seqport_util.cpp

ncbi源码

                                     TSeqPos     uLength)
        const;

    TSeqPos ReverseComplementNcbi2na(CSeq_data*  in_seq,
                                     TSeqPos     uBeginIdx,
                                     TSeqPos     uLength)
        const;

    TSeqPos ReverseComplementNcbi4na(CSeq_data*  in_seq,
                                     TSeqPos     uBeginIdx,
                                     TSeqPos     uLength)
        const;

    // Reverse in copy methods
    TSeqPos ReverseComplementIupacna(const CSeq_data& in_seq,
                                     CSeq_data*       out_seq,
                                     TSeqPos          uBeginIdx,
                                     TSeqPos          uLength)
        const;

    TSeqPos ReverseComplementNcbi2na(const CSeq_data& in_seq,
                                     CSeq_data*       out_seq,
                                     TSeqPos          uBeginIdx,
                                     TSeqPos          uLength)
        const;

    TSeqPos ReverseComplementNcbi4na(const CSeq_data& in_seq,
                                     CSeq_data*       out_seq,
                                     TSeqPos          uBeginIdx,
                                     TSeqPos          uLength)
        const;

    // Append methods
    TSeqPos AppendIupacna(CSeq_data*        out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    TSeqPos AppendNcbi2na(CSeq_data*          out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    TSeqPos AppendNcbi4na(CSeq_data*          out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    TSeqPos AppendNcbieaa(CSeq_data*          out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    TSeqPos AppendNcbistdaa(CSeq_data*        out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    TSeqPos AppendIupacaa(CSeq_data*          out_seq,
                          const CSeq_data&  in_seq1,
                          TSeqPos           uBeginIdx1,
                          TSeqPos           uLength1,
                          const CSeq_data&  in_seq2,
                          TSeqPos           uBeginIdx2,
                          TSeqPos           uLength2)
        const;

    void x_GetSeqFromSeqData(const CSeq_data& data, 
                             const string** str,
                             const vector<char>** vec)
        const;
    void x_GetSeqFromSeqData(CSeq_data& data, 
                             string** str,
                             vector<char>** vec)
        const;
};


auto_ptr<CSeqportUtil_implementation> CSeqportUtil::sm_Implementation;

DEFINE_STATIC_FAST_MUTEX(init_implementation_mutex); /* put back inside x_InitImplementation after Mac CodeWarrior 9.0 comes out */
void CSeqportUtil::x_InitImplementation(void)
{
    CFastMutexGuard   LOCK(init_implementation_mutex);
    if ( !sm_Implementation.get() ) {
        sm_Implementation.reset(new CSeqportUtil_implementation());
    }
}




/////////////////////////////////////////////////////////////////////////////
//  PUBLIC (static wrappers to CSeqportUtil_implementation public methods)::
//


TSeqPos CSeqportUtil::Convert
(const CSeq_data&     in_seq,
 CSeq_data*           out_seq,
 CSeq_data::E_Choice  to_code,
 TSeqPos              uBeginIdx,
 TSeqPos              uLength,
 bool                 bAmbig,
 CRandom::TValue      seed)
{
    return x_GetImplementation().Convert
        (in_seq, out_seq, to_code, uBeginIdx, uLength, bAmbig, seed);
}


TSeqPos CSeqportUtil::Pack
(CSeq_data*   in_seq,
 TSeqPos uLength)
{
    return x_GetImplementation().Pack
        (in_seq, uLength);
}


bool CSeqportUtil::FastValidate
(const CSeq_data&   in_seq,
 TSeqPos            uBeginIdx,
 TSeqPos            uLength)
{
    return x_GetImplementation().FastValidate
        (in_seq, uBeginIdx, uLength);
}


void CSeqportUtil::Validate
(const CSeq_data&   in_seq,
 vector<TSeqPos>*   badIdx,
 TSeqPos            uBeginIdx,
 TSeqPos            uLength)
{
    x_GetImplementation().Validate
        (in_seq, badIdx, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::GetAmbigs
(const CSeq_data&     in_seq,
 CSeq_data*           out_seq,
 vector<TSeqPos>*     out_indices,
 CSeq_data::E_Choice  to_code,
 TSeqPos              uBeginIdx,
 TSeqPos              uLength)
{
    return x_GetImplementation().GetAmbigs
        (in_seq, out_seq, out_indices, to_code, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::GetCopy
(const CSeq_data&   in_seq,
 CSeq_data*         out_seq,
 TSeqPos            uBeginIdx,
 TSeqPos            uLength)
{
    return x_GetImplementation().GetCopy
        (in_seq, out_seq, uBeginIdx, uLength);
}



TSeqPos CSeqportUtil::Keep
(CSeq_data*   in_seq,
 TSeqPos      uBeginIdx,
 TSeqPos      uLength)
{
    return x_GetImplementation().Keep
        (in_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::Append
(CSeq_data*         out_seq,
 const CSeq_data&   in_seq1,
 TSeqPos            uBeginIdx1,
 TSeqPos            uLength1,
 const CSeq_data&   in_seq2,
 TSeqPos            uBeginIdx2,
 TSeqPos            uLength2)
{
    return x_GetImplementation().Append
        (out_seq,
         in_seq1, uBeginIdx1, uLength1, in_seq2, uBeginIdx2, uLength2);
}


