Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/split_query.h>
#include <algo/blast/core/blast_program.h>
#include <algo/blast/core/blast_hspfilter.h>
#include <algo/blast/core/spliced_hits.h>
#include <connect/ncbi_core.h>

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Classes
struct	SSortByScoreStruct
	Auxiliary structure to allow sorting the results by score for the composition-based statistics code. More...

struct	BlastHSPStreamResultBatch
	structure used to hold a collection of hits retrieved from the HSPStream More...

struct	BlastHSPStream
	Default implementation of BlastHSPStream. More...

Typedefs
typedef struct SSortByScoreStruct	SSortByScoreStruct
	Auxiliary structure to allow sorting the results by score for the composition-based statistics code. More...

typedef struct BlastHSPStreamResultBatch	BlastHSPStreamResultBatch
	structure used to hold a collection of hits retrieved from the HSPStream More...

typedef struct BlastHSPStream	BlastHSPStream
	Default implementation of BlastHSPStream. More...

Functions
BlastHSPStreamResultBatch *	Blast_HSPStreamResultBatchInit (Int4 num_hsplists)
	create a new batch to hold HSP results More...

BlastHSPStreamResultBatch *	Blast_HSPStreamResultBatchFree (BlastHSPStreamResultBatch *batch)
	free a batch of HSP results. More...

BlastHSPStreamResultBatch *	Blast_HSPStreamResultBatchReset (BlastHSPStreamResultBatch *batch)
	free the list of HSPLists within a batch More...

BlastHSPStream *	BlastHSPStreamNew (EBlastProgramType program, const BlastExtensionOptions extn_opts, Boolean sort_on_read, Int4 num_queries, BlastHSPWriter writer)
	Initialize the HSP stream. More...

BlastHSPStream *	BlastHSPStreamFree (BlastHSPStream *hsp_stream)
	Frees the BlastHSPStream structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastHSPStreamNew). More...

void	BlastHSPStreamClose (BlastHSPStream *hsp_stream)
	Closes the BlastHSPStream structure for writing. More...

void	BlastHSPStreamSimpleClose (BlastHSPStream *hsp_stream)
	Closes the BlastHSPStream structure for writing without any sorting as done in BlastHSPStreamClose. More...

void	BlastHSPStreamMappingClose (BlastHSPStream hsp_stream, BlastMappingResults results)
	Closes BlastHSPStream structure for mapping and produces BlastMappingResults. More...

void	BlastHSPStreamTBackClose (BlastHSPStream hsp_stream, BlastHSPResults results)
	Closes the BlastHSPStream structure after traceback. More...

int	BlastHSPStreamMerge (SSplitQueryBlk squery_blk, Uint4 chunk_num, BlastHSPStream hsp_stream, BlastHSPStream *combined_hsp_stream)
	Moves the HSPlists from an HSPStream into the list contained by a second HSPStream. More...

int	BlastHSPStreamWrite (BlastHSPStream hsp_stream, BlastHSPList *hsp_list)
	Invokes the user-specified write function for this BlastHSPStream implementation. More...

int	BlastHSPStreamRead (BlastHSPStream hsp_stream, BlastHSPList *hsp_list)
	Invokes the user-specified read function for this BlastHSPStream implementation. More...

int	BlastHSPStreamBatchRead (BlastHSPStream hsp_stream, BlastHSPStreamResultBatch batch)
	Batch read function for this BlastHSPStream implementation. More...

int	BlastHSPStreamRegisterMTLock (BlastHSPStream *hsp_stream, MT_LOCK lock)
	Attach a mutex lock to a stream to protect multiple access during writing. More...

int	BlastHSPStreamRegisterPipe (BlastHSPStream hsp_stream, BlastHSPPipe pipe, EBlastStage stage)
	Insert the user-specified pipe to the end of the pipeline. More...

void	BlastHSPCBSStreamClose (BlastHSPStream *hsp_stream, int hitlist_size)

Variables
const int	kBlastHSPStream_Error
	Standard error return value for BlastHSPStream methods. More...

const int	kBlastHSPStream_Success
	Standard success return value for BlastHSPStream methods. More...

const int	kBlastHSPStream_Eof
	Return value when the end of the stream is reached (applicable to read method only) More...

