seqport_util.hpp

ncbi源码

    // of an input sequence. Attempts to reverse an aa
    // sequence will throw a runtime_error. Returns length of
    // reversed sequence.

    // Reverse a sequence in place
    static TSeqPos Reverse(CSeq_data*   in_seq,
                           TSeqPos      uBeginIdx = 0,
                           TSeqPos      uLength   = 0);

    // Reverse an input sequence and put result in output sequence.
    // Reverses packed bytes as necessary.
    static TSeqPos Reverse(const CSeq_data&   in_seq,
                           CSeq_data*         out_seq,
                           TSeqPos            uBeginIdx = 0,
                           TSeqPos            uLength   = 0);


    // Create the reverse complement of an input sequence. Attempts
    // to reverse-complement an aa sequence will throw a
    // runtime_error.

    // Reverse complement a sequence in place
    static TSeqPos ReverseComplement(CSeq_data*   in_seq,
                                     TSeqPos      uBeginIdx = 0,
                                     TSeqPos      uLength   = 0);

    // Reverse complmenet a sequence and put result in output sequence
    static TSeqPos ReverseComplement(const CSeq_data&   in_seq,
                                     CSeq_data*         out_seq,
                                     TSeqPos            uBeginIdx = 0,
                                     TSeqPos            uLength   = 0);
                                          
    // Given an Ncbistdaa input code index, returns the 3 letter Iupacaa3 code
    // Implementation is efficient
    static const string& GetIupacaa3(TIndex ncbistdaa);
    
    // Given a code type expressible as enum CSeq_data::E_Choice, returns
    // true if the code type is available. See Seq_data_.hpp for definition 
    // of enum CSeq_data::E_Choice.
    static bool IsCodeAvailable(CSeq_data::E_Choice code_type);
    
    // Same as above, but for code types expressible as enum ESeq_code_type.
    // See Seq_code_type_.hpp for definition of enum ESeq_code_type.
    static bool IsCodeAvailable(ESeq_code_type code_type);
    
    // Gets the first and last indices of a code type (e.g., for iupacna,
    // the first index is 65 and the last index is 89). Throws CBadType
    // if code_type is not available
    static TPair GetCodeIndexFromTo(CSeq_data::E_Choice code_type);
    
    // Same as above but takes code type expressed as an ESeq_code_type
    static TPair GetCodeIndexFromTo(ESeq_code_type code_type);
        
    // Given an index for any code type expressible as a
    // CSeq_data::E_Choice, returns the corresponding symbol (code)
    // (e.g., for iupacna, idx 65 causes "A" to be returned)
    // if the code type is available (e.g., ncbi8aa is not currently
    // available). Use IsCodeAvailable() to find out which code types
    // are available. Throws CBadType if code_type not available. Throws
    // CBadIndex if idx out of range for code_type.                    
    static const string& GetCode(CSeq_data::E_Choice code_type, 
                                 TIndex              idx); 

    // Similar to above, but works for all code types expressible as
    // a ESeq_code_type (i.e., iupacaa3 is expressible as an
    // ESeq_code_type but not as a CSeq_data::E_Choice)
    static const string& GetCode(ESeq_code_type code_type, 
                                 TIndex         idx); 
                        
    // Given an index for any code type expressible as a
    // CSeq_data::E_Choice, returns the corresponding name
    // (e.g., for iupacna, idx 65 causes "Adenine" to be returned)
    // if the code type is available (e.g., ncbi8aa is not currently
    // available). Use IsCodeAvailable() to find out which code types
    // are available. Throws CBadType if code_type not available. Throws
    // CBadIndex if idx out of range for code_type.                  
    static const string& GetName(CSeq_data::E_Choice code_type, 
                                 TIndex              idx); 

    // Similar to above, but works for all code types expressible as
    // a ESeq_code_type (i.e., iupacaa3 is expressible as an
    // ESeq_code_type but not as a CSeq_data::E_Choice)
    static const string& GetName(ESeq_code_type code_type, 
                                 TIndex         idx); 