TSeqPos CSeqportUtil::Complement
(CSeq_data*   in_seq,
 TSeqPos      uBeginIdx,
 TSeqPos      uLength)
{
    return x_GetImplementation().Complement
        (in_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::Complement
(const CSeq_data&   in_seq,
 CSeq_data*         out_seq,
 TSeqPos            uBeginIdx,
 TSeqPos            uLength)
{
    return x_GetImplementation().Complement
        (in_seq, out_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::Reverse
(CSeq_data*   in_seq,
 TSeqPos      uBeginIdx,
 TSeqPos      uLength)
{
    return x_GetImplementation().Reverse
        (in_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::Reverse
(const CSeq_data&  in_seq,
 CSeq_data*        out_seq,
 TSeqPos           uBeginIdx,
 TSeqPos           uLength)
{
    return x_GetImplementation().Reverse
        (in_seq, out_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::ReverseComplement
(CSeq_data*  in_seq,
 TSeqPos     uBeginIdx,
 TSeqPos     uLength)
{
    return x_GetImplementation().ReverseComplement
        (in_seq, uBeginIdx, uLength);
}


TSeqPos CSeqportUtil::ReverseComplement
(const CSeq_data&  in_seq,
 CSeq_data*        out_seq,
 TSeqPos           uBeginIdx,
 TSeqPos           uLength)
{
    return x_GetImplementation().ReverseComplement
        (in_seq, out_seq, uBeginIdx, uLength);
}


const string& CSeqportUtil::GetIupacaa3(TIndex ncbistdaa)
{
    return x_GetImplementation().GetIupacaa3(ncbistdaa);
}

bool CSeqportUtil::IsCodeAvailable(CSeq_data::E_Choice code_type)
{
    return x_GetImplementation().IsCodeAvailable(code_type);
}

bool CSeqportUtil::IsCodeAvailable(ESeq_code_type code_type)
{
    return x_GetImplementation().IsCodeAvailable(code_type);
}

CSeqportUtil::TPair CSeqportUtil::GetCodeIndexFromTo
(CSeq_data::E_Choice code_type)
{
    return x_GetImplementation().GetCodeIndexFromTo(code_type);
}

CSeqportUtil::TPair CSeqportUtil::GetCodeIndexFromTo
(ESeq_code_type code_type)
{
    return x_GetImplementation().GetCodeIndexFromTo(code_type);
}

const string& CSeqportUtil::GetCode
(CSeq_data::E_Choice code_type, 
 TIndex              idx) 
{
    return x_GetImplementation().GetCodeOrName(code_type, idx, true);
}

const string& CSeqportUtil::GetCode
(ESeq_code_type code_type, 
 TIndex         idx) 
{
    return x_GetImplementation().GetCodeOrName(code_type, idx, true);
}

const string& CSeqportUtil::GetName
(CSeq_data::E_Choice code_type, 
 TIndex              idx) 
{
    return x_GetImplementation().GetCodeOrName(code_type, idx, false);
}

const string& CSeqportUtil::GetName
(ESeq_code_type code_type, 
 TIndex         idx) 
{
    return x_GetImplementation().GetCodeOrName(code_type, idx, false);
}

CSeqportUtil::TIndex CSeqportUtil::GetIndex
(CSeq_data::E_Choice code_type,
 const string&       code)
{
    return x_GetImplementation().GetIndex(code_type, code);
}

CSeqportUtil::TIndex CSeqportUtil::GetIndex
(ESeq_code_type code_type,
 const string&  code)
{
    return x_GetImplementation().GetIndex(code_type, code);
}

CSeqportUtil::TIndex CSeqportUtil::GetIndexComplement
(CSeq_data::E_Choice code_type,
 TIndex        idx)
{
    return x_GetImplementation().GetIndexComplement(code_type, idx);
}

CSeqportUtil::TIndex CSeqportUtil::GetIndexComplement
(ESeq_code_type code_type,
 TIndex         idx)
{
    return x_GetImplementation().GetIndexComplement(code_type, idx);
}

CSeqportUtil::TIndex CSeqportUtil::GetMapToIndex
(CSeq_data::E_Choice from_type,
 CSeq_data::E_Choice to_type,
 TIndex              from_idx)
{
    return x_GetImplementation().GetMapToIndex(from_type, to_type, from_idx);
}

CSeqportUtil::TIndex CSeqportUtil::GetMapToIndex
(ESeq_code_type from_type,
 ESeq_code_type to_type,
 TIndex         from_idx)
{
    return x_GetImplementation().GetMapToIndex(from_type, to_type, from_idx);
}

CSeqportUtil_implementation::CSeqportUtil_implementation()
{

    // Initialize m_SeqCodeSet
    m_SeqCodeSet = Init();

    // Initialize code tables
    m_Iupacna = InitCodes(eSeq_code_type_iupacna);

    m_Ncbieaa = InitCodes(eSeq_code_type_ncbieaa);

    m_Ncbistdaa = InitCodes(eSeq_code_type_ncbistdaa);

    m_Iupacaa = InitCodes(eSeq_code_type_iupacaa);


    // Initialize na complement tables
    m_Iupacna_complement = InitIupacnaComplement();

    m_Ncbi2naComplement = InitNcbi2naComplement();

    m_Ncbi4naComplement = InitNcbi4naComplement();



    // Initialize na reverse tables
    m_Ncbi2naRev = InitNcbi2naRev();