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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuBlast2Seq.cpp Source File

: m_ac(&

), m_queryRows(0), m_subjectRows(0), m_seqs(0), m_scoringMatrix(matrixName), m_useWhole(

),

m_scoreType(

::eScore_Score), m_psiTargetCd(0)

: m_ac(0), m_seqs(&seqs), m_scoringMatrix(matrixName), m_useWhole(

), m_psiTargetCd(0)

cd_utils::PssmMaker pm(targetCD,

,

);

cd_utils::PssmMakerOptions

;

.requestFrequencyRatios =

;

numBlastsDone = 0;

(

q = 0; q <

->size(); q++)

(

= 0;

< nrows;

++)

totalBlasts = (

)((

)nrows * (((double)nrows-1)/2));

numQueries = nrows-1;

querySeqLoc, subjectSeqLoc;

(

qr = 0; qr < numQueries; qr++)

subStart = qr +1;

batchSize = (nrows -1) - (qr + 1) + 1;

(

sr = subStart; sr < nrows; sr++)

subjectVector.

(bsqSubject);

((

)batchSize == subjectVector.

());

numBlastsDone += batchSize;

notifier(numBlastsDone, totalBlasts);

(

sr = 0; sr < nrows; sr++)

subjectVector.

(bsqSubject);

(index = 0; index < total; ++index)

list< CRef< CSeq_align > >& seqAlignList = (*hits)[index].GetSeqAlign()->Get();

(seqAlignList.empty())

bioseq = (*m_seqs)[

];

(bioseq.

())

list< CRef< CSeq_annot > >& annots = bioseq->

();

(list<

>::const_iterator cit = annots.begin(); cit != annots.end(); cit++)

((*cit)->IsSetData())

((*cit)->GetData().IsLocs())

list< CRef< CSeq_loc > >& locs = (*cit)->GetData().GetLocs();

(seqLoc->

())

tbioseq->

(*bioseq);

tbioseq->

().SetLength(to - from + 1);

tr(seqData.substr(from, to - from + 1));

tbioseq->

().SetSeq_data().SetNcbieaa(tr);

score, idScore;

(

= 0;

< nhits;

++)

list< CRef< CSeq_align > >& seqAlignList = hits[

].GetSeqAlign()->Get();

(seqAlignList.size() > 0)

score = 100*idScore/seqLen;

realQuery =

;

realSubject =

;

totalBeforeQuery = (nrows - 1 + nrows - realQuery)*realQuery/2;

comp = totalBeforeQuery + (realSubject - realQuery - 1);

(from < 0 || to < 0 ||

<=0)

;

(from <= to && to <

&& (to - from + 1 >= 0)) {

(nTermShift == 0 && cTermShift == 0) {

(from == 0 && (to == 0 || to ==

- 1)) {

nTermShift = (nTermShift < 0) ? nTermShift : 0;

cTermShift = (cTermShift < 0) ? cTermShift : 0;

(-nTermShift <

- 1 + cTermShift ) {

(nTermShift >= 0) {

from = (nTermShift <= from) ? from - nTermShift : 0;

from = (-nTermShift < to - 1 + cTermShift) ? from - nTermShift : from;

(cTermShift >= 0) {

to = (cTermShift <=

- 1 - to) ? to + cTermShift :

- 1;

to = (-cTermShift <= to - from - 1 + nTermShift) ? to + cTermShift : to;

->GetRegisteredNames(loader_names);

->RevokeDataLoader(*itr);

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.

Declares the CBlastAdvancedProteinOptionsHandle class.

Declares the CBlastProteinOptionsHandle class.

User-defined methods of the data storage class.

bool GetBioseqForRow(int rowId, CRef< CBioseq > &bioseq)

int GetLowerBound(int row) const

int GetUpperBound(int row) const

const CSeq_id * GetFirstId() const

TSeqPos GetLength(void) const

Handle to the Advanced BLASTP options.

Handle to the protein-protein options to the BLAST algorithm.

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

size_type Size() const

Returns the number of queries found in this query vector.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Handle to the protein-protein options to the BLAST algorithm.

Runs a single iteration of the PSI-BLAST algorithm between 2 sequences.

Search Results for All Queries.

bool GetNamedScore(const string &id, int &score) const

Get score.

bool IsFootprintValid(int from, int to, int len)

void useWholeSequence(bool whole)

int getCompositeIndex(int query, int subject)

CRef< CSeq_align > getPsiBlastAlignement(int row)

bool FillOutSeqLoc(const CRef< CBioseq > &bs, CSeq_loc &seqLoc)

CRef< CPssmWithParameters > m_psiTargetPssm

double getPairwiseScore(int row1, int row2)

void RemoveAllDataLoaders()

const vector< int > * m_subjectRows

vector< double > m_scores

void processBlastHits(int queryRow, CSearchResultSet &hits)

vector< CRef< CSeq_align > > m_alignments

CRef< CBioseq > truncateBioseq(int row)

static const double E_VAL_WHEN_NO_SEQ_ALIGN

static const int DEFAULT_NR_SEQNUM

vector< CRef< CBioseq > > * m_seqs

static const double BLAST_SCALING_FACTOR_DEFAULT

CdBlaster(AlignmentCollection &source, string matrixName=SCORING_MATRIX_DEFAULT)

CRef< CSeq_align > getPairwiseBlastAlignement(int row1, int row2)

static const string SCORING_MATRIX_DEFAULT

void ApplyEndShiftToRange(int &from, int nTermShift, int &to, int cTermShift, int len)

const vector< int > * m_queryRows

double getPairwiseEValue(int row1, int row2)

vector< int > m_batchSizes

static const long DEFAULT_NR_SIZE

vector< CRef< CBioseq > > m_truncatedBioseqs

static const double SCORE_WHEN_NO_SEQ_ALIGN

bool blast(NotifierFunction notifier=0)

double getPsiBlastScore(int row)

static const int CDD_DATABASE_SIZE

void setFootprintExtension(int nExt, int CExt)

CSeq_align::EScoreType m_scoreType

void setPsiBlastTarget(CRef< CPssmWithParameters > pssm)

AlignmentCollection * m_ac

double getPsiBlastEValue(int row)

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

@ eNoCompositionBasedStats

Don't use composition based statistics.

CRef< CSeq_align > ExtractFirstSeqAlign(CRef< CSeq_align > seqAlign)

void(* NotifierFunction)(int Num, int Total)

bool GetNcbieaaString(const CBioseq &bioseq, string &str)

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

void SetDbLength(Int8 len)

Sets DbLength.

void SetDbSeqNum(unsigned int num)

Sets DbSeqNum.

void SetCompositionBasedStats(ECompoAdjustModes mode)

Sets this mode, which mostly specifies whether composition of db sequence is taken into account when ...

void SetHitlistSize(int s)

Sets HitlistSize.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST 2 Sequences engine.

void SetMatrixName(const char *matrix)

Sets MatrixName.

void SetPseudoCount(int p)

Sets PseudoCount.

void SetSegFiltering(bool val)

Enable SEG filtering.

size_type GetNumResults() const

Return the number of results contained by this object.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< string > TRegisteredNames

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

bool NotEmpty(void) const THROWS_NONE

Check if CRef 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.

#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.

TPseudocount GetPseudocount(void) const

Get the Pseudocount member data.

const TParams & GetParams(void) const

Get the Params member data.

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TLength GetLength(void) const

Get the Length member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

const CharType(& source)[N]

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

Declares the CPSIBlastOptionsHandle class.

CRef< objects::CObjectManager > om

#define row(bind, expected)

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