Detailed Description

Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine.

Definition in file blast_hspstream.h.

Typedef Documentation

◆ BlastHSPStream

typedef struct BlastHSPStream BlastHSPStream

Default implementation of BlastHSPStream.

◆ BlastHSPStreamResultBatch

typedef struct BlastHSPStreamResultBatch BlastHSPStreamResultBatch

structure used to hold a collection of hits retrieved from the HSPStream

◆ SSortByScoreStruct

typedef struct SSortByScoreStruct SSortByScoreStruct

Auxiliary structure to allow sorting the results by score for the composition-based statistics code.

Function Documentation

◆ Blast_HSPStreamResultBatchFree()

BlastHSPStreamResultBatch* Blast_HSPStreamResultBatchFree ( BlastHSPStreamResultBatch * batch )

free a batch of HSP results.

Note that the HSPLists themselves are not freed

Parameters

batch Structure to free

Returns: Always NULL

Definition at line 628 of file blast_hspstream.c.

References BlastHSPStreamResultBatch::hsplist_array, NULL, and sfree.

Referenced by BlastHSPStreamToHSPStreamResultsBatch(), and s_BlastHSPStreamResultsBatchArrayReset().

◆ Blast_HSPStreamResultBatchInit()

BlastHSPStreamResultBatch* Blast_HSPStreamResultBatchInit ( Int4 num_hsplists )

create a new batch to hold HSP results

Parameters

num_hsplists Maximum number of results to hold

Returns: Pointer to newly allocated structure

Definition at line 617 of file blast_hspstream.c.

References calloc(), and BlastHSPStreamResultBatch::hsplist_array.

Referenced by BlastHSPStreamToHSPStreamResultsBatch().

◆ Blast_HSPStreamResultBatchReset()

BlastHSPStreamResultBatch* Blast_HSPStreamResultBatchReset ( BlastHSPStreamResultBatch * batch )

free the list of HSPLists within a batch

Parameters

batch Structure to reset

Returns: the input batch

Definition at line 639 of file blast_hspstream.c.

References Blast_HSPListFree(), BlastHSPStreamResultBatch::hsplist_array, i, NULL, and BlastHSPStreamResultBatch::num_hsplists.

Referenced by BLAST_ComputeTraceback_MT(), and s_BlastHSPStreamResultsBatchArrayReset().

◆ BlastHSPCBSStreamClose()

void BlastHSPCBSStreamClose	(	BlastHSPStream *	hsp_stream,
		int	hitlist_size
	)

Definition at line 816 of file blast_hspstream.c.

References BlastHSPList::best_evalue, Blast_HitListSortByEvalue(), BlastHSPStreamClose(), BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, log10(), MAX, BlastHSPStream::results, results, BlastHSPStream::results_sorted, s_FinalizeWriter(), and s_TrimHitList().

Referenced by Blast_RunTracebackSearchWithInterrupt().

◆ BlastHSPStreamBatchRead()

int BlastHSPStreamBatchRead	(	BlastHSPStream *	hsp_stream,
		BlastHSPStreamResultBatch *	batch
	)

Batch read function for this BlastHSPStream implementation.

Parameters

hsp_stream	The BlastHSPStream object [in]
batch	List of HSP lists for the HSPStream to return. The caller acquires ownership of all HSP lists returned [out]

Returns: kBlastHSPStream_Success on success, kBlastHSPStream_Error, or kBlastHSPStream_Eof on end of stream

Definition at line 568 of file blast_hspstream.c.

References BlastHSPStreamClose(), BlastHSPStreamResultBatch::hsplist_array, i, kBlastHSPStream_Eof, kBlastHSPStream_Error, kBlastHSPStream_Success, BlastHSPStreamResultBatch::num_hsplists, BlastHSPStream::num_hsplists, BlastHSPList::oid, BlastHSPStream::results, BlastHSPStream::results_sorted, and BlastHSPStream::sorted_hsplists.

