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

& matrix_name

,

& query_title

)

: m_QueryTitle(query_title),

m_SeqalignSet(seqaligns),

m_MatrixName(matrix_name),

m_DiagnosticsRequest(diags),

m_GapExistence(gap_existence),

m_GapExtension(gap_extension)

(seqaligns.

()) {

(

=0;

<

.size();

++) {

);

);

(evalue >= min_evalue && evalue < max_evalue) {

.push_back(

((*it)->GetSegs().GetDenseg(), evalue));

(

.size() < 2) {

vector<CHit*> new_hits;

new_hits.reserve(

.size());

new_hits.push_back(

[0]);

vector<CHit*>::iterator it(

.begin());

(;it !=

.end();++it) {

(

=

(new_hits.size()) - 1;

>= 0

&& (*it)->m_SubjectId->Match(*new_hits[

]->m_SubjectId);

--) {

* kept_hit = new_hits[

];

intersection(*kept_hit);

(*it)->Subtract(intersection);

((*it)->IsEmpty()) {

new_hits.push_back(*it);

(*it)->FillData(seqdb, *profile_data);

kQueryLength =

(

.size());

kNumCds =

(

.size());

.resize(kQueryLength * (kNumCds), cell);

);

(

=0;

< kNumCds;

++) {

(

hit_idx=0;hit_idx <

.size();hit_idx++) {

[hit_idx]->GetSegments()) {

kNumQueryColumns

= (*it)->m_QueryRange.GetTo() - (*it)->m_QueryRange.GetFrom();

q_from = (*it)->m_QueryRange.GetFrom();

(

=0;

< kNumQueryColumns;

++) {

[hit_idx][q_from +

].

= &(*it)->m_MsaData[

];

[hit_idx]->m_MsaIdx =

(hit_idx);

kQueryLength =

(

.size());

kNumCds =

(

.size());

(

=0;

< kNumCds;

++) {

(

=0;

< kNumCds;

++) {

(

j=0;j < kQueryLength;j++) {

);

(

->iobsr <= 0.0) {

);

(

->wfreqs[k] < 0.0) {

s +=

->wfreqs[k];

(

(s - 1.0) > 1e-5) {

);

: m_Evalue(evalue), m_MsaIdx(-1)

kNumDims = denseg.

();

kNumSegments = denseg.

();

m_SubjectId.Reset(denseg.

()[1].GetNonNullPointer());

vector<TSignedSeqPos>& starts = denseg.

();

vector<TSeqPos>& lens = denseg.

();

(

seg=0;seg < kNumSegments;seg++) {

query_offset = starts[query_index];

subject_offset = starts[subject_index];

query_index += kNumDims;

subject_index += kNumDims;

m_SegmentList.push_back(

CHitSegment(

(query_offset, query_offset + lens[seg]),

(subject_offset, subject_offset

query_offset += lens[seg];

subject_offset += lens[seg];

: m_SubjectId(hit.m_SubjectId),

m_Evalue(hit.m_Evalue),

m_MsaIdx(hit.m_MsaIdx)

(vector<CHitSegment*>, it, m_SegmentList) {

(vector<CHitSegment*>, it, m_SegmentList) {

+= (*it)->GetLength();

(*it)->FillData(db_oid, profile_data);

(!m_SubjectId.Empty());

(vector<CHitSegment*>, it, m_SegmentList) {

(m_SegmentList.empty()) {

(vector<CHitSegment*>, it, m_SegmentList) {

(!(*it)->IsEmpty()) {

vector<TRange>::const_iterator r_itr = ranges.begin();

vector<CHitSegment*>::iterator seg_it = m_SegmentList.begin();

vector<CHitSegment*> new_segs;

(seg_it != m_SegmentList.end() && r_itr != ranges.end()) {

= (app == eSubject ? (*seg_it)->m_SubjectRange

: (*seg_it)->m_QueryRange);

(r_itr != ranges.end() && r_itr->GetTo() < seg_range.

()) {

(r_itr == ranges.end()) {

(intersection == seg_range) {

(intersection.

()) {

(r_itr != ranges.end() && r_itr->GetFrom() < seg_range.

()) {

r_itr->GetFrom()) - seg_range.

();

d_to =

(seg_range.

(),

r_itr->GetTo()) - seg_range.

();

new_segs.push_back(new_seg);

(seg_it != m_SegmentList.end()) {

(vector<CHitSegment*>, it, m_SegmentList) {

new_segs.push_back(*it);

m_SegmentList.swap(new_segs);

vector<TRange> ranges;

ranges.push_back(app == eQuery ? (*it)->m_QueryRange

: (*it)->m_SubjectRange);

IntersectWith(ranges, app);

(IsEmpty() || hit.

()) {

from = hit.

