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NCBI C++ ToolKit: src/algo/blast/api/blast_results.cpp Source File

(src && src->

>= 0) {

: m_GumbelBlk(0), m_UngappedKarlinBlk(0), m_GappedKarlinBlk(0), m_PsiUngappedKarlinBlk(0),

m_PsiGappedKarlinBlk(0), m_SearchSpace(0), m_LengthAdjustment(0)

(

= 0;

< context_per_query;

++) {

query_number * context_per_query +

;

(

->is_valid) {

(

>= context_per_query) {

ctx_index = query_number * context_per_query +

;

pair<double, double> k,

pair<double, double> h,

effective_search_space,

: m_GumbelBlk(0), m_UngappedKarlinBlk(0), m_GappedKarlinBlk(0), m_PsiUngappedKarlinBlk(0),

m_PsiGappedKarlinBlk(0), m_SearchSpace(0), m_LengthAdjustment(0)

(

!= &other) {

: m_QueryId(

), m_Alignment(align), m_Errors(errs),

m_AncillaryData(ancillary_data), m_RID(

), m_PhiQueryInfo(0)

(flt_query_regions.begin(), flt_query_regions.end(),

((**iter).GetSeverity() >= min_severity) {

errs.push_back(*iter);

( !retval.empty() ) {

retval += (*iter)->GetMessage(

) +

;

( !retval.empty() ) {

retval += (*iter)->GetMessage(

) +

;

num_aligns = 1;

CSeq_align_set::Tdata::iterator itr=

->Set().begin();

previous_id = &((*itr)->GetSeq_id(1));

((*itr)->GetSegs().IsDisc())

sub_id = &((*itr)->GetSeq_id(1));

(!sub_id->

(*previous_id))

(num_aligns > max_size)

previous_id = sub_id;

(! (align_set.

() || align_set->

().empty())) {

: m_ResultType(res_type), m_NumQueries(0), m_IsPhiBlast(

)

: m_ResultType(res_type)

(ancillary_data.empty()) {

ancillary_data.resize(aligns.size());

(queries, aligns, msg_vec, ancillary_data, query_masks, phi_query_info);

: m_ResultType(res_type)

vector< CConstRef<CSeq_id> > queries;

(

= 0;

< aligns.size();

++) {

(queries, aligns, msg_vec, ancillary_data,

);

(orig_masks.empty()) {

orig_masks.size() !=

.size()) {

kNumQueries = orig_masks.size();

kNumSubjects =

.size() / kNumQueries;

(mqr.begin(), mqr.end(), back_inserter(masks[

]));

[

]->SetMaskedQueryRegions(masks[0]);

[

]->SetMaskedQueryRegions(masks[

]);

(queries.size() == aligns.size());

(aligns.size() == msg_vec.size());

(aligns.size() == ancillary_data.size());

num_repeated_ids = 1;

(

i_id = 1; i_id < queries.size(); i_id++)

(queries[i_id]->Match(queries[0].GetObject()))

(

= 0;

< aligns.size();

++) {

#define sfree(x)

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

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

const unsigned int kQueryIndex

Index into multiple sequence alignment structure for the query sequence.

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

Blast_KarlinBlk * Blast_KarlinBlkNew(void)

Callocs a Blast_KarlinBlk.

Blast_KarlinBlk * Blast_KarlinBlkFree(Blast_KarlinBlk *kbp)

Deallocates the KarlinBlk.

Int2 Blast_KarlinBlkCopy(Blast_KarlinBlk *kbp_to, Blast_KarlinBlk *kbp_from)

Copies contents of one Karlin block to another.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EResultType

Specifies the style of Seq-aligns that should be built from the internal BLAST data structures.

@ eDatabaseSearch

Seq-aligns in the style of a database search.

@ eSequenceComparison

Seq-aligns in the BLAST 2 Sequence style (one alignment per query-subject pair)

unsigned int BLAST_GetNumberOfContexts(EBlastProgramType program)

Get the number of contexts for a given program.

Class used to return ancillary data from a blast search, i.e.

Defines BLAST error codes (user errors included)

Search Results for All Queries.

Search Results for One Query.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

Collection of masked regions for a single query sequence.

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

static const char si[8][64]

TSeqLocInfoVector m_SubjectMasks

the matching subjects masks

bool HasErrors() const

Returns true if there are errors among the results for this object.

void GetSubjectMasks(TSeqLocInfoVector &subj_masks) const

Retrieve the masked locations for the subject sequences in the contained alignment.

~CBlastAncillaryData()

Destructor.

CSearchResults & operator[](size_type i)

Allow array-like access with integer indices to CSearchResults contained by this object.

static CConstRef< CSeq_id > s_ExtractSeqId(CConstRef< CSeq_align_set > align_set)

Find the first alignment in a set of blast results, and.

size_type m_NumQueries

Number of queries.

Blast_KarlinBlk * m_PsiGappedKarlinBlk

PSI-BLAST gapped Karlin parameters for one query (if applicable)

TSeqLocInfoVector m_QueryMasks

Stores the masked query regions, for convenience and usage in CBl2Seq.

bool m_IsPhiBlast

True if this object contains PHI-BLAST results.

void GetMaskedQueryRegions(TMaskedQueryRegions &flt_query_regions) const

Retrieve the query regions which were masked by BLAST.

