NCBI C++ ToolKit
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BlastHSPStream Struct Reference

Search Toolkit Book for BlastHSPStream

Default implementation of BlastHSPStream. More...

#include <algo/blast/core/blast_hspstream.h>

+ Collaboration diagram for BlastHSPStream:

Public Attributes

EBlastProgramType program
 BLAST program type. More...
 
Int4 num_hsplists
 number of HSPlists saved More...
 
Int4 num_hsplists_alloc
 number of entries in sorted_hsplists More...
 
BlastHSPList ** sorted_hsplists
 list of all HSPlists from 'results' combined, sorted in order of decreasing subject OID More...
 
BlastHSPResultsresults
 Structure for saving HSP lists. More...
 
Boolean results_sorted
 Have the results already been sorted? Set to true after the first read call. More...
 
SSortByScoreStructsort_by_score
 
MT_LOCK x_lock
 Mutex for writing and reading results. More...
 
BlastHSPWriterwriter
 writer to be applied when writing More...
 
Boolean writer_initialized
 Is writer already initialized? More...
 
Boolean writer_finalized
 Is writer ever finalized? More...
 
BlastHSPPipepre_pipe
 registered preliminary pipeline (unused for now) More...
 
BlastHSPPipetback_pipe
 registered traceback pipeline More...
 

Detailed Description

Default implementation of BlastHSPStream.

Definition at line 92 of file blast_hspstream.h.

Member Data Documentation

◆ num_hsplists

Int4 BlastHSPStream::num_hsplists

◆ num_hsplists_alloc

Int4 BlastHSPStream::num_hsplists_alloc

number of entries in sorted_hsplists

Definition at line 95 of file blast_hspstream.h.

Referenced by BlastHSPStreamClose(), and BlastHSPStreamNew().

◆ pre_pipe

BlastHSPPipe* BlastHSPStream::pre_pipe

registered preliminary pipeline (unused for now)

Definition at line 111 of file blast_hspstream.h.

Referenced by BlastHSPStreamFree(), BlastHSPStreamNew(), BlastHSPStreamRegisterPipe(), and s_FinalizeWriter().

◆ program

EBlastProgramType BlastHSPStream::program

BLAST program type.

Definition at line 93 of file blast_hspstream.h.

Referenced by BlastHSPStreamMerge(), BlastHSPStreamNew(), and CBlastPrelimSearch::x_BuildStdSegList().

◆ results

BlastHSPResults* BlastHSPStream::results

◆ results_sorted

Boolean BlastHSPStream::results_sorted

Have the results already been sorted? Set to true after the first read call.

Non-NULL if the results should be sorted by score as opposed to subject OID. This is necessary to meet a pre-condition of the composition-based statistics processing

Definition at line 100 of file blast_hspstream.h.

Referenced by BlastHSPCBSStreamClose(), BlastHSPStreamBatchRead(), BlastHSPStreamClose(), BlastHSPStreamMerge(), BlastHSPStreamNew(), BlastHSPStreamRead(), and BlastHSPStreamWrite().

◆ sort_by_score

SSortByScoreStruct* BlastHSPStream::sort_by_score

◆ sorted_hsplists

BlastHSPList** BlastHSPStream::sorted_hsplists

list of all HSPlists from 'results' combined, sorted in order of decreasing subject OID

Definition at line 96 of file blast_hspstream.h.

Referenced by BlastHSPStreamBatchRead(), BlastHSPStreamClose(), BlastHSPStreamFree(), BlastHSPStreamNew(), BlastHSPStreamRead(), and s_BlastHSPStreamCountNumOids().

◆ tback_pipe

BlastHSPPipe* BlastHSPStream::tback_pipe

registered traceback pipeline

Definition at line 113 of file blast_hspstream.h.

Referenced by BlastHSPStreamFree(), BlastHSPStreamNew(), BlastHSPStreamRegisterPipe(), and BlastHSPStreamTBackClose().

◆ writer

BlastHSPWriter* BlastHSPStream::writer

◆ writer_finalized

Boolean BlastHSPStream::writer_finalized

Is writer ever finalized?

Definition at line 110 of file blast_hspstream.h.

Referenced by BlastHSPStreamMappingClose(), BlastHSPStreamNew(), and s_FinalizeWriter().

◆ writer_initialized

Boolean BlastHSPStream::writer_initialized

Is writer already initialized?

Definition at line 109 of file blast_hspstream.h.

Referenced by BlastHSPStreamMappingClose(), BlastHSPStreamNew(), BlastHSPStreamWrite(), and s_FinalizeWriter().

◆ x_lock

MT_LOCK BlastHSPStream::x_lock

The documentation for this struct was generated from the following file:
Modified on Mon Feb 26 04:00:14 2024 by modify_doxy.py rev. 669887