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NCBI C++ ToolKit: CCmdLineBlastXMLReportData Class Reference
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Strategy class to gather the data for generating BLAST XML output. More...
#include <algo/blast/format/data4xmlformat.hpp>
CCmdLineBlastXMLReportData (CRef< blast::CBlastQueryVector > queries, const blast::CSearchResultSet &results, const blast::CBlastOptions &opts, const string &dbname, bool db_is_aa, int qgencode=BLAST_GENETIC_CODE, int dbgencode=BLAST_GENETIC_CODE, bool is_remote=false, int dbfilt_algorithm=-1) Constructor. More...
CCmdLineBlastXMLReportData (CRef< blast::CBlastQueryVector > queries, const blast::CSearchResultSet &results, const blast::CBlastOptions &opts, const vector< align_format::CAlignFormatUtil::SDbInfo > &dbInfo, int qgencode=BLAST_GENETIC_CODE, int dbgencode=BLAST_GENETIC_CODE, bool is_remote=false, int dbfilt_algorithm=-1) Constructor. More...
~CCmdLineBlastXMLReportData () Destructor. More...
string GetBlastProgramName (void) const @inheritDoc More...
blast::EProgram GetBlastTask (void) const @inheritDoc More...
string GetDatabaseName (void) const @inheritDoc More...
double GetEvalueThreshold (void) const @inheritDoc More...
int GetGapOpeningCost (void) const @inheritDoc More...
int GetGapExtensionCost (void) const @inheritDoc More...
int GetMatchReward (void) const @inheritDoc More...
int GetMismatchPenalty (void) const @inheritDoc More...
string GetPHIPattern (void) const @inheritDoc More...
string GetFilterString (void) const @inheritDoc More...
string GetMatrixName (void) const @inheritDoc More...
CBlastFormattingMatrix * GetMatrix (void) const @inheritDoc More...
unsigned int GetNumQueries (void) const @inheritDoc More...
const TMaskedQueryRegions * GetMaskLocations (int query_index) const @inheritDoc More...
int GetDbNumSeqs (void) const @inheritDoc More...
Int8 GetDbLength (void) const @inheritDoc More...
int GetLengthAdjustment (int) const @inheritDoc More...
Int8 GetEffectiveSearchSpace (int query_index) const @inheritDoc More...
double GetLambda (int query_index) const @inheritDoc More...
double GetKappa (int query_index) const @inheritDoc More...
double GetEntropy (int query_index) const @inheritDoc More...
const objects::CSeq_loc * GetQuery (int query_index) const @inheritDoc More...
objects::CScope * GetScope (int query_index) const @inheritDoc More...
const CSeq_align_set * GetAlignment (int query_index) const @inheritDoc More...
bool GetGappedMode (void) const @inheritDoc More...
int GetMasterGeneticCode () const @inheritDoc More...
int GetSlaveGeneticCode () const @inheritDoc More...
vector< string > GetMessages () const @inheritDoc More...
virtual ~IBlastXMLReportData () Our virtual destructor. More...
Strategy class to gather the data for generating BLAST XML output.
Definition at line 50 of file data4xmlformat.hpp.
◆ CCmdLineBlastXMLReportData() [1/2]
Constructor.
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Parameters
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queries Query sequences [in] results results set containing one query per element or one iteration per element in the case of PSI-BLAST [in] opts Blast options container [in] dbname Name of database to search ("" if none) [in] db_is_aa true if database contains protein sequences [in] qgencode Genetic code used to translate query sequences (if applicable) [in] dbgencode Genetic code used to translate database sequences (if applicable) [in] dbfilt_algorithm DB Filtering algorithm to use, -1 means not applicable FIXME: this is not being reported
Definition at line 46 of file data4xmlformat.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), m_DbName, m_Queries, results, and x_Init().
◆ CCmdLineBlastXMLReportData() [2/2]
Constructor.
