libopenms-dev 1.11.1-5 / usr / include / OpenMS / VISUAL / APPLICATIONS / TOPPViewBase.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    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
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm, Timo Sachsenberg $
// --------------------------------------------------------------------------

#ifndef OPENMS_VISUAL_APPLICATIONS_TOPPVIEWBASE_H
#define OPENMS_VISUAL_APPLICATIONS_TOPPVIEWBASE_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/TOPPViewBehaviorInterface.h>
#include <OpenMS/VISUAL/TOPPViewSpectraViewBehavior.h>
#include <OpenMS/VISUAL/TOPPViewIdentificationViewBehavior.h>

//STL
#include <map>

//QT
#include <QtGui/QMainWindow>
#include <QtGui/QButtonGroup>
#include <QtGui/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 DBConnection;
  class FileWatcher;

  /**
    @brief Main window of TOPPView tool

    @improvement Use DataRepository singleton to share data between TOPPView and the canvas classes (Hiwi)

        @improvement For painting single mass traces with no width we currently paint each line twice (once going down, and then coming back up).
        This could be more efficient...

    @improvement Keep spectrum browser widgets of all layers in memory in order to avoid rebuilding the entire tree view every time the active layer changes (Hiwi, Johannes)

    @todo Add TOPPView live-tutorial (Stephan, Marc)

    @ingroup TOPPView_elements
  */
  class OPENMS_GUI_DLLAPI TOPPViewBase :
    public QMainWindow,
    public DefaultParamHandler
  {
    Q_OBJECT

    friend class TestTOPPView;

public:
    ///@name Type definitions
    //@{
    //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;
    ///Peak spectrum type
    typedef ExperimentType::SpectrumType SpectrumType;
    //@}

    ///Constructor
    TOPPViewBase(QWidget* parent = 0);
    ///Destructor
    ~TOPPViewBase();

    /**
      @brief Opens and displays data from a file

      Loads the data and adds it to the application by calling addData_()

      @param filename The file to open
      @param show_options If the options dialog should be shown (otherwise the defaults are used)
      @param caption Sets the layer name and window caption of the data. If unset the file name is used.
      @param add_to_recent If the file should be added to the recent files after opening
      @param window_id in which window the file is opened if opened as a new layer (0 or default equals current window).
      @param spectrum_id determines the spectrum to show in 1D view.
    */
    void addDataFile(const String& filename, bool show_options, bool add_to_recent, String caption = "", UInt window_id = 0, Size spectrum_id = 0);
    /**
      @brief Opens and displays a data from a database

      Loads the data and adds it to the application by calling addData_()

      @param db_id The id in the database
      @param show_options If the options dialog should be shown (otherwise the defaults are used)
      @param caption Sets the layer name and window caption of the data. If unset the file name is used.
      @param window_id in which window the file is opened if opened as a new layer (0 or default equals current window).
    */
    void addDataDB(UInt db_id, bool show_options, String caption = "", UInt window_id = 0);

    /**
      @brief Adds a peak or feature map to the viewer

      @param feature_map The feature data (empty if not feature data)
      @param consensus_map The consensus feature data (empty if not consensus feature data)
      @param peptides The peptide identifications (empty if not ID data)
      @param peak_map The peak data (empty if not peak data)
      @param data_type Type of the data
      @param show_as_1d Force dataset to be opened in 1D mode (even if it contains several spectra)
      @param show_options If the options dialog should be shown (otherwise the defaults are used)
      @param filename source file name (if the data came from a file)
      @param caption Sets the layer name and window caption of the data. If unset the file name is used. If set, the file is not monitored foro changes.
      @param window_id in which window the file is opened if opened as a new layer (0 or default equals current
      @param spectrum_id determines the spectrum to show in 1D view.
    */
    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);

    /// Opens all the files in the string list
    void loadFiles(const StringList& list, QSplashScreen* splash_screen);

    /**
      @brief Loads the preferences from the filename given.

