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NCBI C++ ToolKit: include/algo/blast/format/data4xml2format.hpp Source File

blast::CSearchResults&

,

vector<align_format::CAlignFormatUtil::SDbInfo> & dbsInfo);

blast::CSearchResults&

,

blast::CSearchResultSet& resultSet,

vector<align_format::CAlignFormatUtil::SDbInfo> & dbsInfo);

blast::CSearchResultSet& resultSet,

->GetGapExtensionCost();

->GetQuerySeqLoc();

(

vector<align_format::CAlignFormatUtil::SDbInfo> & dbsInfo);

BLAST formatter utilities.

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

Defines interface for retrieving sequence identifiers.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

256x256 matrix used for calculating positives etc.

Strategy class to gather the data for generating BLAST XML output.

string GetBl2seqMode(void) const

string GetMessages(int num) const

Get error messages.

void x_InitSubjects(CConstRef< blast::IBlastSeqInfoSrc > subjectsInfo)

Int8 m_NumSequences

Number of sequences in all BLAST databases involved in this search.

static const unsigned int kMatrixCols

Number of columns used in score matrices.

CRef< objects::CScope > GetScope() const

Returns scope .

string GetFilterString(void) const

Returns filtering option string.

CBlastFormattingMatrix * GetMatrix(void) const

Returns a 256x256 ASCII-alphabet matrix, needed for formatting.

void x_FillScoreMatrix(const char *matrix_name=BLAST_DEFAULT_MATRIX)

Initialize the score matrix to be used for formatting (if applicable)

double GetKappa(int num) const

Returns Karlin-Altschul K parameter for a given query.

int GetDbGeneticCode() const

slave genetic code

string GetPHIPattern(void) const

Returns pattern string, for PHI BLAST search only.

vector< CConstRef< CSeq_align_set > > m_Alignments

the alignments

int GetCompositionBasedStats(void) const

string GetMatrixName(void) const

Returns matrix name.

string GetEntrezQuery(void) const

double GetEntropy(int num) const

Returns Karlin-Altschul H parameter for a given query.

blast::EProgram GetBlastTask(void) const

@inheritDoc

int GetQueryGeneticCode() const

master genetic code

int GetGapExtensionCost(void) const

@inheritDoc

CCmdLineBlastXML2ReportData(CConstRef< blast::CBlastSearchQuery > query, const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts, CRef< objects::CScope > scope, CConstRef< blast::IBlastSeqInfoSrc > subjectsInfo)

Constructor bl2seq in db mode.

int GetGapOpeningCost(void) const

@inheritDoc

bool CanGetTaxInfo(void) const

int GetLengthAdjustment(int num) const

Returns length adjustment for a given query.

int GetMismatchPenalty(void) const

@inheritDoc

CConstRef< blast::CBlastOptions > m_Options

BLAST algorithm options.

CBlastFormattingMatrix * m_Matrix

Score matrix used to determine neighboring protein residues.

string GetDatabaseName(void) const

@inheritDoc

Int8 GetEffectiveSearchSpace(int num) const

Returns effective search space for a given query.

CCmdLineBlastXML2ReportData(CConstRef< blast::CBlastSearchQuery > query, const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts, CRef< objects::CScope > scope, const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo)

Constructor db search.

CCmdLineBlastXML2ReportData(CConstRef< blast::CBlastSearchQuery > query, const blast::CSearchResultSet &resultSet, CConstRef< blast::CBlastOptions > opts, CRef< objects::CScope > scope, CConstRef< blast::IBlastSeqInfoSrc > subjectsInfo)

Constructor iterative bl2seq or bl2seq in orginal mode.

int GetNumOfSearchResults(void) const

bool IsBl2seq(void) const

TMaskedQueryRegions m_QueryMasks

const TMaskedQueryRegions & GetMaskLocations(void) const

Returns list of mask locations for a given query.

bool IsGappedSearch(void) const

Int8 m_NumBases

Number of bases in all BLAST databases involved in this search.

CConstRef< objects::CSeq_loc > GetQuerySeqLoc(void) const

CConstRef< blast::CBlastSearchQuery > m_Query

CRef< objects::CScope > m_Scope

int GetMatchReward(void) const

@inheritDoc

bool IsIterativeSearch(void) const

double GetEvalueThreshold(void) const

@inheritDoc

CCmdLineBlastXML2ReportData(CConstRef< blast::CBlastSearchQuery > query, const blast::CSearchResultSet &resultSet, CConstRef< blast::CBlastOptions > opts, CRef< objects::CScope > scope, const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo)

Constructor iterative db search.

CConstRef< CSeq_align_set > GetAlignmentSet(int num) const

Returns a vector continaing set of alignments found for a given query.

string m_DbName

name of blast database

void x_InitDB(const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo)

vector< string > m_Errors

Error messages.

Int8 GetDbNumSeqs(void) const

Returns number of database sequences.

list< string > GetSubjectIds(void) const

Int8 GetDbLength(void) const

Returns database length.

~CCmdLineBlastXML2ReportData()

Destructor.

list< string > m_SubjectIds

string GetBlastProgramName(void) const

@inheritDoc

void x_InitResults(const blast::CSearchResults &results)

vector< CRef< blast::CBlastAncillaryData > > m_AncillaryData

ancillary results data

double GetLambda(int num) const

Returns Karlin-Altschul Lambda parameter for a given query.

void x_InitCommon(const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts)

Interface for filling the top layer of the XML report.

Collection of masked regions for a single query sequence.

AutoPtr< Char, CDeleter< Char > > TAutoCharPtr

Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc)

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Definition of SSeqLoc structure.

Uniform BLAST Search Interface.

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