Referenced by BlastHSPStreamToHSPStreamResultsBatch().

◆ BlastHSPStreamClose()

void BlastHSPStreamClose ( BlastHSPStream * hsp_stream )

Closes the BlastHSPStream structure for writing.

Any subsequent attempt to write to the stream will return error.

Parameters

hsp_stream The stream to close [in] [out]

Closes the BlastHSPStream structure for writing.

Also perform sorting of results here to prepare them for reading.

Parameters

hsp_stream The HSP stream to close [in] [out]

Definition at line 133 of file blast_hspstream.c.

References Blast_HSPResultsReverseOrder(), Blast_HSPResultsReverseSort(), BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, MAX, MT_LOCK_Delete(), NULL, BlastHSPStream::num_hsplists, BlastHSPStream::num_hsplists_alloc, BlastHSPList::query_index, BlastHSPStream::results, results, BlastHSPStream::results_sorted, s_FinalizeWriter(), s_SortHSPListByOid(), BlastHSPStream::sort_by_score, SSortByScoreStruct::sort_on_read, BlastHSPStream::sorted_hsplists, TRUE, and BlastHSPStream::x_lock.

Referenced by Blast_RunFullSearch(), Blast_RunTracebackSearchWithInterrupt(), BlastHSPCBSStreamClose(), BlastHSPStreamBatchRead(), BlastHSPStreamRead(), and testHSPStream().

◆ BlastHSPStreamFree()

BlastHSPStream* BlastHSPStreamFree ( BlastHSPStream * hsp_stream )

Frees the BlastHSPStream structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastHSPStreamNew).

If the destructor function pointer is not set, a memory leak could occur.

Parameters

hsp_stream BlastHSPStream to free [in]

Returns: NULL

Frees the BlastHSPStream structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastHSPStreamNew).

Free the BlastHSPStream with its HSP list collector data structure.

Parameters

hsp_stream The HSP stream to free [in]

Returns: NULL.

Definition at line 46 of file blast_hspstream.c.

References Blast_HSPListFree(), Blast_HSPResultsFree(), BlastHSPWriter::FreeFnPtr, MT_LOCK_Delete(), BlastHSPPipe::next, NULL, BlastHSPStream::num_hsplists, BlastHSPStream::pre_pipe, BlastHSPStream::results, sfree, BlastHSPStream::sort_by_score, BlastHSPStream::sorted_hsplists, BlastHSPStream::tback_pipe, BlastHSPStream::writer, and BlastHSPStream::x_lock.

Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), Deleter< BlastHSPStream >::Delete(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), testHSPStream(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().

◆ BlastHSPStreamMappingClose()

void BlastHSPStreamMappingClose	(	BlastHSPStream *	hsp_stream,
		BlastMappingResults *	results
	)

Closes BlastHSPStream structure for mapping and produces BlastMappingResults.

Parameters

hsp_stream	The stream to close [in] [out]
results	The results [in] [out]

Definition at line 209 of file blast_hspstream.c.

References BlastHSPWriter::data, BlastHSPWriter::FinalFnPtr, BlastHSPWriter::InitFnPtr, MT_LOCK_Delete(), BlastHSPStream::results, results, TRUE, BlastHSPStream::writer, BlastHSPStream::writer_finalized, BlastHSPStream::writer_initialized, and BlastHSPStream::x_lock.

Referenced by CMagicBlast::Run(), and CMagicBlast::RunEx().

◆ BlastHSPStreamMerge()

int BlastHSPStreamMerge	(	SSplitQueryBlk *	squery_blk,
		Uint4	chunk_num,
		BlastHSPStream *	stream1,
		BlastHSPStream *	stream2
	)

Moves the HSPlists from an HSPStream into the list contained by a second HSPStream.

