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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSimpleB2SWrapper.cpp Source File

(seq1,

, 0, 0);

(seq2,

, 0, 0);

full = (from == 0 && to == 0);

(full || from > to) {

isNameKnown =

;

querySeqLoc, subjectSeqLoc;

subjectVector.

(bsqSubject);

(

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

(score &&

.size() > 0) {

(eval &&

.size() > 0) {

invLen1 = (len1) ? 1.0/(double) len1 : 0;

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

()->Get();

(seqAlignList.size() == 0)

;

score = 0.0, eVal =

, percIdent = 0.0;

percIdent = 100.0 * invLen1 * (double) nIdent;

User-defined methods of the data storage class.

Declares the CBlastAdvancedProteinOptionsHandle class.

Declares the CBlastProteinOptionsHandle class.

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.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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

Search Results for All Queries.

Search Results for One Query.

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

Get score.

ECompoAdjustModes m_caMode

CRef< CSeq_align > getBestB2SAlignment(double *score=NULL, double *eval=NULL, double *percIdent=NULL) const

bool FillOutSeqLoc(const SB2SSeq &s, CSeq_loc &seqLoc)

double SetEValueThreshold(double eValueThold)

static const double E_VAL_WHEN_NO_SEQ_ALIGN

static const unsigned int HITLIST_SIZE_DEFAULT

double SetPercIdThreshold(double percIdThold)

double getPairwiseScore(unsigned int hitIndex) const

double getPairwisePercIdent(unsigned int hitIndex) const

void SetSeq(CRef< CBioseq > &seq, bool isSeq1, unsigned int from, unsigned int to)

unsigned int SetHitlistSize(unsigned int hitlistSize)

static const double DO_NOT_USE_PERC_ID_THRESHOLD

CSimpleB2SWrapper(double percIdThold=DO_NOT_USE_PERC_ID_THRESHOLD, string matrixName=SCORING_MATRIX_DEFAULT)

CRef< CBlastAdvancedProteinOptionsHandle > m_options

static const unsigned int MAX_HITLIST_SIZE

static const Int8 CDD_DATABASE_SIZE

vector< double > m_percIdents

Int8 SetEffSearchSpace(Int8 effSearchSpace)

vector< double > m_scores

bool getPairwiseBlastAlignment(unsigned int hitIndex, CRef< CSeq_align > &seqAlign) const

void processBlastHits(ncbi::blast::CSearchResults &)

Int8 SetDbLength(Int8 dbLength)

static void RemoveAllDataLoaders()

void InitializeToDefaults()

string SetMatrixName(string matrixName)

static const Int8 DO_NOT_USE_EFF_SEARCH_SPACE

static const double E_VAL_DEFAULT

double getPairwiseEValue(unsigned int hitIndex) const

vector< CRef< CSeq_align > > m_alignments

static const ECompoAdjustModes COMPOSITION_ADJ_DEF

unsigned int m_hitlistSize

static const string SCORING_MATRIX_DEFAULT

ECompoAdjustModes SetCompoAdjustMode(ECompoAdjustModes caMode)

static const double SCORE_WHEN_NO_SEQ_ALIGN

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

@ eNoCompositionBasedStats

Don't use composition based statistics.

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

int GetSeqLength(const CBioseq &bioseq)

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

void SetDbLength(Int8 len)

Sets DbLength.

void SetDbSeqNum(unsigned int num)

Sets DbSeqNum.

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

void SetEffectiveSearchSpace(Int8 eff)

Sets EffectiveSearchSpace.

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 SetSegFiltering(bool val)

Enable SEG filtering.

void SetPercentIdentity(double p)

Sets PercentIdentity.

size_type GetNumResults() const

Return the number of results contained by this object.

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.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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 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 END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

const TId & GetId(void) const

Get the Id member data.

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

Declares the CPSIBlastOptionsHandle class.

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