NCBI C++ ToolKit
Classes | Typedefs | Functions
hspfilter_collector.h File Reference

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently return them in sorted order. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_program.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_hspfilter.h>
#include <algo/blast/core/blast_hits.h>
#include <connect/ncbi_core.h>
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Classes

struct  BlastHSPCollectorParams
 Keeps prelim_hitlist_size and HitSavingOptions together. More...

Typedefs

typedef struct
BlastHSPCollectorParams 
BlastHSPCollectorParams
 Keeps prelim_hitlist_size and HitSavingOptions together.

Functions

BlastHSPCollectorParamsBlastHSPCollectorParamsNew (const BlastHitSavingOptions *hit_options, Int4 compositionBasedStats, Boolean gapped_calculation)
 Sets up parameter set for use by collector.
BlastHSPCollectorParamsBlastHSPCollectorParamsFree (BlastHSPCollectorParams *opts)
 Deallocates the BlastHSPCollectorParams structure passed in.
BlastHSPWriterInfoBlastHSPCollectorInfoNew (BlastHSPCollectorParams *params)
 WriterInfo to create a default writer: the collecter.

Detailed Description

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently return them in sorted order.

Definition in file hspfilter_collector.h.


Typedef Documentation

Keeps prelim_hitlist_size and HitSavingOptions together.


Function Documentation

Deallocates the BlastHSPCollectorParams structure passed in.

Parameters:
optsstructure to deallocate [in]
Returns:
NULL

Definition at line 349 of file hspfilter_collector.c.

References sfree.

Referenced by BlastHSPCullingParamsNew().

BlastHSPCollectorParams* BlastHSPCollectorParamsNew ( const BlastHitSavingOptions hit_options,
Int4  compositionBasedStats,
Boolean  gapped_calculation 
)

Sets up parameter set for use by collector.

Parameters:
programBlast program type.[in]
hit_optionsfield hitlist_size and hsp_num_max needed, a pointer to this structure will be stored on resulting structure.[in]
ext_optionsfield compositionBasedStats needed here. [in]
scoring_optionsgapped_calculation needed here. [in]
Returns:
the pointer to the allocated parameter

Definition at line 323 of file hspfilter_collector.c.

References BlastHspNumMax(), BlastHitSavingOptions::hitlist_size, BlastHSPCollectorParams::hsp_num_max, MAX, MIN, BlastHSPCollectorParams::prelim_hitlist_size, BlastHSPCollectorParams::program, and BlastHitSavingOptions::program_number.

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

Modified on Wed Jul 23 17:21:52 2014 by modify_doxy.py rev. 426318