bam_ui_data_source.hpp

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#ifndef PKG_SEQUENCE___BAM_UI_DATA_SOURCE__HPP
#define PKG_SEQUENCE___BAM_UI_DATA_SOURCE__HPP
 
/*  $Id: bam_ui_data_source.hpp 45702 2020-10-27 15:13:28Z shkeda $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Liangshou Wu
 *
 * File Description:
 *
 */
 
#include <corelib/ncbistl.hpp>
 
#include <gui/framework/ui_data_source.hpp>
#include <gui/framework/service.hpp>
 
#include <gui/core/ui_tool_manager.hpp>
#include <gui/core/pt_item.hpp>
#include <gui/core/project_selector_panel.hpp>
 
#include <gui/utils/extension.hpp>
#include <gui/utils/ui_object.hpp>
#include <gui/objutils/reg_settings.hpp>
 
#include <gui/widgets/loaders/bam_load_option_panel.hpp>
 
#include <objects/seq/Seq_annot.hpp>
 
 
BEGIN_NCBI_SCOPE
 
 
/** @addtogroup GUI_PKG_NCBI_INTERNAL
*
* @{
*/
 
/// commands introduced by BAM data source
enum EBamCommands  {
    eCmdLoadBamFile = 12350,
};
 
class CBamUIDataSourceType;
 
///////////////////////////////////////////////////////////////////////////////
/// CBamUIDataSource
 
class  CBamUIDataSource :
    public CObject,
    public IExtension,
    public IServiceLocatorConsumer,
    public IUIDataSource,
    public IDataLoaderProvider,
    public IExplorerItemCmdContributor
{
public:
    CBamUIDataSource(CBamUIDataSourceType& type);
    ~CBamUIDataSource();
 
    /// @name IExtension interface implementation
    /// @{
    virtual string  GetExtensionIdentifier() const;
    virtual string  GetExtensionLabel() const;
    /// @}
 
    /// @name IServiceLocatorConsumer implementation
    /// @{
    virtual void    SetServiceLocator(IServiceLocator* locator);
    /// @}
 
    /// @name IUIDataSource interface implementation
    /// @{
    virtual IUIDataSourceType&  GetType() const;
 
    virtual const IUIObject&    GetDescr();
 
    virtual bool    IsOpen();
    virtual bool    Open();
    virtual bool    Close();
 
    virtual void    EditProperties();
 
    virtual IUIToolManager*    GetLoadManager();
 
    virtual int GetDefaultCommand();
    virtual wxEvtHandler* CreateEvtHandler();
    /// @}
 
    /// @name IDataLoaderProvider implementation
    /// @{
    virtual string AddDataLoader(const objects::CUser_object& obj);
 
    virtual string GetLoaderName(const objects::CUser_object& obj) const;
    /// @}
 
    /// @name IExplorerItemCmdContributor implementation
    /// @{
    virtual IExplorerItemCmdContributor::TContribution GetMenu(wxTreeCtrl& treeCtrl, PT::TItems& items);
    /// @}
 
private:
    bool x_GetBamInputs(const objects::CUser_object& obj,
                       string& path, string& files,
                       string& idx, string& target_assm) const;
 
    bool x_GetSrzAccession(const objects::CUser_object& obj, string& srz) const;
    bool x_GetCSraInputs(const objects::CUser_object& obj, string& file) const;
    bool x_GetSraAccession(const objects::CUser_object& obj, string& sra) const;
 
protected:
    mutable CRef<CBamUIDataSourceType>  m_Type;
 
    CUIObject   m_Descr;
 
    IServiceLocator*    m_SrvLocator;
 
    bool    m_Open;
};
 
 
///////////////////////////////////////////////////////////////////////////////
/// CBamUIDataSourceType
 
class  CBamUIDataSourceType :
    public CObject,
    public IUIDataSourceType,
    public IExtension
{
public:
    CBamUIDataSourceType();
 
    /// @name IUIDataSourceType interface implementation
    /// @{
    virtual const IUIObject&    GetDescr();
    virtual IUIDataSource*  CreateDataSource();
    virtual bool    AutoCreateDefaultDataSource();
    /// @}
 
    /// @name IExtension interface implementation
    /// @{
    virtual string  GetExtensionIdentifier() const;
    virtual string  GetExtensionLabel() const;
    /// @}
 
protected:
    CUIObject   m_Descr;
};
 
 
///////////////////////////////////////////////////////////////////////////////
/// CBamUILoadManager
 
class CBamIndexingPanel;
class CBamRefSequencesPanel;
class CBamCoverageGraphPanel;
class CBamIdMappingPanel;
 
class  CBamUILoadManager :
    public CObject,
    public IUIToolManager,
    public IRegSettings
{
public:
    CBamUILoadManager();
 
    /// @name IUIToolManager interface implementation
    /// @{
    virtual void    SetServiceLocator(IServiceLocator* srv_locator);
    virtual void    SetParentWindow(wxWindow* parent);
    virtual const IUIObject&  GetDescriptor() const;
    virtual void    InitUI();
    virtual void    CleanUI();
    virtual wxPanel*    GetCurrentPanel();
    virtual bool        CanDo(EAction action);
    virtual bool        IsFinalState();
    virtual bool        IsCompletedState();
    virtual bool    DoTransition(EAction action);
    virtual IAppTask*      GetTask();
    /// @}
 
    /// @name IRegSettings interface implementation
    /// @{
    virtual void    SetRegistryPath(const string& path);
    virtual void    LoadSettings();
    virtual void    SaveSettings() const;
    /// @}
 
protected:
    enum EState {
        eInvalid = -1,
        eSelectBam,
        eBamIndex,
        eCoverageGraph,
        eRefSequences,
        eSelectProject,
        eCompleted
    };
 
protected:
    void x_GetBamRefSeqs(const CBamLoadOptionPanel::TBamWithIndexFiles &files, const string &mappedAcc);
    void x_GetCSraRefSeqs(const CBamLoadOptionPanel::TBamFiles &accessions);
    void x_GetSrzRefSeqs(const CBamLoadOptionPanel::TBamFiles &accessions);
 
protected:
    IServiceLocator* m_SrvLocator;
    wxWindow*        m_ParentWindow;
 
    CUIObject        m_Descriptor;
    EState           m_State;
 
    string           m_RegPath;
    mutable string   m_SavedInput;   // input saved in the registry
    mutable string   m_SamtoolsPath; // samtools path saved in the registry
    string           m_AssmAcc;
    vector<CConstRef<objects::CSeq_id> >     m_RefSeqIds;
 
    CBamLoadOptionPanel*     m_OptionPanel;
    CBamIndexingPanel*       m_IndexingPanel;
    CBamRefSequencesPanel*   m_RefSequencesPanel;
    CBamCoverageGraphPanel*  m_GraphPanel;
    CProjectSelectorPanel*   m_ProjectSelPanel;
    SProjectSelectorParams   m_ProjectParams; //TODO
};
 
 
/* @} */
 
END_NCBI_SCOPE;
 
#endif  // PKG_SEQUENCE___BAM_UI_DATA_SOURCE__HPP