().front()->m_QueryRange.GetFrom();

to = hit.

().back()->m_QueryRange.GetTo();

(m_SegmentList.front()->m_QueryRange.GetFrom() >= to

|| m_SegmentList.back()->m_QueryRange.GetTo() <= from) {

vector<CHitSegment*>::iterator it = m_SegmentList.begin();

vector<CHitSegment*> new_segments;

new_segments.reserve(m_SegmentList.size());

(it != m_SegmentList.end() && (*it)->m_QueryRange.GetTo() <= from) {

new_segments.push_back(*it);

(it == m_SegmentList.end() || (*it)->m_QueryRange.GetFrom() > to) {

((*it)->m_QueryRange.GetTo() > to) {

((*it)->m_QueryRange.GetFrom() < from) {

d_to = from - (*it)->m_QueryRange.GetTo();

(*it)->AdjustRanges(0, d_to);

((*it)->m_QueryRange.GetFrom() < (*it)->m_QueryRange.GetTo());

new_segments.push_back(*it);

((*it)->m_QueryRange.GetFrom() < (*it)->m_QueryRange.GetTo());

new_segments.push_back(new_seg);

(;it != m_SegmentList.end();++it) {

new_segments.push_back(*it);

((*it)->m_QueryRange.GetFrom() >= from) {

d_to = from - (*it)->m_QueryRange.GetTo();

(*it)->AdjustRanges(0, d_to);

((*it)->m_QueryRange.GetFrom() < (*it)->m_QueryRange.GetTo());

new_segments.push_back(*it);

(it != m_SegmentList.end()

&& (*it)->m_QueryRange.GetTo() <= to) {

(it != m_SegmentList.end()) {

((*it)->m_QueryRange.GetFrom() < to) {

d_from = to - (*it)->m_QueryRange.GetFrom();

(*it)->AdjustRanges(d_from, 0);

((*it)->m_QueryRange.GetFrom()

< (*it)->m_QueryRange.GetTo());

new_segments.push_back(*it);

(it != m_SegmentList.end()) {

new_segments.push_back(*it);

m_SegmentList.swap(new_segments);

.resize(m_QueryRange.GetTo() - m_QueryRange.GetFrom(), d);

x_FillResidueCounts(db_oid, profile_data);

x_FillObservations(db_oid, profile_data);

(m_QueryRange.GetFrom() >= 0 && m_QueryRange.GetTo() >= 0);

(m_SubjectRange.GetFrom() >= 0 && m_SubjectRange.GetTo() >= 0);

kQueryLength = m_QueryRange.GetTo() - m_QueryRange.GetFrom();

kSubjectLength = m_SubjectRange.GetTo() - m_SubjectRange.GetFrom();

(kQueryLength != kSubjectLength) {

m_QueryRange.SetFrom(m_QueryRange.GetFrom() + d_from);

m_QueryRange.SetTo(m_QueryRange.GetTo() + d_to);

m_SubjectRange.SetFrom(m_SubjectRange.GetFrom() + d_from);

m_SubjectRange.SetTo(m_SubjectRange.GetTo() + d_to);

m_QueryRange.GetFrom() > m_QueryRange.GetTo()

|| m_SubjectRange.GetFrom() > m_SubjectRange.GetTo();

(profile_data()->freq_header);

(db_oid < num_profiles);

* db_counts =

db_seq_length = db_seq_offsets[db_oid + 1] - db_seq_offsets[db_oid];

(m_SubjectRange.GetTo() <= db_seq_length);

(

=0;

< num_columns;

++) {

(double)counts[(m_SubjectRange.GetFrom() +

) *

+ j]

/ (

)sum_freqs;

(profile_data()->obsr_header);

(db_oid < num_profiles);

* data_start

(

=0;

< data_size;

+=2) {

(

j=0;j < num;j++) {

obsr.push_back(

);

num_columns = m_SubjectRange.GetTo() - m_SubjectRange.GetFrom();

(

=0;

< num_columns;

++) {

User-defined methods of the data storage class.

Declares the BLAST exception class.

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.

Defines BLAST error codes (user errors included)

Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deall...

Defines system exceptions occurred while running BLAST.

Represents one alignment segment of a RPS-BLAST hit.

Class used for sorting hits by subject seq-id and e-value.

Class used for sorting hit segments by range.

Class used for sorting ranges.

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

const CSeq_id & GetSeq_id(TDim row) const

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

#define GAP_IN_ALIGNMENT

Representation of GAP in Seq-align.

virtual ~CCddInputData()

Virtual destructor.

CRef< objects::CBioseq > m_QueryBioseq

Query as Bioseq.

static const char kGapChar('-')

The representation of a gap in ASCII format.

void AdjustRanges(int d_from, int d_to)

Change ranges on query and subject by given values.

