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NCBI C++ ToolKit: src/algo/cobalt/rps.cpp Source File

(blockstream.bad() || blockstream.fail())

);

blockstream >> block_idx;

blocklist.push_back(

(oid, start, end));

(!blockstream.eof()) {

(blockstream.eof()) {

blockstream >> block_idx;

blockstream >> start;

blocklist.push_back(

(oid, start, end));

vector<SSegmentLoc>& blocklist,

(

= 0;

< rps_hits.

();

++) {

**pssm = profile_data.

() + db_seq_offsets[db_seq];

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

vector<SSegmentLoc>::iterator

itr = lower_bound(blocklist.begin(), blocklist.end(),

(itr != blocklist.end() &&

(itr != blocklist.end() &&

itr->GetTo() < target.

()) {

vector<SSegmentLoc>::iterator prev_itr(itr);

vector<SSegmentLoc>::iterator next_itr(itr);

(itr != blocklist.begin()) {

(itr != blocklist.end() && itr->seq_index == db_seq

&& itr->GetFrom() < target.

()) {

kMaxFudge = 6;

q_range, new_s_range;

s_range(itr->range.IntersectionWith(target.

));

(!s_range.

() && itr->range.Contains(s_range));

left_fudge, right_fudge;

(itr == blocklist.begin() ||

prev_itr == blocklist.begin() ||

prev_itr->seq_index != db_seq) {

left_fudge = s_range.

() -

prev_itr->GetTo() - last_fudge - 1;

left_fudge =

(left_fudge, kMaxFudge);

(itr == blocklist.end() ||

next_itr == blocklist.end() ||

next_itr->seq_index != db_seq) {

right_fudge = (next_itr->GetFrom() - s_range.

() - 1) / 2;

right_fudge =

(right_fudge, kMaxFudge);

last_fudge = right_fudge;

(prev_itr != itr) {

(next_itr != blocklist.end()) {

printf(

,

q_range.

() - left_fudge));

q_range.

() + right_fudge));

(

*)

.GetSequence() + q_range.

(),

tback_size = tback.size();

last_tback = tback_size - 1;

q_start = q_range.

();

q_stop = q_range.

();

s_start = s_range.

();

s_stop = s_range.

();

(

k = 0; k < tback_size &&

(tback[k] != tback[k-1])

(

k = tback_size - 1; k >= 0 &&

(k == tback_size - 1)

(tback[k] != tback[k+1])

q_range.

(q_start, q_stop);

s_range.

(s_start, s_stop);

(first_tback, last_tback));

score, final_script));

);

vector<int>& indices,

(queries.size() == indices.size());

num_queries = queries.size();

->SetCompositionBasedStats(

);

blaster(query_factory, opts, search_database);

(

= 0;

< num_queries;

++) {

& curr_score = **score_itr;

(curr_score.

().

() ==

)

align_score, denseg));

);

printf(

);

(

= 0;

< rps_hits.

();

++) {

printf(

,

(rps_hits.

()) {

(

= 0;

< rps_hits.

();

++) {

(j = 0; j <

; j++) {

vector<TOffsetPair> sub_list(

(j = 0; j < (

)sub_list.size(); j += 2) {

q = start_pair.first;

s = start_pair.second;

(stop_pair.second - stop_pair.first ==

start_pair.second - start_pair.first);

(

k = 0; k < stop_pair.first - start_pair.first; k++) {

(1 - domain_res_freq_boost) *

matrix(q+k,

.GetLetter(q+k)) += domain_res_freq_boost;

);

(

j = 0; j <

.GetLength(); j++) {

matrix(j, k) = (1 - local_res_freq_boost) *

std_freqs->

[k];

matrix(j,

.GetLetter(j)) += local_res_freq_boost;

);