      If the filename is empty, the application name + ".ini" is used as filename
    */
    void loadPreferences(String filename = "");

    /// Stores the preferences (used when this window is closed)
    void savePreferences();

    /// Returns the parameters for a SpectrumCanvas of dimension @p dim
    Param getSpectrumParameters(UInt dim);

    /// Returns the active Layer data (0 if no layer is active)
    const LayerData* getCurrentLayer() const;

    //@name Accessors for the main gui components.
    //@brief The top level enhanced workspace and the EnhancedTabWidgets resing in the EnhancedTabBar.
    //@{
    /// returns a pointer to the EnhancedWorkspace containing SpectrumWidgets
    EnhancedWorkspace* getWorkspace() const;

    /// returns a pointer to the active SpectrumWidget (0 if none is active)
    SpectrumWidget* getActiveSpectrumWidget() const;

    /// returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window)
    Spectrum1DWidget* getActive1DWidget() const;

    /// returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window)
    Spectrum2DWidget* getActive2DWidget() const;

    /// returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window)
    Spectrum3DWidget* getActive3DWidget() const;
    //@}

    /// returns a pointer to the active SpectrumCanvas (0 if none is active)
    SpectrumCanvas* getActiveCanvas() const;


    /// returns a pointer to the SpectraIdentificationViewWidget
    SpectraIdentificationViewWidget* getSpectraIdentificationViewWidget();

    /// Opens the provided spectrum widget in a new window
    void showSpectrumWidgetInWindow(SpectrumWidget* sw, const String& caption);

public slots:
    /// changes the current path according to the currently active window/layer
    void updateCurrentPath();
    /// shows the URL stored in the data of the sender QAction
    void showURL();
    /// shows the file dialog for opening files
    void openFileDialog();
    /// shows the file dialog for opening example files
    void openExampleDialog();
    /// shows the DB dialog for opening files
    void openDatabaseDialog();
    /// shows the goto dialog
    void showGoToDialog();
    /// shows the preferences dialog
    void preferencesDialog();
    /// Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data
    void layerStatistics();
    /// lets the user edit the meta data of a layer
    void editMetadata();
    /// get's called if a layer got activated
    void layerActivated();
    /// gets called when a layer changes in zoom
    void layerZoomChanged();
    /// link the zoom of individual windows
    void linkZoom();
    /// get's called if a layer got deactivated
    void layerDeactivated();
    /// Activation of 1D spectrum
    void activate1DSpectrum(int index);
    /// Activation of 1D with multiple entries (e.g. chromatograms)
    void activate1DSpectrum(std::vector<int, std::allocator<int> > indices);
    /// Deactivation of 1D spectrum
    void deactivate1DSpectrum(int index);
    /// closes the active window
    void closeFile();
    /// updates the toolbar
    void updateToolBar();
    /// adapts the layer bar to the active window
    void updateLayerBar();
    /// adapts view bar to the active window
    void updateViewBar();
    /// changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar()
    void viewChanged(int);
    /// adapts the filter bar to the active window
    void updateFilterBar();
    /// enabled/disabled menu entries depending on the current state
    void updateMenu();
    /// brings the tab corresponding to the active window in front
    void updateTabBar(QWidget* w);
    /// tile the open windows vertically
    void tileVertical();
    /// tile the open windows horizontally
    void tileHorizontal();
    /**
      @brief Shows a status message in the status bar.