Parameters

squery_blk	Information needed to map HSPs from one HSPstream to the combined HSPstream [in]
chunk_num	Used to choose a subset of the information in squery_blk [in]
hsp_stream	The stream to merge [in][out]
combined_hsp_stream	The stream that will contain the HSPLists of the first stream [in][out]

Moves the HSPlists from an HSPStream into the list contained by a second HSPStream.

The HSPs from the first stream are moved to the second stream.

Parameters

squery_blk	Structure controlling the merge process [in]
chunk_num	Unique integer assigned to hsp_stream [in]
stream1	The stream to merge [in][out]
stream2	The stream that will contain the HSPLists of the first stream [in][out]

Definition at line 399 of file blast_hspstream.c.

References ASSERT, BLAST_ContextToFrame(), BLAST_GetNumberOfContexts(), Blast_HitListMerge(), Blast_HSPListSortByScore(), BlastHSP::context, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, INT4_MIN, kBlastHSPStream_Error, kBlastHSPStream_Success, MAX, NULL, NUM_FRAMES, BlastSeg::offset, BlastHSPList::oid, BlastHSPStream::program, BlastHSP::query, BlastHSPList::query_index, BlastHSPStream::results, results1, results2, BlastHSPStream::results_sorted, s_FinalizeWriter(), BlastHSP::score, sfree, SplitQueryBlk_AllowGap(), SplitQueryBlk_GetChunkOverlapSize(), SplitQueryBlk_GetContextOffsetsForChunk(), SplitQueryBlk_GetQueryContextsForChunk(), SplitQueryBlk_GetQueryIndicesForChunk(), BlastHSP::subject, and UINT4_MAX.

Referenced by CBlastPrelimSearch::Run().

◆ BlastHSPStreamNew()

BlastHSPStream* BlastHSPStreamNew	(	EBlastProgramType	program,
		const BlastExtensionOptions *	extn_opts,
		Boolean	sort_on_read,
		Int4	num_queries,
		BlastHSPWriter *	writer
	)

Initialize the HSP stream.

Parameters

program	Type of BlAST program [in]
extn_opts	Extension options to determine composition-based statistics mode [in]
sort_on_read	Should results be sorted on the first read call? Only applicable if composition-based statistics is on [in]
num_queries	Number of query sequences in this BLAST search [in]
writer	Writer to be registered [in]

Definition at line 653 of file blast_hspstream.c.

References Blast_HSPResultsNew(), Blast_QueryIsProtein(), Blast_QueryIsPssm(), calloc(), BlastExtensionOptions::compositionBasedStats, FALSE, SSortByScoreStruct::first_query_index, malloc(), NULL, BlastHSPStream::num_hsplists, BlastHSPStream::num_hsplists_alloc, BlastHSPStream::pre_pipe, BlastHSPStream::program, BlastHSPStream::results, BlastHSPStream::results_sorted, BlastHSPStream::sort_by_score, SSortByScoreStruct::sort_on_read, BlastHSPStream::sorted_hsplists, BlastHSPStream::tback_pipe, BlastHSPStream::writer, BlastHSPStream::writer_finalized, BlastHSPStream::writer_initialized, and BlastHSPStream::x_lock.

Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateHspStream(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), testHSPStream(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), and CTracebackTestFixture::x_MakeStream().

◆ BlastHSPStreamRead()

int BlastHSPStreamRead	(	BlastHSPStream *	hsp_stream,
		BlastHSPList **	hsp_list_out
	)

Invokes the user-specified read function for this BlastHSPStream implementation.

Parameters

hsp_stream	The BlastHSPStream object [in]
hsp_list	List of HSPs for the HSPStream to return. The caller acquires ownership of the hsp_list [out]

Returns: kBlastHSPStream_Success on success, kBlastHSPStream_Error, or kBlastHSPStream_Eof on end of stream

Invokes the user-specified read function for this BlastHSPStream implementation.

Once an HSP list is read from the stream, it relinquishes ownership and removes it from the internal results data structure.