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Parameters
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queries Query sequences [in] results results set containing one query per element or one iteration per element in the case of PSI-BLAST [in] opts Blast options container [in] dbInfo vector of SDbInfo containing db names and type [in] qgencode Genetic code used to translate query sequences (if applicable) [in] dbgencode Genetic code used to translate database sequences (if applicable) [in] dbfilt_algorithm DB Filtering algorithm to use, -1 means not applicable FIXME: this is not being reported
◆ ~CCmdLineBlastXMLReportData() CCmdLineBlastXMLReportData::~CCmdLineBlastXMLReportData ( ) ◆ GetAlignment() ◆ GetBlastProgramName() string CCmdLineBlastXMLReportData::GetBlastProgramName ( void ) const inlinevirtual ◆ GetBlastTask() ◆ GetDatabaseName() string CCmdLineBlastXMLReportData::GetDatabaseName ( void ) const inlinevirtual ◆ GetDbLength() Int8 CCmdLineBlastXMLReportData::GetDbLength ( void ) const inlinevirtual ◆ GetDbNumSeqs() int CCmdLineBlastXMLReportData::GetDbNumSeqs ( void ) const inlinevirtual ◆ GetEffectiveSearchSpace() Int8 CCmdLineBlastXMLReportData::GetEffectiveSearchSpace ( int query_index ) const inlinevirtual ◆ GetEntropy() double CCmdLineBlastXMLReportData::GetEntropy ( int query_index ) const virtual ◆ GetEvalueThreshold() double CCmdLineBlastXMLReportData::GetEvalueThreshold ( void ) const inlinevirtual ◆ GetFilterString() string CCmdLineBlastXMLReportData::GetFilterString ( void ) const inlinevirtual ◆ GetGapExtensionCost() int CCmdLineBlastXMLReportData::GetGapExtensionCost ( void ) const inlinevirtual ◆ GetGapOpeningCost() int CCmdLineBlastXMLReportData::GetGapOpeningCost ( void ) const inlinevirtual ◆ GetGappedMode() bool CCmdLineBlastXMLReportData::GetGappedMode ( void ) const inlinevirtual ◆ GetKappa() double CCmdLineBlastXMLReportData::GetKappa ( int query_index ) const virtual ◆ GetLambda() double CCmdLineBlastXMLReportData::GetLambda ( int query_index ) const virtual ◆ GetLengthAdjustment() int CCmdLineBlastXMLReportData::GetLengthAdjustment ( int query_index ) const virtual ◆ GetMaskLocations() ◆ GetMasterGeneticCode() int CCmdLineBlastXMLReportData::GetMasterGeneticCode ( ) const inlinevirtual ◆ GetMatchReward() int CCmdLineBlastXMLReportData::GetMatchReward ( void ) const inlinevirtual ◆ GetMatrix() ◆ GetMatrixName() string CCmdLineBlastXMLReportData::GetMatrixName ( void ) const inlinevirtual ◆ GetMessages() vector<string> CCmdLineBlastXMLReportData::GetMessages ( void ) const inlinevirtual ◆ GetMismatchPenalty() int CCmdLineBlastXMLReportData::GetMismatchPenalty ( void ) const inlinevirtual ◆ GetNumQueries() unsigned int CCmdLineBlastXMLReportData::GetNumQueries ( void ) const inlinevirtual ◆ GetPHIPattern() string CCmdLineBlastXMLReportData::GetPHIPattern ( void ) const inlinevirtual ◆ GetQuery() const objects::CSeq_loc* CCmdLineBlastXMLReportData::GetQuery ( int query_index ) const inlinevirtual ◆ GetScope() objects::CScope* CCmdLineBlastXMLReportData::GetScope ( int query_index ) const inlinevirtual ◆ GetSlaveGeneticCode() int CCmdLineBlastXMLReportData::GetSlaveGeneticCode ( ) const inlinevirtual ◆ x_FillScoreMatrix()
Initialize the score matrix to be used for formatting (if applicable)
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Parameters
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matrix_name Name of score matrix. NULL defaults to BLOSUM62 [in]
Definition at line 185 of file data4xmlformat.cpp.
References Blast_ProgramNameFromType(), i, kMatrixCols, m_Matrix, m_Options, NCBI_THROW, NCBISM_Blosum45, NCBISM_Blosum50, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Blosum90, NCBISM_Identity, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, NCBISM_Unpack(), NULL, SNCBIFullScoreMatrix::s, and util::strcmp().
Referenced by x_Init().
◆ x_Init() void CCmdLineBlastXMLReportData::x_Init ( CRef< blast::CBlastQueryVector > queries, const blast::CSearchResultSet & results, const blast::CBlastOptions & opts, const vector< align_format::CAlignFormatUtil::SDbInfo > & dbInfo, int qgencode, int dbgencode, bool is_remote, int dbfilt_algorith ) private
Definition at line 103 of file data4xmlformat.cpp.
References ePSIBlast, GetNumQueries(), i, ITERATE, kEmptyStr, m_Alignments, m_AncillaryData, m_Errors, m_Masks, m_NoHitsFound, m_NumBases, m_NumSequences, m_Options, m_Queries, results, and x_FillScoreMatrix().
Referenced by CCmdLineBlastXMLReportData().
◆ kMatrixCols const unsigned int CCmdLineBlastXMLReportData::kMatrixCols = 28 staticprivate ◆ m_Alignments ◆ m_AncillaryData vector<CRef<blast::CBlastAncillaryData> > CCmdLineBlastXMLReportData::m_AncillaryData private ◆ m_DbGeneticCode int CCmdLineBlastXMLReportData::m_DbGeneticCode private ◆ m_DbName string CCmdLineBlastXMLReportData::m_DbName private ◆ m_Errors vector<string> CCmdLineBlastXMLReportData::m_Errors private ◆ m_Masks ◆ m_Matrix ◆ m_NoHitsFound bool CCmdLineBlastXMLReportData::m_NoHitsFound private ◆ m_NumBases Int8 CCmdLineBlastXMLReportData::m_NumBases private ◆ m_NumSequences int CCmdLineBlastXMLReportData::m_NumSequences private ◆ m_Options const blast::CBlastOptions& CCmdLineBlastXMLReportData::m_Options private
BLAST algorithm options.
Definition at line 251 of file data4xmlformat.hpp.
Referenced by GetBlastProgramName(), GetBlastTask(), GetEvalueThreshold(), GetFilterString(), GetGapExtensionCost(), GetGapOpeningCost(), GetGappedMode(), GetMatchReward(), GetMatrixName(), GetMismatchPenalty(), GetPHIPattern(), x_FillScoreMatrix(), and x_Init().
◆ m_Queries CRef<blast::CBlastQueryVector> CCmdLineBlastXMLReportData::m_Queries private ◆ m_QueryGeneticCode int CCmdLineBlastXMLReportData::m_QueryGeneticCode private
The documentation for this class was generated from the following files:
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