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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__seqsrc__impl_8h_source.html below:

NCBI C++ ToolKit: include/algo/blast/core/blast_seqsrc_impl.h Source File

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Blast_GiList* (*GetGisFnPtr)

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Structures for BLAST messages.

const char *(* GetStrFnPtr)(void *seqsrc_impl, void *arg)

Function pointer typedef to return a null terminated string, used to return the name of a BlastSeqSrc...

BlastSeqSrc *(* BlastSeqSrcDestructor)(BlastSeqSrc *seqrc)

Function pointer typedef to deallocate a BlastSeqSrc structure, always returns NULL.

void(* SetInt4FnPtr)(void *seqsrc_impl, int arg)

Function pointer typedef to set a 4-byte integer.

void(* ReleaseSeqBlkFnPtr)(void *seqsrc_impl, BlastSeqSrcGetSeqArg *arg)

Function pointer typedef to release sequences obtained from the data structure embedded in the BlastS...

BlastSeqSrc *(* BlastSeqSrcConstructor)(BlastSeqSrc *seqsrc, void *arg)

Function pointer typedef to create a new BlastSeqSrc structure.

Int8(* GetInt8FnPtr)(void *seqsrc_impl, void *arg)

Function pointer typedef to return a 8-byte integer.

Boolean(* GetBoolFnPtr)(void *seqsrc_impl, void *arg)

Function pointer typedef to return a boolean value, used to return whether a given BlastSeqSrc implem...

Int4(* GetInt4FnPtr)(void *seqsrc_impl, void *arg)

Function pointer typedef to return a 4-byte integer.

void(* SetSeqRangeFnPtr)(void *seqsrc_impl, BlastSeqSrcSetRangesArg *arg)

Function pointer typedef to set partial fetching range.

#define DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(member_type, member)

void(* ResetChunkIteratorFnPtr)(void *seqsrc_impl)

Function pointer typedef to reset the internal "bookmark" of the last chunk provided for iteration by...

BlastSeqSrc *(* BlastSeqSrcCopier)(BlastSeqSrc *)

Function pointer typedef to modify the contents of a BlastSeqSrc structure, copied by BlastSeqSrcCopy...

Int2(* GetSeqBlkFnPtr)(void *seqsrc_impl, BlastSeqSrcGetSeqArg *arg)

Function pointer typedef to retrieve sequences from data structure embedded in the BlastSeqSrc struct...

Int4(* AdvanceIteratorFnPtr)(void *seqsrc_impl, BlastSeqSrcIterator *itr)

Function pointer typedef to obtain the next ordinal id to fetch from the BlastSeqSrc structure.

BlastSeqSrcItrType

Defines the type of data contained in the BlastSeqSrcIterator structure.

@ eOidRange

Data is a range of contiguous ordinal ids (indices)

@ eOidList

Data is a list of discontiguous ordinal ids (indices)

Int2(* GetNextChunkFnPtr)(void *seqsrc_impl, BlastSeqSrcIterator *itr)

Function pointer typedef to obtain the next chunk of ordinal ids for the BLAST engine to search.

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

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

Type and macro definitions from C toolkit that are not defined in C++ toolkit.

static Int4 GetSeqLen(const DataBlk &entry)

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

Complete type definition of Blast Sequence Source Iterator.

unsigned int chunk_sz

Size of the chunks to advance over the BlastSeqSrc, also size of oid_list member, this is provided to...

BlastSeqSrcItrType itr_type

Indicates which member to access: oid_list or oid_range.

int oid_range[2]

This is a half-closed interval [a,b)

int * oid_list

Array of ordinal ids used when itr_type is eOidList.

unsigned int current_pos

Keep track of this iterator's current position, implementations use UINT4_MAX to indicate this is uni...

Complete type definition of the structure used to create a new BlastSeqSrc.

BlastSeqSrcConstructor constructor

User-defined function to initialize a BlastSeqSrc structure.

void * ctor_argument

Argument to the above function.

Structure used as the argument to function SetRanges.

Complete type definition of Blast Sequence Source ADT.

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