Parameters

hsp_stream	The HSP stream to read from [in]
hsp_list_out	The read HSP list. [out]

Returns: Success, error, or end of reading, when nothing left to read.

Definition at line 271 of file blast_hspstream.c.

References BlastHSPStreamClose(), SSortByScoreStruct::first_query_index, BlastHitList::hsplist_array, BlastHitList::hsplist_count, kBlastHSPStream_Eof, kBlastHSPStream_Error, kBlastHSPStream_Success, NULL, BlastHSPStream::num_hsplists, BlastHSPList::query_index, BlastHSPStream::results, results, BlastHSPStream::results_sorted, BlastHSPStream::sort_by_score, and BlastHSPStream::sorted_hsplists.

Referenced by Blast_HSPResultsFromHSPStream(), Blast_RedoAlignmentCore_MT(), BOOST_AUTO_TEST_CASE(), s_RPSComputeTraceback(), and testHSPStream().

◆ BlastHSPStreamRegisterMTLock()

int BlastHSPStreamRegisterMTLock	(	BlastHSPStream *	hsp_stream,
		MT_LOCK	lock
	)

Attach a mutex lock to a stream to protect multiple access during writing.

Parameters

hsp_stream	The stream to attach [in]
lock	Pointer to locking structure for writing by multiple threads. Locking will not be performed if NULL. [in]

Definition at line 697 of file blast_hspstream.c.

References MT_LOCK_Delete(), and BlastHSPStream::x_lock.

Referenced by BlastSetupPreliminarySearchEx(), CBlastPrelimSearch::SetNumberOfThreads(), and testHSPStream().

◆ BlastHSPStreamRegisterPipe()

int BlastHSPStreamRegisterPipe	(	BlastHSPStream *	hsp_stream,
		BlastHSPPipe *	pipe,
		EBlastStage	stage
	)

Insert the user-specified pipe to the *end* of the pipeline.

Parameters

hsp_stream	The BlastHSPStream object [in]
pipe	The pipe to be registered [in]
stage	At what stage should this pipeline be applied [in]

Definition at line 709 of file blast_hspstream.c.

References ePrelimSearch, eTracebackSearch, BlastHSPPipe::next, NULL, BlastHSPStream::pre_pipe, and BlastHSPStream::tback_pipe.

Referenced by BlastSetupPreliminarySearchEx().

◆ BlastHSPStreamSimpleClose()

void BlastHSPStreamSimpleClose ( BlastHSPStream * hsp_stream )

Closes the BlastHSPStream structure for writing without any sorting as done in BlastHSPStreamClose.

Any subsequent attempt to write to the stream will return error.

Parameters

hsp_stream The stream to close [in] [out]

Definition at line 226 of file blast_hspstream.c.

References MT_LOCK_Delete(), s_FinalizeWriter(), and BlastHSPStream::x_lock.

◆ BlastHSPStreamTBackClose()

void BlastHSPStreamTBackClose	(	BlastHSPStream *	hsp_stream,
		BlastHSPResults *	results
	)

Closes the BlastHSPStream structure after traceback.

This is mainly to provide a chance to apply post-traceback pipes.

Parameters

hsp_stream	The stream to close [in] [out]
results	The traceback results [in] [out]

Closes the BlastHSPStream structure after traceback.

This is mainly to provide a chance to apply post-traceback pipes.

Parameters

hsp_stream	The HSP stream to close [in] [out]
results	The traceback results [in] [out]

Definition at line 241 of file blast_hspstream.c.

References BlastHSPPipe::data, BlastHSPPipe::FreeFnPtr, BlastHSPPipe::next, results, BlastHSPPipe::RunFnPtr, and BlastHSPStream::tback_pipe.

Referenced by BLAST_ComputeTraceback_MT(), Blast_RedoAlignmentCore_MT(), and s_RPSComputeTraceback().