(

j = 0; j <

.GetLength(); j++) {

matrix(j, k) = (1 - local_res_freq_boost) *

std_freqs->

[k];

matrix(j,

.GetLetter(j)) += local_res_freq_boost;

pair<const CSeq_id*, int>&

)

.first->CompareOrdered(*

.first) > 0;

vector<int>& indices,

(!pre_queries.empty());

(pre_queries.size() == indices.size());

vector< pair<const CSeq_id*, int> > queries;

queries.reserve(pre_queries.size());

(

=0;

< pre_queries.size();

++) {

(pre_queries[

].seqloc->GetId());

queries.push_back(make_pair(pre_queries[

].seqloc->GetId(), indices[

]));

);

pair<const CSeq_id*, int> p((*it)->GetId(), -1);

vector< pair<const CSeq_id*, int> >::iterator id_itr

= lower_bound(queries.begin(), queries.end(), p,

(id_itr != queries.end()

&& id_itr->first->CompareOrdered(*p.first) == 0) {

pair<const CSeq_id*, int> p(itr->GetFirstId(), -1);

vector< pair<const CSeq_id*, int> >::iterator id_itr

= lower_bound(queries.begin(), queries.end(), p,

(id_itr != queries.end()

&& id_itr->first->CompareOrdered(*p.first) == 0) {

printf(

);

(

=0;

< pre_queries.size();

++) {

printf(

, indices[

]);

is_presearched =

;

is_presearched =

;

(!is_presearched) {

is_presearched =

;

(!last_query_id || query_id.

(*last_query_id) != 0) {

pair<const CSeq_id*, int> p(&query_id, -1);

vector< pair<const CSeq_id*, int> >::iterator id_itr

= lower_bound(queries.begin(), queries.end(), p,

(id_itr == queries.end()

|| id_itr->first->CompareOrdered(*p.first) != 0) {

query_idx = id_itr->second;

last_query_id = id_itr->first;

& curr_score = **score_itr;

(curr_score.

().

() ==

)

+ denseg.

()[1]->AsFastaString()

+

align_score, denseg));

is_presearched =

;

(!is_presearched) {

printf(

);

printf(

,

vector<int>& indices)

blockfile = rps_db +

;

freqfile = rps_db +

;

(rps_db.empty()) {

do_search =

;

(

=0;

< indices.size();

++) {

vector<int> indices_not_searched;

(

=0;

< queries.size();

++) {

queries_not_searched.push_back(queries[

]);

indices_not_searched.push_back(indices[

]);

);

vector<SSegmentLoc> blocklist;

profile_data.

();

printf(

);

printf(

,

profile_data.

();

*subhit = *subitr;

printf(

);

*subhit = *itr;

printf(

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

pair< TOffset, TOffset > TOffsetPair

Basic type specifying a range on a sequence.

RPS BLAST structure definitions.

#define FREQ_RATIO_SCALE

header for RPS blast frequency ratios ('.freq') file

Declares the CBlastRPSOptionsHandle class.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Blast_ResFreq * Blast_ResFreqFree(Blast_ResFreq *rfp)

Deallocates Blast_ResFreq and prob0 element.

Int2 Blast_ResFreqStdComp(const BlastScoreBlk *sbp, Blast_ResFreq *rfp)

Calculates residues frequencies given a standard distribution.

Blast_ResFreq * Blast_ResFreqNew(const BlastScoreBlk *sbp)

Allocates a new Blast_ResFreq structure and fills in the prob element based upon the contents of sbp.

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

Defines BLAST error codes (user errors included)

Handle to the rpsblast options to the BLAST algorithm.

Interface for the traceback from blast hits.

int GetScore(TRange tback_range, TOffsetPair start_offsets, CSequence &seq1, int **seq2_pssm, int gap_open, int gap_extend)

Compute the score associated with (a portion of) an alignment Assumes that seq1 is a sequence and tha...

