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NCBI C++ ToolKit: src/algo/blast/core/blast_seqsrc.c Source File

( !(destructor_fnptr = (*seq_src->

))) {

retval = (

*) (*destructor_fnptr)(seq_src);

( !(copy_fnptr = (*seq_src->

))) {

kInitialGiListSize = 10;

Blast_GiListNew(

)

Blast_GiListNewEx(kInitialGiListSize);

Blast_GiListNewEx(

list_size)

Blast_GiList* retval = (Blast_GiList*)

(1,

(Blast_GiList));

( !retval->data ) {

Blast_GiListFree(retval);

retval->num_allocated = list_size;

Blast_GiListFree(Blast_GiList* gilist)

(gilist->data);

Blast_GiList_ReallocIfNecessary(Blast_GiList* gilist)

(gilist->num_used+1 > gilist->num_allocated) {

gilist->num_allocated *= 2;

gilist->data = (

*) realloc(gilist->data,

gilist->num_allocated *

(

));

( !gilist->data ) {

Blast_GiList_Append(Blast_GiList* gilist,

gi)

( (retval = Blast_GiList_ReallocIfNecessary(gilist)) != 0) {

gilist->data[gilist->num_used++] = gi;

BlastSeqSrcGetGis(

* seq_src,

* oid)

(

(

)*new_size*2));

(*

)-(*r2);

}

(end > arg->

[2*

+1]) {

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Int2 BlastSeqSrcSetRangesArgAddRange(BlastSeqSrcSetRangesArg *arg, Int4 begin, Int4 end, Int4 len)

add new range

#define DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(member_type, member)

Int4 BlastSeqSrcIteratorNext(const BlastSeqSrc *seq_src, BlastSeqSrcIterator *itr)

Increments the BlastSeqSrcIterator.

Int8 BlastSeqSrcGetTotLenStats(const BlastSeqSrc *seq_src)

Get the total length of all sequences for calculation of expect value etc.

BlastSeqSrcIterator * BlastSeqSrcIteratorFree(BlastSeqSrcIterator *itr)

Frees the BlastSeqSrcIterator structure.

void BlastSeqSrcSetSeqRanges(const BlastSeqSrc *seq_src, BlastSeqSrcSetRangesArg *arg)

Setting the ranges for partial fetching.

BlastSeqSrcIterator * BlastSeqSrcIteratorNewEx(unsigned int chunk_sz)

Allocate and initialize an iterator over a BlastSeqSrc.

Int4 BlastSeqSrcGetSeqLen(const BlastSeqSrc *seq_src, void *oid)

Retrieve sequence length (number of residues/bases)

Boolean BlastSeqSrcGetIsProt(const BlastSeqSrc *seq_src)

Find if the Blast Sequence Source contains protein or nucleotide sequences.

BlastSeqSrc * BlastSeqSrcNew(const BlastSeqSrcNewInfo *bssn_info)

Allocates memory for a BlastSeqSrc structure and then invokes the constructor function defined in its...

BlastSeqSrcIterator * BlastSeqSrcIteratorNew()

Allocate and initialize an iterator over a BlastSeqSrc with a default chunk size for MT-safe iteratio...

void BlastSeqSrcSetRangesArgBuild(BlastSeqSrcSetRangesArg *arg)

build BlastSeqSrcSetRangesArg from range list

void BlastSeqSrcReleaseSequence(const BlastSeqSrc *seq_src, BlastSeqSrcGetSeqArg *getseq_arg)

Deallocate individual sequence.

BlastSeqSrc * BlastSeqSrcCopy(const BlastSeqSrc *seq_src)

Copy function: needed to guarantee thread safety.

Int4 BlastSeqSrcGetAvgSeqLen(const BlastSeqSrc *seq_src)

Get the average length of all sequences in the sequence source.

char * BlastSeqSrcGetInitError(const BlastSeqSrc *seq_src)

Function to retrieve NULL terminated string containing the description of an initialization error or ...

void BlastSeqSrcSetNumberOfThreads(BlastSeqSrc *seq_src, int n_threads)

Set the number of threads for MT mode.

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined construct...

Int4 BlastSeqSrcGetNumSeqsStats(const BlastSeqSrc *seq_src)

Get the number of sequences used for calculation of expect values etc.

