libopenms-dev 1.11.1-5 / usr / include / OpenMS / VISUAL / TOPPASToolVertex.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.
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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.
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// --------------------------------------------------------------------------
// $Maintainer: Johannes Junker $
// $Authors: Johannes Junker, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_VISUAL_TOPPASTOOLVERTEX_H
#define OPENMS_VISUAL_TOPPASTOOLVERTEX_H

#include <OpenMS/VISUAL/TOPPASVertex.h>
#include <OpenMS/DATASTRUCTURES/Param.h>

#include <QtCore/QVector>

namespace OpenMS
{
  /**
      @brief A vertex representing a TOPP tool

      Besides TOPPASScene, this class contains most of the remaining functionality of
      TOPPAS regarding the execution of pipelines. Once a pipeline run is started
      from TOPPASScene, the execution is propagated from tool to tool and the
      TOPP tools are actually called from here.

      @ingroup TOPPAS_elements
  */
  class OPENMS_GUI_DLLAPI TOPPASToolVertex :
    public TOPPASVertex
  {
    Q_OBJECT

public:
    /// current status of the vertex
    enum TOOLSTATUS {TOOL_READY, TOOL_SCHEDULED, TOOL_RUNNING, TOOL_SUCCESS, TOOL_CRASH, TOOLSTATUS_SIZE};

    /// Stores the information for input/output files/lists
    struct IOInfo
    {
      ///Standard constructor
      IOInfo() :
        type(IOT_FILE),
        param_name(),
        valid_types()
      {
      }

      ///Copy constructor
      IOInfo(const IOInfo & rhs) :
        type(rhs.type),
        param_name(rhs.param_name),
        valid_types(rhs.valid_types)
      {
      }

      ///The type
      enum IOType
      {
        IOT_FILE,
        IOT_LIST
      };

      ///Comparison operator
      bool operator<(const IOInfo & rhs) const
      {
        if (type != rhs.type)
        {
          return type == IOT_FILE;
        }
        else
        {
          return param_name.compare(rhs.param_name) < 0;
        }
      }

      ///Assignment operator
      IOInfo & operator=(const IOInfo & rhs)
      {
        type = rhs.type;
        param_name = rhs.param_name;
        valid_types = rhs.valid_types;

        return *this;
      }

      ///The type of the parameter
      IOType type;
      ///The name of the parameter
      String param_name;
      ///The valid file types for this parameter
      StringList valid_types;
    };

    /// Default constructor
    TOPPASToolVertex();
    /// Constructor
    TOPPASToolVertex(const String & name, const String & type = "");
    /// Copy constructor
    TOPPASToolVertex(const TOPPASToolVertex & rhs);
    /// Destructor
    virtual ~TOPPASToolVertex();
    /// Assignment operator
    TOPPASToolVertex & operator=(const TOPPASToolVertex & rhs);

    /// returns the name of the TOPP tool
    virtual String getName() const;
    /// Returns the type of the tool
    const String & getType() const;
    /// Fills @p input_infos with the required input file/list parameters together with their valid types.
    void getInputParameters(QVector<IOInfo> & input_infos) const;
    /// Fills @p output_infos with the required output file/list parameters together with their valid types.
    void getOutputParameters(QVector<IOInfo> & output_infos) const;
    // documented in base class
    virtual void paint(QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget);
    // documented in base class
    virtual QRectF boundingRect() const;
    // documented in base class
    virtual QPainterPath shape() const;
    // documented in base class
    virtual void setTopoNr(UInt nr);
    // documented in base class
    virtual void reset(bool reset_all_files = false);
    /// Sets the Param object of this tool
    void setParam(const Param & param);
    /// Returns the Param object of this tool
    const Param & getParam();
    /// Checks if all parent nodes have finished the tool execution and, if so, runs the tool
    void run();
    /// Updates the vector containing the lists of current output files for all output parameters
    /// using the input files as guidance
    /// Returns true on success, on failure the error_message is filled
    bool updateCurrentOutputFileNames(const RoundPackages & pkg, String & error_message);
    /// return if tool failed or is ready etc.
    TOOLSTATUS getStatus() const;
    /// Lets the user edit the parameters of the tool
    void editParam();
    /// Returns the number of iterations this tool has to perform
    int numIterations();
    /// Returns the full directory (including preceding tmp path)
    String getFullOutputDirectory() const;
    /// Returns the directory where this tool stores its output files
    String getOutputDir() const;
    /// Creates all necessary directories
    void createDirs();
    /// Opens the folder where the file is contained
    void openContainingFolder();
    /// Opens the files in TOPPView
    void openInTOPPView();
    /// Refreshes the parameters of this tool, returns if their has been a change
    bool refreshParameters();
    /// underlying TOPP tool found and parameters fetched?! (done in C'Tor)
    bool isToolReady() const;
    /// Toggle breakpoint
    void toggleBreakpoint();
    /// Called when the QProcess in the queue is called: emits 'toolStarted()'
    virtual void emitToolStarted();
    /// invert status of recycling (overriding base class)
    virtual bool invertRecylingMode();

