NCBI C++ Toolkit Cross Reference

/*  $Id: table2asn.hpp 102515 2024-05-20 15:38:38Z foleyjp $
* ===========================================================================
*
*                            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:  Jonathan Kans, Clifford Clausen,
*           Aaron Ucko, Sergiy Gotvyanskyy
*
* File Description:
*   Converter of various files into ASN.1 format, main application function
*
*/

#include <objtools/readers/message_listener.hpp>
#include <misc/data_loaders_util/data_loaders_util.hpp>
#include <util/format_guess.hpp>

#include "table2asn_context.hpp"
#include "async_token.hpp"
#include "multireader.hpp"

BEGIN_NCBI_SCOPE

using namespace objects;

class CSerialObject;

class CTable2AsnLogger;
class CMultiReader;
class CTable2AsnValidator;
class CMask;
class CTable2AsnStructuredCommentsReader;
class CFeatureTableReader;
class CMemorySrcFileMap;

namespace objects::edit {
    class CHugeFile;
}

namespace objects::feature {
    class CFeatTree;
}

class CTbl2AsnApp : public CNcbiApplication
{
public:
    CTbl2AsnApp();

    void Init() override;
    int Run() override;
    int DryRun() override
    {
        return Run();
    }

    using TAnnotMap = CMultiReader::TAnnotMap;

private:

    static const CDataLoadersUtil::TLoaders default_loaders = CDataLoadersUtil::fGenbank | CDataLoadersUtil::fVDB | CDataLoadersUtil::fGenbankOffByDefault | CDataLoadersUtil::fSRA;
    void Setup(const CArgs& args);

    void ProcessOneFile(bool isAlignment, bool manageDiagnosticStreams = true, bool manageDataStream=true);
    void ProcessOneFile(CNcbiOstream* output);
    void xProcessOneFile(CFormatGuess::EFormat format, 
            CRef<CSerialObject> pInputObject, 
            TAnnotMap& annotMap,
            CNcbiOstream* output);
    void ProcessHugeFile(edit::CHugeFile& hugeFile, CNcbiOstream* output);
    void ProcessOneFile(CFormatGuess::EFormat format, const string& contentType, unique_ptr<CNcbiIstream>& pIstr, CNcbiOstream* output);
    void ProcessOneEntry(CFormatGuess::EFormat inputFormat, CRef<CSerialObject> obj, CRef<CSerialObject>& result);
    void ProcessSingleEntry(CFormatGuess::EFormat inputFormat, TAsyncToken& token);
    void MakeFlatFile(CSeq_entry_Handle seh, CRef<CSeq_submit> submit, std::ostream& ostream);
    void ProcessTopEntry(CFormatGuess::EFormat inputFormat, bool need_update_date, CRef<CSeq_submit>& submit, CRef<CSeq_entry>& entry);
    bool ProcessOneDirectory(const CDir& directory, const CMask& mask, bool recurse);
    void ProcessAlignmentFile(CNcbiOstream* output);
    void ReportUnusedSourceQuals();

    void xProcessSecretFiles1Phase(bool readModsFromTitle, CSeq_entry& result);
    void ProcessSecretFiles1Phase(bool readModsFromTitle, TAsyncToken&);

    void ProcessSecretFiles2Phase(CSeq_entry& result) const;
    void ProcessCMTFiles(CSeq_entry& result) const;
    void LoadPEPFile(const string& pathname);
    void LoadRNAFile(const string& pathname);
    void LoadPRTFile(const string& pathname);
    void LoadDSCFile(const string& pathname);
    void LoadAdditionalFiles();
    void LoadCMTFile(const string& pathname, unique_ptr<CTable2AsnStructuredCommentsReader>& comments);
    void LoadAnnotMap(const string& pathname, TAnnotMap& annotMap);
    void AddAnnots(CSeq_entry& entry);
    void SetupAndOpenDiagnosticStreams();
    void SetupAndOpenDataStreams();
    void CloseDiagnosticStreams();
    void CloseDataStreams();
    void xProcessHugeEntries();
    size_t xGetNumThreads() const; 

    void x_SetAlnArgs(CArgDescriptions& arg_desc);

    struct TAdditionalFiles
    {
        unique_ptr<CTable2AsnStructuredCommentsReader> m_struct_comments;
        CMultiReader::TAnnotMap m_AnnotMap;
        set<string> m_MatchedAnnots;
        CRef<CSeq_entry> m_replacement_proteins;
        CRef<CSeq_entry> m_possible_proteins;
        CRef<CSeq_descr> m_descriptors;
        unique_ptr<CMemorySrcFileMap> mp_src_qual_map;
        unique_ptr<CFeatureTableReader> m_feature_table_reader;
    };

    TAdditionalFiles m_global_files;
    unique_ptr<TAdditionalFiles> m_secret_files;

    unique_ptr<CMultiReader> m_reader;
    CRef<CTable2AsnValidator> m_validator;
    CRef<CTable2AsnLogger> m_logger;
    CTable2AsnContext    m_context;

    static const Int8 TBL2ASN_MAX_ALLOWED_FASTA_SIZE = INT8_C(0x7FFFFFFF);
};


class CTable2AsnLogger : public CMessageListenerLenient, public CDiagHandler
{
public:
    CTable2AsnLogger() : m_enable_log(false) {}
    bool m_enable_log;

    void PutProgress(
        const string& sMessage,
        const Uint8   iNumDone = 0,
        const Uint8   iNumTotal = 0) override;

    bool PutMessage(const IObjtoolsMessage& message) override;

    void Post(const SDiagMessage& mess) override;
};


END_NCBI_SCOPE