◆ BlastHSPStreamWrite()

int BlastHSPStreamWrite	(	BlastHSPStream *	hsp_stream,
		BlastHSPList **	hsp_list
	)

Invokes the user-specified write function for this BlastHSPStream implementation.

Parameters

hsp_stream	The BlastHSPStream object [in]
hsp_list	List of HSPs for the HSPStream to keep track of. The caller releases ownership of the hsp_list [in]

Returns: kBlastHSPStream_Success on success, otherwise kBlastHSPStream_Error

Invokes the user-specified write function for this BlastHSPStream implementation.

The HSP stream assumes ownership of the HSP list and sets the dereferenced pointer to NULL.

Parameters

hsp_stream	Stream to write to. [in] [out]
hsp_list	Pointer to the HSP list to save in the collector. [in]

Returns: Success or error, if stream is already closed for writing.

Definition at line 339 of file blast_hspstream.c.

References BlastHSPWriter::data, eMT_Lock, eMT_Unlock, FALSE, BlastHSPWriter::InitFnPtr, kBlastHSPStream_Error, kBlastHSPStream_Success, MT_LOCK_Do, NULL, BlastHSPStream::results, BlastHSPStream::results_sorted, BlastHSPWriter::RunFnPtr, TRUE, BlastHSPStream::writer, BlastHSPStream::writer_initialized, and BlastHSPStream::x_lock.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), DoAnchoredSearch(), CHspStreamWriteThread::Main(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_RPSPreliminarySearchEngine(), testHSPStream(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().

Variable Documentation

◆ kBlastHSPStream_Eof

const int kBlastHSPStream_Eof

extern

Return value when the end of the stream is reached (applicable to read method only)

Definition at line 262 of file blast_hspstream.c.

Referenced by Blast_HSPResultsFromHSPStream(), Blast_RedoAlignmentCore_MT(), BlastHSPStreamBatchRead(), BlastHSPStreamRead(), BlastHSPStreamToHSPStreamResultsBatch(), BOOST_AUTO_TEST_CASE(), s_RPSComputeTraceback(), and testHSPStream().

◆ kBlastHSPStream_Error

const int kBlastHSPStream_Error

extern

Standard error return value for BlastHSPStream methods.

Definition at line 260 of file blast_hspstream.c.

Referenced by BlastHSPStreamBatchRead(), BlastHSPStreamMerge(), BlastHSPStreamRead(), BlastHSPStreamWrite(), and testHSPStream().

◆ kBlastHSPStream_Success

const int kBlastHSPStream_Success

extern

Standard success return value for BlastHSPStream methods.

Definition at line 261 of file blast_hspstream.c.

Referenced by BlastHSPStreamBatchRead(), BlastHSPStreamMerge(), BlastHSPStreamRead(), BlastHSPStreamToHSPStreamResultsBatch(), BlastHSPStreamWrite(), BOOST_AUTO_TEST_CASE(), CHspStreamWriteThread::Main(), and testHSPStream().

Classes

Typedefs

Functions

Variables

Detailed Description

Typedef Documentation

◆ BlastHSPStream

◆ BlastHSPStreamResultBatch

◆ SSortByScoreStruct

Function Documentation

◆ Blast_HSPStreamResultBatchFree()

◆ Blast_HSPStreamResultBatchInit()

◆ Blast_HSPStreamResultBatchReset()

◆ BlastHSPCBSStreamClose()

◆ BlastHSPStreamBatchRead()

◆ BlastHSPStreamClose()

◆ BlastHSPStreamFree()

◆ BlastHSPStreamMappingClose()

◆ BlastHSPStreamMerge()

◆ BlastHSPStreamNew()

◆ BlastHSPStreamRead()

◆ BlastHSPStreamRegisterMTLock()

◆ BlastHSPStreamRegisterPipe()

◆ BlastHSPStreamSimpleClose()

◆ BlastHSPStreamTBackClose()

◆ BlastHSPStreamWrite()

Variable Documentation

◆ kBlastHSPStream_Eof

◆ kBlastHSPStream_Error

◆ kBlastHSPStream_Success