public slots:

    /// Called when the execution of this tool has finished
    void executionFinished(int ec, QProcess::ExitStatus es);
    /// Called when the running TOPP tool produces output
    void forwardTOPPOutput();
    /// Called when the tool is started
    void toolStartedSlot();
    /// Called when the tool has finished
    void toolFinishedSlot();
    /// Called when the tool has crashed
    void toolCrashedSlot();
    /// Called when the tool has failed
    void toolFailedSlot();
    /// Called when the tool was scheduled for running
    virtual void toolScheduledSlot();
    /// Called by an incoming edge when it has changed
    virtual void inEdgeHasChanged();
    /// Called by an outgoing edge when it has changed
    virtual void outEdgeHasChanged();

signals:

    /// Emitted when the tool is started
    void toolStarted();
    /// Emitted when the tool is finished
    void toolFinished();
    /// Emitted when the tool crashes
    void toolCrashed();
    /// Emitted when the tool execution fails
    void toolFailed(const QString & message = "");
    /// Emitted from forwardTOPPOutput() to forward the signal outside
    void toppOutputReady(const QString & out);

protected:

    ///@name reimplemented Qt events
    //@{
    void mouseDoubleClickEvent(QGraphicsSceneMouseEvent * e);
    //@}

    /// determines if according to current status_, a parameter change would invalidate the pipeline status (e.g., because this node was already processed)
    bool doesParamChangeInvalidate_();
    /// renames SUFFICES of the output files created by the TOPP tool by inspecting file content
    bool renameOutput_();
    /// Initializes the parameters with standard values (from -write_ini), uses the parameters from the old_ini_file if given, returns if parameters have changed (if old_ini_file was given)
    bool initParam_(const QString & old_ini_file = "");
    /// Fills @p io_infos with the required input/output file/list parameters. If @p input_params is true, input params are returned, otherwise output params.
    void getParameters_(QVector<IOInfo> & io_infos, bool input_params) const;
    /// Writes @p param to the @p ini_file
    void writeParam_(const Param & param, const QString & ini_file);
    /// Helper method for finding good boundaries for wrapping the tool name. Returns a string with whitespaces at the preferred boundaries.
    QString toolnameWithWhitespacesForFancyWordWrapping_(QPainter * painter, const QString & str);

    /// The name of the tool
    String name_;
    /// The type of the tool, or "" if it does not have a type
    String type_;
    /// The temporary path
    String tmp_path_;
    /// The parameters of the tool
    Param param_;
    /// current status of the tool
    TOOLSTATUS status_;
    /// tool initialization status: if C'tor was successful in finding the TOPP tool, this is set to 'true'
    bool tool_ready_;

    /// UID for output files
    static UInt uid_;

    /// Breakpoint set?
    bool breakpoint_set_;

    /// smart naming of round-based filenames
    /// when basename is not unique we take the preceding directory name
    void smartFileNames_(std::vector< QStringList >& filenames);

  };
}

#endif