      If @p time is 0 the status message is displayed until showStatusMessage is called with an empty message or a new message.
      Otherwise the message is displayed for @p time ms.
    */
    void showStatusMessage(std::string msg, OpenMS::UInt time);
    /// shows m/z and rt in the status bar
    void showCursorStatus(double mz, double rt);
    /// shows m/z and rt in the status bar (inverting RT and m/z)
    void showCursorStatusInvert(double mz, double rt);
    /// Apply TOPP tool
    void showTOPPDialog();
    /// Annotates current layer with ID data
    void annotateWithID();
    /// Shows the theoretical spectrum generation dialog
    void showSpectrumGenerationDialog();
    /// Shows the spectrum alignment dialog
    void showSpectrumAlignmentDialog();
    /// Shows the spectrum with index @p index of the active layer in 1D
    void showSpectrumAs1D(int index);
    void showSpectrumAs1D(std::vector<int, std::allocator<int> > indices);
    /// Shows the current peak data of the active layer in 2D
    void showCurrentPeaksAs2D();
    /// Shows the current peak data of the active layer in 3D
    void showCurrentPeaksAs3D();
    /// Shows the 'About' dialog
    void showAboutDialog();
    /// Saves the whole current layer data
    void saveLayerAll();
    /// Saves the visible layer data
    void saveLayerVisible();
    /// Toggles the grid lines
    void toggleGridLines();
    /// Toggles the axis legends
    void toggleAxisLegends();
    /// Shows current layer preferences
    void showPreferences();
    /// dialog for inspecting database meta data
    void metadataDatabaseDialog();
    /// dialog for inspecting file meta data
    void metadataFileDialog();

    /** @name Toolbar slots
    */
    //@{
    void setDrawMode1D(int);
    void setIntensityMode(int);
    void changeLayerFlag(bool);
    void changeLabel(QAction*);
    void changeUnassigned(QAction*);
    void resetZoom();
    void toggleProjections();
    //@}

    /// Loads a file given by the passed string
    void loadFile(QString);

protected slots:
    /** @name Layer manager and filter manager slots
    */
    //@{
    /// slot for layer manager selection change
    void layerSelectionChange(int);
    /// Enables/disables the data filters for the current layer
    void layerFilterVisibilityChange(bool);
    /// slot for layer manager context menu
    void layerContextMenu(const QPoint& pos);
    /// slot for log window context menu
    void logContextMenu(const QPoint& pos);
    /// slot for layer manager visibility change (check box)
    void layerVisibilityChange(QListWidgetItem* item);
    /// slot for filter manager context menu
    void filterContextMenu(const QPoint& pos);
    /// slot for editing a filter
    void filterEdit(QListWidgetItem* item);
    /// slot for editing the preferences of the current layer
    void layerEdit(QListWidgetItem* /*item*/);
    //@}

    /// slot for the finished signal of the TOPP tools execution
    void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus);
    /// aborts the execution of a TOPP tool
    void abortTOPPTool();
    /// retuns the last invoked TOPP tool with the same parameters
    void rerunTOPPTool();
    /// shows the spectrum browser and updates it
    void showSpectrumBrowser();
    /// shows the spectrum metadata
    void showSpectrumMetaData(int spectrum_index);

    /** @name Tabbar slots
    */
    //@{
    /// Closes the window corresponding to the data of the tab with identifier @p id
    void closeByTab(int id);
    /// Raises the window corresponding to the data of the tab with identifier @p id
    void enhancedWorkspaceWindowChanged(int id);
    /// Opens a file from the recent files menu
    void openRecentFile();
    /// Slot for drag-and-drop of layer manager to tabbar
    void copyLayer(const QMimeData* data, QWidget* source, int id = -1);
    //@}

    /// Appends process output to log window
    void updateProcessLog();

    /// Called if a data file has been externally changed
    void fileChanged_(const String&);
protected:
    /// Initializes the default parameters on TOPPView construction.
    void initializeDefaultParameters_();

    /// unique list of files referenced by all layers
    std::set<String> getFilenamesOfOpenFiles_();

    /// Tries to open a db connection (queries the user for the DB password)
    void connectToDB_(DBConnection& db);
    /**
        @brief Shows a dialog where the user can select files
    */
    QStringList getFileList_(const String& path_overwrite = "");

    /// Returns the enhanced tabbar widget with id @p id
    EnhancedTabBarWidgetInterface* window_(int id) const;

