TOPPViewBase.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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/SpectrumCanvas.h>
#include <OpenMS/VISUAL/SpectrumWidget.h>
#include <OpenMS/SYSTEM/FileWatcher.h>
#include <OpenMS/VISUAL/SpectraViewWidget.h>
#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.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 EnhancedWorkspace;
  class EnhancedTabBar;
  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;
    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, 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() const;

    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 showURL();
    void openFileDialog();
    void openExampleDialog();
    void showGoToDialog();
    void preferencesDialog();
    void layerStatistics();
    void editMetadata();
    void layerActivated();
    void layerZoomChanged();
    void linkZoom();
    void layerDeactivated();
    void closeFile();
    void updateToolBar();
    void updateLayerBar();
    void updateViewBar();
    void viewChanged(int);
    void updateFilterBar();
    void updateMenu();
    void updateTabBar(QMdiSubWindow* w);
    void tileVertical();
    void tileHorizontal();
    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, std::allocator<int> > indices);
    void showCurrentPeaksAs2D();
    void showCurrentPeaksAs3D();
    void showAboutDialog();
    void saveLayerAll();
    void saveLayerVisible();
    void toggleGridLines();
    void toggleAxisLegends();
    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);

protected slots:
    void layerSelectionChange(int);
    void layerFilterVisibilityChange(bool);
    void layerContextMenu(const QPoint& pos);
    void logContextMenu(const QPoint& pos);
    void layerVisibilityChange(QListWidgetItem* item);
    void filterContextMenu(const QPoint& pos);
    void filterEdit(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* layer_manager_;


    QListWidget* filters_;
    QCheckBox* filters_check_box_;

    FileWatcher* watcher_;

    bool watcher_msgbox_;

    bool zoom_together_;

    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_;

    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;
      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_;

    // static helper functions
public:
    static bool containsMS1Scans(const ExperimentType& exp);

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

    static bool hasMS1Zeros(const ExperimentType& exp);

    static bool hasPeptideIdentifications(const ExperimentType& map);

private:
    static const String CAPTION_3D_SUFFIX_;
  }; //class

} //namespace