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NCBI C++ ToolKit: Implementing the BlastSeqSrc interface

Implementations of this interface should provide life-cycle functions as well as functions which satisfy the BlastSeqSrc interface.

These functions must have C linkage, as these functions are invoked by the BlastSeqSrc framework. An initialization function must also be provided, this is intended to be invoked by client code which wants to use a specific BlastSeqSrc implementation through the BlastSeqSrc interface. For example, MyDatabaseFormat implementation would define the following functions:

• Initialization function

  Complete type definition of Blast Sequence Source ADT.

• Life-cycle functions
• BlastSeqSrc interface

  extern "C" {

  void MyDatabaseFormatSetNumberOfThreads(int);

  Int4

  MyDatabaseFormatGetNumSeqs(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatGetNumSeqsStats(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatGetMaxSeqLen(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatGetMinSeqLen(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatGetAvgSeqLen(

  void

  *,

  void

  *);

  Int8

  MyDatabaseFormatGetTotLen(

  void

  *,

  void

  *);

  Int8

  MyDatabaseFormatGetTotLenStats(

  void

  *,

  void

  *);

  const char* MyDatabaseFormatGetName(void*, void*);

  Boolean

  MyDatabaseFormatGetIsProt(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatGetSeqLen(

  void

  *,

  void

  *);

  Int4

  MyDatabaseFormatResetChunkIterator(

  void

  *);

  }

  int16_t Int2

  2-byte (16-bit) signed integer

  int32_t Int4

  4-byte (32-bit) signed integer

  int64_t Int8

  8-byte (64-bit) signed integer

  Uint1 Boolean

  bool replacment for C

  Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature,...

  Complete type definition of Blast Sequence Source Iterator.

Since the life-cycle and BlastSeqSrc interface functions above are called by the BlastSeqSrc framework (BlastSeqSrc* functions declared in blast_seqsrc.h), no exceptions should be thrown in C++ implementations. When not obvious, please see the required signature's documentation for determining what to implement (see blast_seqsrc_impl.h).

For ease of maintenance, please follow the following conventions:

• Client implementations' initialization function should be called XBlastSeqSrcInit, where X is the name of the implementation
• Client implementations should reside in a file named seqsrc_X.[hc] or seqsrc_X.[ch]pp, where X is the name of the implementation.

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