libopenms-dev 1.11.1-5 / usr / include / OpenMS / VISUAL / MetaDataBrowser.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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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_VISUAL_METADATABROWSER_H
#define OPENMS_VISUAL_METADATABROWSER_H

#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

//QT
#include <QtGui/QDialog>
#include <QtGui/QTreeWidget>
class QTreeWidgetItem;
class QPushButton;
class QStackedWidget;
class QHBoxLayout;
class QVBoxLayout;
class QGridLayout;

namespace OpenMS
{
  class BaseVisualizerGUI;
  class Acquisition;
  class AcquisitionInfo;
  class ContactPerson;
  class Digestion;
  class ExperimentalSettings;
  class Gradient;
  class HPLC;
  class PeptideIdentification;
  class Instrument;
  class IonDetector;
  class IonSource;
  class MassAnalyzer;
  class MetaInfo;
  class MetaInfoDescription;
  class MetaInfoInterface;
  class MetaInfoRegistry;
  class Modification;
  class PeptideHit;
  class Precursor;
  class DataProcessing;
  class ProteinHit;
  class ProteinIdentification;
  class Sample;
  class SampleTreatment;
  class Software;
  class SourceFile;
  class SpectrumSettings;
  class Tagging;
  class DocumentIdentifier;
  class Product;

  /**
      @brief A meta data visualization widget

      @image html MetaDataBrowser.png

      It contains a tree view showing all objects of the meta data to be viewed in hierarchical order.

      The meta info data of the tree items are shown in the right part of the viewer, when they are selected in the tree.

      If the data has beed modified exec() returns @em true . Otherwise @em false is returned.

      @improvement Add generic mechanism to add items to data vectors e.g. for Instrument - IonSource (Hiwi)

      @ingroup Visual
  */
  class OPENMS_GUI_DLLAPI MetaDataBrowser :
    public QDialog
  {
    Q_OBJECT

public:

    /// Constructor with flag for edit mode
    MetaDataBrowser(bool editable = FALSE, QWidget * parent = 0, bool modal = FALSE);

    /// Adds a peak map
    template <class PeakType>
    void add(MSExperiment<PeakType> & exp)
    {
      add(static_cast<ExperimentalSettings &>(exp));
      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    /// Adds a peak spectrum
    template <class PeakType>
    void add(MSSpectrum<PeakType> & spectrum)
    {
      //spectrum settings
      add(static_cast<SpectrumSettings &>(spectrum));

      //MetaInfoDescriptions
      for (Size i = 0; i < spectrum.getFloatDataArrays().size(); ++i)
      {
        add(spectrum.getFloatDataArrays()[i]);
      }
      for (Size i = 0; i < spectrum.getIntegerDataArrays().size(); ++i)
      {
        add(spectrum.getIntegerDataArrays()[i]);
      }
      for (Size i = 0; i < spectrum.getStringDataArrays().size(); ++i)
      {
        add(spectrum.getStringDataArrays()[i]);
      }

      add(static_cast<MetaInfoInterface &>(spectrum));

      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    /// Adds a feature map
    template <class FeatureType>
    void add(FeatureMap<FeatureType> & map)
    {
      //identifier
      add(static_cast<DocumentIdentifier &>(map));

      //protein ids
      for (Size i = 0; i < map.getProteinIdentifications().size(); ++i)
      {
        add(map.getProteinIdentifications()[i]);
      }

      //unassigned peptide ids
      for (Size i = 0; i < map.getUnassignedPeptideIdentifications().size(); ++i)
      {
        add(map.getUnassignedPeptideIdentifications()[i]);
      }

      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    /// Adds a feature
    void add(Feature & feature);
    /// Adds a consensus feature
    void add(ConsensusFeature & feature);

    /// Adds a consensus map
    void add(ConsensusMap & map);

    /**
        @brief A generic function to add data.

        The meta data information of all classes that for which a visualize_ method exists can be visualized.
    */
    template <class MetaDataType>
    void add(MetaDataType & meta_data_object)
    {
      visualize_(meta_data_object);
      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    /// Check if mode is editable or not
    bool isEditable();

    /// Defines friend classess that can use the functionality of the subclasses.
    friend class ProteinIdentificationVisualizer;
    friend class PeptideIdentificationVisualizer;

public slots:

    /// Set a list of error strings due to invalid date format.
    void setStatus(std::string status);

protected slots:

    /// Raises the corresponding viewer from the widget stack according to the item selected in the tree.
    void showDetails_();

    /// Saves all changes and close explorer
    void saveAll_();

protected:

    ///@name Visualizer for the different classes
    //@{
    void visualize_(ExperimentalSettings & meta, QTreeWidgetItem * parent = 0);
    void visualize_(SpectrumSettings & meta, QTreeWidgetItem * parent = 0);
    void visualize_(MetaInfoInterface & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Sample & meta, QTreeWidgetItem * parent = 0);
    void visualize_(HPLC & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Digestion & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Modification & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Tagging & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Gradient & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Software & meta, QTreeWidgetItem * parent = 0);
    void visualize_(ScanWindow & meta, QTreeWidgetItem * parent = 0);
    void visualize_(SourceFile & meta, QTreeWidgetItem * parent = 0);
    void visualize_(ContactPerson & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Instrument & meta, QTreeWidgetItem * parent = 0);
    void visualize_(IonSource & meta, QTreeWidgetItem * parent = 0);
    void visualize_(IonDetector & meta, QTreeWidgetItem * parent = 0);
    void visualize_(MassAnalyzer & meta, QTreeWidgetItem * parent = 0);
    void visualize_(DataProcessing & meta, QTreeWidgetItem * parent = 0);
    void visualize_(ProteinIdentification & meta, QTreeWidgetItem * parent = 0);
    void visualize_(ProteinHit & meta, QTreeWidgetItem * parent = 0);
    void visualize_(PeptideHit & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Acquisition & meta, QTreeWidgetItem * parent = 0);
    void visualize_(AcquisitionInfo & meta, QTreeWidgetItem * parent = 0);
    void visualize_(MetaInfoDescription & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Precursor & meta, QTreeWidgetItem * parent = 0);
    void visualize_(Product & meta, QTreeWidgetItem * parent = 0);
    void visualize_(InstrumentSettings & meta, QTreeWidgetItem * parent = 0);
    void visualize_(PeptideIdentification & meta, QTreeWidgetItem * parent = 0);
    void visualize_(DocumentIdentifier & meta, QTreeWidgetItem * parent = 0);
    //@}

    /// Visualizes all elements of a container
    template <typename ContainerType>
    void visualizeAll_(ContainerType & container, QTreeWidgetItem * parent)
    {
      for (typename ContainerType::iterator it = container.begin(); it != container.end(); ++it)
      {
        visualize_(*it, parent);
      }
    }

    /// Connects the Signals of all visualier classes with Slot setStatus()
    void connectVisualizer_(BaseVisualizerGUI * ptr);

    /// Filters hits according to a score @a threshold. Takes the score orientation into account
    void filterHits_(DoubleReal threshold, bool higher_better, int tree_item_id);
    /// Shows hits.
    void showAllHits_(int tree_item_id);

    /// A list of setting errors due to invalid formats.
    std::string status_list_;

    /// Indicates the mode
    bool editable_;

    /// A widgetstack that keeps track of all widgets.
    QStackedWidget * ws_;
    /// Save button
    QPushButton * saveallbutton_;
    /// Close Button
    QPushButton * closebutton_;
    /// Cancel Button
    QPushButton * cancelbutton_;
    /// Undo Button
    QPushButton * undobutton_;

    /// The tree.
    QTreeWidget * treeview_;
  };
}
#endif