    // Given a code (symbol) for any code type expressible as a
    // CSeq_data::E_Choice, returns the corresponding index
    // (e.g., for iupacna, symbol "A" causes 65 to be returned)
    // if the code type is available (e.g., ncbi8aa is not currently
    // available). Use IsCodeAvailable() to find out which code types
    // are available.Throws CBadType if code_type not available. Throws
    // CBadSymbol if code is not a valid symbol for code_type.                     
    static TIndex GetIndex(CSeq_data::E_Choice code_type, const string& code);
    
    // Similar to above, but works for all code types expressible as
    // a ESeq_code_type (i.e., iupacaa3 is expressible as an
    // ESeq_code_type but not as a CSeq_data::E_Choice)
    static TIndex GetIndex(ESeq_code_type code_type, const string& code);
    
    // Get the index that is the complement of the index for the
    // input CSeq_data::E_Choice code type (e.g., for iupacna, the
    // complement of index 66 is 86). Throws CBadType if complements for 
    // code_type not available. Throws CBadIndex if idx out of range for 
    // code_type    
    static TIndex GetIndexComplement(CSeq_data::E_Choice code_type,
                                     TIndex              idx);

    // Same as above, but for code type expressible as ESeq_code_type.                                  
    static TIndex GetIndexComplement(ESeq_code_type code_type,
                                     TIndex         idx);
    
    // Takes an index for a from_type code and returns the index for to_type
    // (e.g., GetMapToIndex(CSeq_data::e_Iupacna, CSeq_data::e_Ncbi2na,
    // 68) returns 2). Returns 255 if no map value exists for a legal
    // index (e.g., GetMapToIndex(CSeq_data::e_Iupacna, CSeq_data::e_Ncbi2na,
    // 69) returns 255). Throws CBadType if map for from_type to to_type not
    // available. Throws CBadIndex if from_idx out of range for from_type.
    static TIndex GetMapToIndex(CSeq_data::E_Choice from_type,
                             CSeq_data::E_Choice    to_type,
                             TIndex                 from_idx);
    
    // Same as above, but uses ESeq_code_type.                        
    static TIndex GetMapToIndex(ESeq_code_type from_type,
                                ESeq_code_type to_type,
                                TIndex         from_idx);

private:
    
    // we maintain a singleton internally
    // these variables and functions control access to the singleton

    static auto_ptr<CSeqportUtil_implementation> sm_Implementation;

    static void                         x_InitImplementation(void);
    static CSeqportUtil_implementation& x_GetImplementation (void);
};


inline
CSeqportUtil_implementation& CSeqportUtil::x_GetImplementation(void)
{
    if ( !sm_Implementation.get() ) {
        x_InitImplementation();
    }
    return *sm_Implementation;
}


END_objects_SCOPE
END_NCBI_SCOPE

#endif  /* OBJECTS_SEQ___SEQPORT_UTIL__HPP */

 /*
 * ---------------------------------------------------------------------------
 * $Log: seqport_util.hpp,v $
 * Revision 1000.2  2003/11/21 18:20:24  gouriano
 * PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.10
 *
 * Revision 1.10  2003/11/21 14:44:59  grichenk
 * Replaced runtime_error with CException
 *
 * Revision 1.9  2003/11/06 16:10:56  shomrat
 * changed signature of Pack method
 *
 * Revision 1.8  2002/12/26 12:42:59  dicuccio
 * Added Win32 export specifiers
 *
 * Revision 1.7  2002/09/13 20:43:01  ucko
 * +#include <memory> (for auto_ptr<>)
 *
 * Revision 1.6  2002/09/13 18:35:33  dicuccio
 * Fixed problem with static object initialization and type information.
 * First pass at reformatting code.
 *
 * Revision 1.5  2002/05/14 15:12:06  clausen
 * Added IsCodeAvailable, GetCodeIndexFromTo, GetName, GetIndexComplement, GetMapToIndex
 *
 * Revision 1.4  2002/05/03 21:28:03  ucko
 * Introduce T(Signed)SeqPos.
 *
 * Revision 1.3  2002/01/10 19:20:45  clausen
 * Added GetIupacaa3, GetCode, and GetIndex
 *
 * Revision 1.2  2001/09/07 14:16:49  ucko
 * Cleaned up external interface.
 *
 * Revision 1.1  2001/08/24 00:34:22  vakatov
 * Initial revision
 *
 * ===========================================================================
 */