    ///@name dock widgets
    //@{
    QDockWidget* layer_dock_widget_;
    QDockWidget* views_dockwidget_;
    QDockWidget* filter_dock_widget_;
    //@}

    ///@name Spectrum selection widgets
    //@{
    SpectraViewWidget* spectra_view_widget_;
    SpectraIdentificationViewWidget* spectra_identification_view_widget_;
    //@}

    /// Layer management widget
    QListWidget* layer_manager_;

    ///@name Filter widgets
    //@{
    QListWidget* filters_;
    QCheckBox* filters_check_box_;
    //@}

    /// Watcher that tracks file changes (in order to update the data in the different views)
    FileWatcher* watcher_;

    /// Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again, if file changes again before the messagebox is closed)
    bool watcher_msgbox_;

    /// Stores whether the individual windows should zoom together (be linked) or not
    bool zoom_together_;

    QAction* linkZoom_action_;

    /// Log output window
    QTextEdit* log_;

    /** @name Toolbar
    */
    //@{
    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_;
    //@}

    /// Main workspace
    EnhancedWorkspace* ws_;

    ///Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()
    EnhancedTabBar* tab_bar_;

    /** @name Status bar
    */
    //@{
    /// Label for messages in the status bar
    QLabel* message_label_;
    /// m/z label for messages in the status bar
    QLabel* mz_label_;
    /// RT label for messages in the status bar
    QLabel* rt_label_;
    //@}

    /// @name Recent files
    //@{
    ///adds a Filename to the recent files
    void addRecentFile_(const String& filename);
    ///update the recent files menu
    void updateRecentMenu_();
    /// list of the recently opened files
    QStringList recent_files_;
    /// list of the recently opened files actions (menu entries)
    std::vector<QAction*> recent_actions_;
    //@}


    /// @name TOPP tool execution
    //@{
    /// Runs the TOPP tool according to the information in topp_
    void runTOPPTool_();
    ///Information needed for execution of TOPP tools
    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_;
    //@}

    /// check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values.
    void checkPreferences_();
    ///@name reimplemented Qt events
    //@{
    void closeEvent(QCloseEvent* event);
    //@}

    ///Log message states
    enum LogState
    {
      LS_NOTICE, ///< Notice
      LS_WARNING, ///< Warning
      LS_ERROR ///< Fatal error
    };
    /// Shows a log message in the log_ window
    void showLogMessage_(LogState state, const String& heading, const String& body);

    ///Additional context menu for 2D layers
    QMenu* add_2d_context_;

    /// Apply TOPP tool. If @p visible is true, only the visible data is used, otherwise the whole layer is used.
    void showTOPPDialog_(bool visible);

    /// The current path (used for loading and storing).
    /// Depending on the preferences this is static or changes with the current window/layer.
    String current_path_;

    /// Tabwidget that hold the different views on the loaded data
    QTabWidget* views_tabwidget_;
    /// The current TOPPView view behavior
    TOPPViewBehaviorInterface* view_behavior_;
    /// TOPPView behavior for the identification view
    TOPPViewIdentificationViewBehavior* identificationview_behavior_;
    /// TOPPView behavior for the spectra view
    TOPPViewSpectraViewBehavior* spectraview_behavior_;

    // static helper functions
public:
    /// Returns true if @p contains at least one MS1 spectrum
    static bool containsMS1Scans(const ExperimentType& exp);

    /// Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities is noise.
    float estimateNoiseFromRandomMS1Scans(const ExperimentType& exp, UInt n_scans = 10);

    /// Counts the number of exact zero valued intensities in all MS1 spectra
    static UInt countMS1Zeros(const ExperimentType& exp);

    /// Returns true if the experiment map contains peptide identifications
    static bool hasPeptideIdentifications(const ExperimentType& map);

private:
    /// Suffix appended to caption of tabs when layer is shown in 3D
    static const String CAPTION_3D_SUFFIX_;
  }; //class

} //namespace

#endif