CRef< objects::CSeq_align_set > m_Alignment

alignments for this query

void SetRID(const string &rid)

Sets the RID for these results.

vector< CConstRef< objects::CSeq_id > > TQueryIdVector

List of query ids.

TSeqLocInfoVector GetFilteredQueryRegions() const

Retrieves the filtered query regions.

void TrimSeqAlign(objects::CSeq_align_set::Tdata::size_type max_size)

Trim align_set size @parm size max num of alignments to keep (0 will erase all)

void SetSubjectMasks(const TSeqLocInfoVector &subj_masks)

Set the masked locations for the subject sequences in the contained alignment.

CSearchResultSet(EResultType res_type=eDatabaseSearch)

Simplest constructor.

static void s_InitializeKarlinBlk(Blast_KarlinBlk *src, Blast_KarlinBlk **dest)

~CSearchResults()

Our destructor.

TQueryMessages m_Errors

error/warning messages for this query

string GetQueryId() const

Get the query id as a string.

TMaskedQueryRegions m_Masks

this query's masked regions

EResultType m_ResultType

Type of results stored in this object.

CBlastAncillaryData & operator=(const CBlastAncillaryData &rhs)

Assignment operator.

bool HasWarnings() const

Returns true if there are warnings among the results for this object.

Int8 m_LengthAdjustment

Length adjustment for boundary conditions.

void SetMaskedQueryRegions(const TMaskedQueryRegions &flt_query_regions)

Mutator for the masked query regions, intended to be used by internal BLAST APIs to populate this obj...

vector< value_type >::size_type size_type

size_type type definition

void SetFilteredQueryRegions(const TSeqLocInfoVector &masks)

Sets the filtered query regions.

string GetWarningStrings() const

Retrieve a string with the query identifier followed by the warnings produced, returns a empty string...

Blast_KarlinBlk * m_GappedKarlinBlk

Gapped Karlin parameters for one query.

CConstRef< objects::CSeq_id > m_QueryId

this query's id

vector< CRef< CSearchResults > > m_Results

Vector of results.

static void s_InitializeGumbelBlk(Blast_GumbelBlk *src, Blast_GumbelBlk **dest)

Blast_KarlinBlk * m_PsiUngappedKarlinBlk

PSI-BLAST ungapped Karlin parameters for one query (if applicable)

Blast_KarlinBlk * m_UngappedKarlinBlk

Ungapped Karlin parameters for one query.

void push_back(value_type &element)

Add a value to the back of this container.

SPHIQueryInfo * m_PhiQueryInfo

PHI-BLAST information.

TQueryMessages GetErrors(int min_severity=eBlastSevError) const

Accessor for the error/warning messsages for this query.

CConstRef< objects::CSeq_id > GetSeqId() const

Accessor for the query's sequence identifier.

void x_Init(TQueryIdVector &queries, TSeqAlignVector aligns, TSearchMessages msg_vec, TAncillaryVector ancillary_data, const TSeqLocInfoVector *query_masks, const SPHIQueryInfo *phi_query_info=NULL)

Initialize the result set.

CBlastAncillaryData(EBlastProgramType program_type, int query_number, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info)

constructor

vector< CRef< CBlastAncillaryData > > TAncillaryVector

typedef for a vector of CRef<CBlastAncillaryData>

Int8 m_SearchSpace

Search space used when calculating e-values for one query.

Blast_GumbelBlk * m_GumbelBlk

Gumbel parameters for one query.

void do_copy(const CBlastAncillaryData &other)

Workhorse for copy constructor and assignment operator.

string GetErrorStrings() const

Retrieve a string with the query identifier followed by the errors produced, returns a empty string i...

size_type GetNumResults() const

Return the number of results contained by this object.

CSearchResults(CConstRef< objects::CSeq_id > query, CRef< objects::CSeq_align_set > align, const TQueryMessages &errs, CRef< CBlastAncillaryData > ancillary_data, const TMaskedQueryRegions *query_masks=NULL, const string &rid=kEmptyStr, const SPHIQueryInfo *phi_query_info=NULL)

Constructor.

CSearchResults & GetResults(size_type qi, size_type si)

Retrieve results for a query-subject pair contained by this object.

bool HasAlignments() const

Return true if there are any alignments for this query.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

@ e_YES

SeqIds compared, but are different.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a 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.

bool IsDisc(void) const

Check if variant Disc is selected.

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

SPHIQueryInfo * SPHIQueryInfoFree(SPHIQueryInfo *pat_info)

Frees the pattern information structure.

SPHIQueryInfo * SPHIQueryInfoCopy(const SPHIQueryInfo *pat_info)

Copies the SPHIQueryInfo structure.

vector< TMaskedQueryRegions > TSeqLocInfoVector

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

The context related information.

The query related information.

BlastContextInfo * contexts

Information per context.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp_psi

K-A parameters for position-based alignments.

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Blast_KarlinBlk ** kbp_gap_psi

K-A parameters for psi alignments.

Blast_GumbelBlk * gbp

Gumbel parameters for FSC.

Structure to hold the Gumbel parameters (for FSC).

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.

In PHI BLAST, structure containing information about all pattern occurrences in query.

voidp calloc(uInt items, uInt size)

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