CEditScript MakeEditScript(TRange tback_range)

Return an edit script corresponding to a subset of the complete traceback available.

vector< TOffsetPair > ListMatchRegions(TOffsetPair start_offsets)

Compile a list of regions in the current edit script that contain substitutions.

An ordered collection of CHit objects.

int Size() const

Retrieve number of hits in list.

void SetKeepHit(int index, bool keep)

Set whether a hit in the hitlist will be scheduled for deletion.

void PurgeAllHits()

Delete all hits unconditionally.

bool Empty()

Determine whether a list contains no hits.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

void PurgeUnwantedHits()

Delete all hits scheduled to be deleted.

bool GetKeepHit(int index)

Determine whether a hit in the hitlist has been scheduled for deletion.

void SortByScore()

Sort the hits in the hitlist in order of decreasing score.

void MatchOverlappingSubHits(CHitList &matched_list)

For each pair of hits with the same sequence2, produce a list of hits between sequence1 of the first ...

void AddToHitList(CHit *hit)

Append a hit to the hitlist.

A generalized representation of a pairwise alignment.

TSubHit & GetSubHit()

Retrieve a list of subhits.

void ResolveSubHitConflicts(CSequence &seq1, int **seq2_pssm, CNWAligner::TScore gap_open, CNWAligner::TScore gap_extend)

If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is a...

void InsertSubHit(CHit *hit)

Add a to a CHit's list of subhits.

void GetRangeFromSeq2(TRange seq_range2, TRange &seq_range1, TRange &new_seq_range2, TRange &traceback_range)

Retrieve the seq1 range corresponding to a specified seq2 range.

void AddUpSubHits()

Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits.

int m_Score

Score of alignment.

CEditScript & GetEditScript()

Retrieve the traceback associated with a CHit.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

static const int kMinHitSize

Not always used, but useful to avoid extremely small hits.

TRange m_SeqRange2

The range of offsets on the second sequence.

bool HasSubHits()

Query if a CHit has a hierarchy of subhits available.

vector< CHit * > TSubHit

Hits can be grouped hierarchically.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

TScore GetEndGapExtendPenalty(void) const

Get gap extension penalty for end gaps in pairwise global alignment of profiles.

string GetRpsDb(void) const

Get RPS Blast data base name.

double GetLocalResFreqBoost(void) const

Get frequency boost for a letter that appears in query sequence in given position.

int GetDomainHitlistSize(void) const

Get hitlist size (per sequence) for domain searches.

CConstRef< objects::CBlast4_archive > GetDomainHits(void) const

Get pre-computed domain hits.

TScore GetGapExtendPenalty(void) const

Get gap extension penlaty for middle gaps in pairwise global alignment of profiles.

bool CanGetDomainHits(void) const

Are pre-computed domain hits set.

TScore GetGapOpenPenalty(void) const

Get gap opening penalty for middle gaps in pairwise global alignment of profiles.

TScore GetEndGapOpenPenalty(void) const

Get gap opening penalty for end gaps in pairwise global alignment of profiles.

double GetRpsEvalue(void) const

Get e-value threshold for accepting RPS Blast hits.

@ eToPrototype

All cluster elements are aligner to cluster prototype.

bool GetVerbose(void) const

Get verbose mode.

double GetDomainResFreqBoost(void) const

Get boost for residue frequencies in conserved domains from RPS data base.

Simultaneously align multiple protein sequences.

vector< CSequence > m_AllQueryData

CMultiAlignerOptions::EInClustAlnMethod m_ClustAlnMethod

SProgress m_ProgressMonitor

vector< CRef< objects::CSeq_loc > > m_tQueries

void x_MakeClusterResidueFrequencies()

Compute profile residue frequencies for clusters.

void x_AssignRPSResFreqs(CHitList &rps_hits, CProfileData &profile_data)

@ eInterrupt

Alignment interruped through callback function.

vector< CSequence > m_QueryData

vector< bool > m_IsDomainSearched

Marks sequences with pre-computed domain hits.