BlastSeqSrcSetRangesArg * BlastSeqSrcSetRangesArgNew(Int4 num_ranges)

new setrangearg

const unsigned int kBlastSeqSrcDefaultChunkSize

How many database sequences to process in one database chunk.

static int BeginCompareHSPs(const void *x, const void *y)

Int4 BlastSeqSrcGetMaxSeqLen(const BlastSeqSrc *seq_src)

Get the length of the longest sequence in the sequence source.

Boolean BlastSeqSrcGetSupportsPartialFetching(const BlastSeqSrc *seq_src)

Find if the Blast Sequence Source supports partial fetching.

const char * BlastSeqSrcGetName(const BlastSeqSrc *seq_src)

Get the Blast Sequence source name (e.g.

Int2 BlastSeqSrcGetSequence(const BlastSeqSrc *seq_src, BlastSeqSrcGetSeqArg *getseq_arg)

Retrieve an individual sequence.

BlastSeqSrcSetRangesArg * BlastSeqSrcSetRangesArgFree(BlastSeqSrcSetRangesArg *arg)

free setrangearg

Int4 BlastSeqSrcGetMinSeqLen(const BlastSeqSrc *seq_src)

Get the length of the longest sequence in the sequence source.

void BlastSeqSrcResetChunkIterator(BlastSeqSrc *seq_src)

Reset the internal "bookmark" of the last chunk for iteration provided by this object.

Declaration of ADT to retrieve sequences for the BLAST engine.

#define BLAST_SEQSRC_OVERHANG

Extension for each new range added.

#define BLAST_SEQSRC_MINLENGTH

Default minimal sequence length.

#define BLAST_SEQSRC_MINGAP

Minimal gap allowed in range list.

Definitions needed for implementing the BlastSeqSrc interface and low level details of the implementa...

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.

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.

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

#define MIN(a, b)

returns smaller of a and b.

void * BlastMemDup(const void *orig, size_t size)

Copies memory using memcpy and malloc.

Uint1 Boolean

bool replacment for C

#define FALSE

bool replacment for C indicating false.

#define UINT4_MAX

largest number represented by unsigned int.

#define ASSERT

macro for assert.

#define MAX(a, b)

returns larger of a and b.

static const sljit_gpr r1

static const sljit_gpr r2

static Int4 GetSeqLen(const DataBlk &entry)

const Int2 kOutOfMemory

Failure due to out-of-memory condition.

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...

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.

Int4 capacity

initial allocation

Int4 * ranges

Ranges in sorted order [in].

Int4 num_ranges

Number of actual ranges contained.

Complete type definition of Blast Sequence Source ADT.

GetInt4FnPtr GetMaxSeqLen

Get length of longest seq in set.

GetInt4FnPtr GetSeqLen

Retrieve given sequence length.

SetInt4FnPtr SetNumberOfThreads

Set number of threads.

GetBoolFnPtr GetSupportsPartialFetching

Find if database supports partial fetching.

SetSeqRangeFnPtr SetSeqRange

Setting ranges for partial fetching.

GetInt4FnPtr GetNumSeqs

Get number of sequences in set.

GetInt4FnPtr GetAvgSeqLen

Get average length of sequences in the set.

GetInt4FnPtr GetNumSeqsStats

Number of sequences for statistical purposes.

GetInt4FnPtr GetMinSeqLen

Get length of longest seq in set.

GetSeqBlkFnPtr GetSequence

Retrieve individual sequence.

GetInt8FnPtr GetTotLenStats

Total length of all seqs for statistical purposes.

ResetChunkIteratorFnPtr ResetChunkIterator

Reset the implementation's chunk "bookmark".

BlastSeqSrcConstructor NewFnPtr

Constructor.

void * DataStructure

ADT holding the sequence data.

ReleaseSeqBlkFnPtr ReleaseSequence

Deallocate individual sequence (if applicable)

char * InitErrorStr

initialization error string

GetBoolFnPtr GetIsProt

Find if database is a protein or nucleotide.

BlastSeqSrcDestructor DeleteFnPtr

Destructor.

BlastSeqSrcCopier CopyFnPtr

Copier.

GetStrFnPtr GetName

Get the name of the database.

AdvanceIteratorFnPtr IterNext

Gets next oid from the iterator.

GetInt8FnPtr GetTotLen

Get tot length of all seqs in set.

voidp calloc(uInt items, uInt size)

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