TRange m_QueryRange

Segment range on query.

vector< CHit * > m_Hits

RPS-BLAST hits in internal representation.

bool IsEmpty(void) const

Is hit empty.

string m_DbName

CDD database name.

CHit(const objects::CDense_seg &denseg, double evalue)

Constructor.

vector< CHitSegment * > m_SegmentList

List of hit segments.

void x_CreateMsa(void)

Create multiple alignment of CDs.

void x_ProcessAlignments(double min_evalue, double max_evalue)

Process RPS-BLAST hits.

void x_RemoveMultipleCdHits(void)

Remove multiple hits to the same CD.

vector< CHitSegment * > & GetSegments(void)

Get hit segments.

void Subtract(const CHit &hit)

Subtract from another hit from this hit using query ranges.

PSIBlastOptions m_Opts

Delta BLAST options for PSSM Engine.

int GetLength(void) const

Get hit length in residues, counts number of matching residues, gaps are not counted.

void Process(void)

Pre-process CD matches to query.

double m_MinEvalue

Min e-value threshold for all hits to be included in PSSM computation.

PSICdMsaCell ** m_Msa

Pointer to MSA.

CConstRef< objects::CSeq_align_set > m_SeqalignSet

RPS-BLAST hits for the query.

CCddInputData(const Uint1 *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > seqaligns, const PSIBlastOptions &opts, const string &dbname, const string &matrix_name="BLOSUM62", int gap_existence=0, int gap_extension=0, PSIDiagnosticsRequest *diags=NULL, const string &query_title="")

Constructor.

bool x_ValidateHits(void) const

Validate internal representation of RPS-BLAST hits.

PSICdMsa m_CddData

MSA of CDs and CD data.

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

vector< Uint1 > m_QueryData

Query sequence.

PSIMsaDimensions m_MsaDimensions

MSA dimensions, used by PSSM engine.

void x_FillResidueCounts(int db_oid, const CBlastRPSInfo &profile_data)

Populate arrays of weighted residue counts.

void x_FillObservations(int db_oid, const CBlastRPSInfo &profile_data)

Populate arrays of effective numbers of observations.

void FillData(int db_oid, const CBlastRPSInfo &profile_data)

Allocate and populate arrays for MSA data (weighted residue counts and effective observations used fo...

static const int kAlphabetSize

bool Validate(void) const

Validate hit.

vector< PSICdMsaCell > m_MsaData

MSA data.

Uint4 TFreqs

Type used for residue frequencies stored in CDD.

void IntersectWith(const vector< TRange > &segments, EApplyTo app)

Intersect hit segments with list of ranges and store result in hit segments.

bool Validate(void) const

Validate hit segment.

unsigned int GetQueryLength(void)

Get query length.

string m_QueryTitle

Query title (for PSSM)

static const int kRpsScaleFactor

Scale of residue frequencies and number of independent observations stored in CDD.

bool x_ValidateMsa(void) const

Validate multiple alignment of CDs.

void x_ExtractQueryForPssm(void)

Create query as Bioseq.

bool IsEmpty(void) const

Does the hit segment represent an empty range.

void FillData(const CSeqDB &seqdb, const CBlastRPSInfo &profile_data)

Allocate and populate arrays of data for PSSM computation.

Uint4 TObsr

Type used for number of independent observations stored in CDD.

void x_FillHitsData(void)

Read data needed for PSSM computation from CDD and populate arrays.

EApplyTo

Master selection for operations involving ranges.

@ fDeltaBlast

Flags set for DELTA-BLAST.

unsigned int TSeqPos

Type for sequence locations and lengths.

#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 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.

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.

bool Empty(void) const THROWS_NONE

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

TThisType IntersectionWith(const TThisType &r) const

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

TTitle & SetTitle(void)

Select the variant.

@ eRepr_raw

continuous sequence

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

A callback function used to compare two keys in a database.

bool is_aligned(T *p) noexcept

Check pointer alignment.

constexpr auto sort(_Init &&init)

static PCRE2_SIZE * offsets

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

Data needed for PSSM computation stored in MSA cell for single column in CD aligned to a position in ...

double iobsr

Effective number of independent observations in a CD column.

double * wfreqs

Frequencies for each residue in CD column.

Alignment cell that represents one column of CD aligned to a position in the query.

Uint1 is_aligned

Does this cell represent column aligned to a CD.

PSICdMsaCellData * data

Data needed for PSSM computation.

PSIMsaDimensions * dimensions

Query length and number of aligned cds.

unsigned char * query

Query sequence as Ncbistdaa.

PSICdMsaCell ** msa

Multiple alignment of CDs.

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

Uint4 num_seqs

Number of distinct sequences aligned with the query (does not include the query)

Uint4 query_length

Length of the query.

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