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NCBI C++ ToolKit: src/algo/blast/proteinkmer/blastkmerresults.cpp Source File

: m_QueryId(

), m_Stats(stats), m_SeqDB(seqdb), m_Errors(errs)

x_InitScoreVec(scores);

(TBlastKmerPrelimScoreVector::iterator iter=scores.begin(); iter != scores.end(); ++iter)

(seqids.size() > 0)

( !id->

() )

= seqids.front();

pair<CRef<CSeq_id>,

> retval(

, (*iter).second);

(TBlastKmerScoreVector::const_iterator iter=scores.begin(); iter != scores.end(); ++iter)

seqloc->

().Assign(*((*iter).first));

unique_ptr<SSeqLoc> ssl(

(*seqloc, *scope));

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

errs.push_back(*iter);

(

=0;

<ids.size();

++)

seqid->

(*(queryVector[queryNum].seqloc->GetId()));

errs.push_back(

);

EBlastSeverity

Blast error message severities .

CRef< CBlastKmerResults > MakeEmptyResults(TSeqLocVector &queryVector, int queryNum, const string &errMsg, EBlastSeverity severity)

Empty results (use on error)

vector< pair< CRef< CSeq_id >, double > > TBlastKmerScoreVector

Vector of pairs of seq-ids and scores.

vector< pair< uint32_t, double > > TBlastKmerPrelimScoreVector

Vector of pairs of database OIDs and scores.

CBlastKmerResultsSet()

Default constructor.

void x_Init(TQueryIdVector &ids, TBlastKmerPrelimScoreVectorSet &scores, TBlastKmerStatsVector &stats, CRef< CSeqDB > seqdb, TSearchMessages msg_vec)

vector< BlastKmerStats > TBlastKmerStatsVector

Vector of KmerStats.

void push_back(value_type &element)

Add an element to m_Results.

CBlastKmerResults & operator[](size_type i)

vector< CRef< CBlastKmerResults > > m_Results

Vectors of results.

vector< CConstRef< objects::CSeq_id > > TQueryIdVector

List of query ids.

size_t m_NumQueries

Number or queries.

vector< TBlastKmerPrelimScoreVector > TBlastKmerPrelimScoreVectorSet

Vector of TBlastKmerScoreVector (scores)

This class represents the results for one KMER search (one query).

void GetTSL(TSeqLocVector &tsl, CRef< CScope > scope) const

Get the results as a TSeqLocVector.

TQueryMessages m_Errors

error/warning messages for this query

bool HasWarnings() const

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

TQueryMessages GetErrors(int min_severity=eBlastSevError) const

Accessor for the error/warning messsages for this query.

TBlastKmerScoreVector m_Scores

Vector of Seq-ids and scores.

CRef< CSeqDB > m_SeqDB

Database searched.

const TBlastKmerScoreVector & GetScores() const

Get the vector of GIs and scores for the matches.

void x_InitScoreVec(TBlastKmerPrelimScoreVector &scores)

Saves the matches as TBlastKmerScoreVector.

bool HasErrors() const

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

Error or Warning Message from search.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

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...

string GetQueryId() const

Get the query id as a string.

void SetQueryId(const string &id)

Set the query id as a string.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const string AsFastaString(void) const

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

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

static int BestRank(const CRef< CSeq_id > &id)

@ e_YES

SeqIds compared, but are different.

void Reset(void)

Reset reference object.

#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.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsGi(void) const

Check if variant Gi is selected.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure for ancillary data on KMER search.

Structure to represent a single sequence to be fed to BLAST.

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