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

  // Calls BlastSeqSrcNew in behalf of client code, client should free using
  // BlastSeqSrcFree
  BlastSeqSrc* MyDatabaseFormatBlastSeqSrcInit(...);

• Life-cycle functions

  extern "C" {
  // required signature: BlastSeqSrcConstructor
  BlastSeqSrc* MyDatabaseFormatNew(BlastSeqSrc*, void*);
  // required signature: BlastSeqSrcDestructor
  BlastSeqSrc* MyDatabaseFormatFree(BlastSeqSrc*);
  // required signature: BlastSeqSrcCopier
  BlastSeqSrc* MyDatabaseFormatCopy(BlastSeqSrc*);
  }

• BlastSeqSrc interface

  extern "C" {
  // required signature: SetInt4FnPtr
  void MyDatabaseFormatSetNumberOfThreads(int);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetNumSeqs(void*, void*);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetNumSeqsStats(void*, void*);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetMaxSeqLen(void*, void*);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetMinSeqLen(void*, void*);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetAvgSeqLen(void*, void*);
  // required signature: GetInt8FnPtr
  Int8 MyDatabaseFormatGetTotLen(void*, void*);
  // required signature: GetInt8FnPtr
  Int8 MyDatabaseFormatGetTotLenStats(void*, void*);
  // required signature: GetStrFnPtr
  const char* MyDatabaseFormatGetName(void*, void*);
  // required signature: GetBoolFnPtr
  Boolean MyDatabaseFormatGetIsProt(void*, void*);
  // required signature: GetSeqBlkFnPtr
  Int2 MyDatabaseFormatGetSequence(void*, BlastSeqSrcGetSeqArg*);
  // required signature: GetInt4FnPtr
  Int4 MyDatabaseFormatGetSeqLen(void*, void*);
  // required signature: ReleaseSeqBlkFnPtr
  void MyDatabaseFormatReleaseSequence(void*, BlastSeqSrcGetSeqArg*);
  // required signature: AdvanceIteratorFnPtr
  Int4 MyDatabaseFormatItrNext(void*, BlastSeqSrcIterator* itr);
  // required signature: ResetChunkIteratorFnPtr
  Int4 MyDatabaseFormatResetChunkIterator(void*);
  }

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.