void x_AssignDefaultResFreqs()

vector< vector< TRange > > m_RPSLocs

void x_LoadBlockBoundaries(string blockfile, vector< SSegmentLoc > &blocklist)

Given an RPS blast database, load a list of block offsets for each database sequence.

void x_FindRPSHits(blast::TSeqLocVector &queries, const vector< int > &indices, CHitList &rps_hits)

CConstRef< CMultiAlignerOptions > m_Options

void x_SetDomainHits(const blast::TSeqLocVector &queruies, const vector< int > &indices, const objects::CBlast4_archive &archive)

Set pre-computed domain hits using BLAST archive format.

void x_FindDomainHits(blast::TSeqLocVector &queries, const vector< int > &indices)

Run RPS blast on seletced input sequences and postprocess the results.

void x_RealignBlocks(CHitList &rps_hits, vector< SSegmentLoc > &blocklist, CProfileData &profile_data)

static const int kRpsScaleFactor

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Represent databases of PSSM data and residue frequencies.

Int4 ** GetResFreqs() const

Assuming the database is a list of columns of profiles, frequencies, retrieve a list of all of the pr...

@ eGetResFreqs

Retrieve residue frequencies.

@ eGetPssm

Retrieve PSSMs.

void Clear()

Free previously loaded PSSM or profile data.

void Load(EMapChoice choice, string dbname, string resfreq_file="")

Load information from a given database.

Int4 * GetSeqOffsets() const

Retrieve a list of offsets where database sequences begin.

Int4 ** GetPssm() const

Assuming the database is a list of PSSM columns, retrieve a list of all of the PSSMs in the database ...

Search Results for All Queries.

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).

Class for representing protein sequences.

Template class for iteration on objects of class C (non-medifiable version)

Interface for CMultiAligner.

void SetStartWg(TScore value)

TTranscript GetTranscript(bool reversed=true) const

void SetEndWs(TScore value)

virtual CNWAligner::TScore Run(void)

void SetEndWg(TScore value)

vector< ETranscriptSymbol > TTranscript

void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)

void SetEndSpaceFree(bool Left1, bool Right1, bool Left2, bool Right2)

void SetStartWs(TScore value)

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

CRef< CSearchResultSet > Run()

Executes the search.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

void SetHitlistSize(int s)

Sets HitlistSize.

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

@ eBlastDbIsProtein

protein

#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.

int CompareOrdered(const CSeq_id &sid2) const

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

int32_t Int4

4-byte (32-bit) signed integer

position_type GetLength(void) const

bool IntersectingWith(const TThisType &r) const

TThisType & Set(position_type from, position_type to)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

const TRequest & GetRequest(void) const

Get the Request member data.

const TQueue_search & GetQueue_search(void) const

Get the variant data.

const TBioseq_set & GetBioseq_set(void) const

Get the variant data.

bool IsBioseq_set(void) const

Check if variant Bioseq_set is selected.

const TSeq_loc_list & GetSeq_loc_list(void) const

Get the variant data.

const TQueries & GetQueries(void) const

Get the Queries member data.

const TAlignments & GetAlignments(void) const

Get the Alignments member data.

const TResults & GetResults(void) const

Get the Results member data.

const TBody & GetBody(void) const

Get the Body member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TStr & GetStr(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

vector< CRef< CScore > > TScore

TInt GetInt(void) const

Get the variant data.

const TValue & GetValue(void) const

Get the Value member data.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

TReal GetReal(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

unsigned int

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

Main class to perform a BLAST search on the local machine.

const TYPE & Get(const CNamedParameterList *param)

constexpr auto sort(_Init &&init)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

bool compare_seqids(const pair< const CSeq_id *, int > &a, const pair< const CSeq_id *, int > &b)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure used for scoring calculations.

Stores the letter frequency of a sequence or database.

double * prob

letter probs, (possible) non-zero offset.

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