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType;
    typedef ExperimentType::SpectrumType SpectrumType;

    enum class TOOL_SCAN
    {
      SKIP_SCAN,
      SCAN_IF_NEWER_VERSION,
      FORCE_SCAN
    };

    explicit TOPPViewBase(TOOL_SCAN scan_mode = TOOL_SCAN::SCAN_IF_NEWER_VERSION, QWidget* parent = nullptr);
    ~TOPPViewBase() override;

    enum class LOAD_RESULT
    {
      OK,
      FILE_NOT_FOUND,       
      FILETYPE_UNKNOWN,     
      FILETYPE_UNSUPPORTED, 
      LOAD_ERROR            
    };

    LOAD_RESULT 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,
                 LayerDataBase::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 getCanvasParameters(UInt dim) const;

    const LayerDataBase* getCurrentLayer() const;

    LayerDataBase* getCurrentLayer();

    //@name Accessors for the main gui components.
    //@brief The top level enhanced workspace and the EnhancedTabWidgets resing in the EnhancedTabBar.
    EnhancedWorkspace* getWorkspace();

    PlotWidget* getActivePlotWidget() const;

    Plot1DWidget* getActive1DWidget() const;

    Plot2DWidget* getActive2DWidget() const;

    Plot3DWidget* getActive3DWidget() const;

    PlotCanvas* getActiveCanvas() const;

    void showPlotWidgetInWindow(PlotWidget* sw, const String& caption);

public slots:
    void updateCurrentPath();
    void openFilesByDialog(const String& initial_directory = "");
    void showGoToDialog() const;
    void preferencesDialog();
    void layerStatistics() const;
    void editMetadata();
    void layerActivated();
    void layerZoomChanged() const;
    void linkZoom();
    void layerDeactivated();
    void closeTab();

    void rerunTOPPTool();

    void updateBarsAndMenus();
    void updateToolBar();
    void updateLayerBar();
    void updateViewBar();
    void updateMenu();
    void updateFilterBar();
    void showStatusMessage(std::string msg, OpenMS::UInt time);
    void showCursorStatus(double mz, double rt);
    void showCursorStatusInvert(double mz, double rt);
    void showTOPPDialog();
    void annotateWithAMS();
    void annotateWithID();
    void annotateWithOSW();
    void showSpectrumGenerationDialog();
    void showSpectrumAlignmentDialog();
    void showCurrentPeaksAs2D();
    void showCurrentPeaksAs3D();
    void showCurrentPeaksAsIonMobility();
    void showCurrentPeaksAsDIA();
    void saveLayerAll() const;
    void saveLayerVisible() const;
    void toggleGridLines() const;
    void toggleAxisLegends() const;
    void toggleInterestingMZs() const;
    void showPreferences() const;
    void metadataFileDialog();

    void setDrawMode1D(int) const;
    void setIntensityMode(int);
    void changeLayerFlag(bool);
    void changeLabel(QAction*);
    void changeUnassigned(QAction*);
    void resetZoom() const;
    void toggleProjections();

    void openFile(const String& filename);

    void layerFilterVisibilityChange(bool) const;

    void showSpectrumMetaData(int spectrum_index) const;

protected slots:
    void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus);
    void abortTOPPTool();
    void showSpectrumBrowser();

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

    void updateProcessLog();

    void fileChanged_(const String&);
protected:
    void initializeDefaultParameters_();

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


    QDockWidget* layer_dock_widget_;
    QDockWidget* views_dockwidget_;
    QDockWidget* filter_dock_widget_;

    LayerListView* layers_view_;

    DataSelectionTabs* selection_view_;


    FilterList* filter_list_;

    FileWatcher* watcher_ = nullptr;

    bool watcher_msgbox_ = false;

    bool zoom_together_ = false;

    LogWindow* log_;

    TOOL_SCAN scan_mode_;
    TVToolDiscovery tool_scanner_;

    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)
    QMdiSubWindow* lastActiveSubwindow_ = nullptr; // due to Qt bugs or confusing features we need to save the current Window id in the children of the workspace;
    EnhancedTabBar tab_bar_;
    RecentFilesMenu recent_files_;  // needs to be declared before 'menu_', because its needed there
    TOPPViewMenu menu_;

    QLabel* message_label_;
    QLabel* mz_label_;
    QLabel* rt_label_;


    void addRecentFile_(const String& filename);




    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;
      QElapsedTimer timer;
      bool visible_area_only;
    } topp_;

    void checkPreferences_();

    void closeEvent(QCloseEvent* event) override;

    QMenu* add_2d_context_;

    void showTOPPDialog_(bool visible);

    String current_path_;

private:
    static const String CAPTION_3D_SUFFIX_;

    TheoreticalSpectrumGenerationDialog spec_gen_dialog_;
  }; //class

} //namespace