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NCBI C++ ToolKit: src/algo/blast/format/build_archive.cpp Source File

retval->SetLambda(kablk->

);

retval->SetK(kablk->

);

retval->SetH(kablk->

);

retval->SetLambda(-1.0);

retval->SetGapped(gapped);

blast::CBlastOptionsHandle& options_handle,

archive->SetRequest(*net_request);

isPsiblast =

;

list<CRef<CBlast4_mask> >& net_masks = net_results->SetMasks();

first_time =

;

effective_search_space = 0;

length_adjustment = 0;

(*result)->GetSeqAlign();

seqalign_set->

().insert(seqalign_set->

().end(),

result_set->

().begin(),

result_set->

().end());

list<CRef<CBlast4_ka_block> >& ka_list = net_results->SetKa_blocks();

(*result)->GetMaskedQueryRegions(query_masks);

mask_vector.push_back(query_masks);

list<CRef<CBlast4_mask> > masks =

net_masks.insert(net_masks.end(), masks.begin(), masks.end());

list<string>& search_stats = net_results->SetSearch_stats();

search_stats.push_back(

+

(effective_search_space));

search_stats.push_back(

+

(effective_search_space));

search_stats.push_back(

+

(length_adjustment));

net_results->SetAlignments(*seqalign_set);

archive->SetResults(*net_results);

blast::CBlastOptionsHandle& options_handle,

num_iters)

blast::CBlastOptionsHandle& options_handle,

blast::IQueryFactory& subjects)

blast::CBlastOptionsHandle& options_handle,

num_iters)

User-defined methods of the data storage class.

Declares singleton objects to store the version and reference for the BLAST engine.

Declares the CBlastOptionsBuilder class.

Definition of classes which constitute the results of running a BLAST search.

build_archive declarations

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

Search Results for All Queries.

Collection of masked regions for a single query sequence.

const Blast_KarlinBlk * GetGappedKarlinBlk() const

Retrieve gapped Karlin parameters.

const Blast_KarlinBlk * GetPsiGappedKarlinBlk() const

Retrieve PSI-BLAST gapped Karlin parameters.

CRef< objects::CBlast4_archive > BlastBuildArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results, CRef< CSearchDatabase > search_db, unsigned int num_iters=0)

Returns a blast archive object.

static objects::CBlast4_get_search_results_reply::TMasks ConvertToRemoteMasks(const TSeqLocInfoVector &masking_locations, EBlastProgramType program, vector< string > *warnings=NULL)

Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects.

Int8 GetLengthAdjustment() const

Retrieve the length adjustment for boundary conditions.

const Blast_KarlinBlk * GetPsiUngappedKarlinBlk() const

Retrieve PSI-BLAST ungapped Karlin parameters.

static CRef< CBlast4_ka_block > s_Convert_to_CBlast_ka_block(const Blast_KarlinBlk *kablk, bool gapped)

static CRef< objects::CBlast4_archive > s_BuildArchiveAll(CRef< CExportStrategy > export_strategy, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results)

const Blast_KarlinBlk * GetUngappedKarlinBlk() const

Retrieve ungapped Karlin parameters.

Int8 GetSearchSpace() const

Retrieve the search space for this query sequence.

virtual string Print(void) const

Print version information.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

void SetIdent(const TIdent &value)

Assign a value to Ident data member.

const TService & GetService(void) const

Get the Service member data.

bool IsQueue_search(void) const

Check if variant Queue_search is selected.

const TQueue_search & GetQueue_search(void) const

Get the variant data.

bool CanGetBody(void) const

Check if it is safe to call GetBody method.

const TBody & GetBody(void) const

Get the Body member data.

Tdata & Set(void)

Assign a value to data member.

const Tdata & Get(void) const

Get the member data.

Names used in blast4 network communications.

Declares the CRemoteBlast class.

Declares the CImportStrategy and CExportStrategy.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

Structure to hold the Karlin-Altschul parameters.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

Uniform BLAST Search Interface.

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