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NCBI C++ ToolKit: CCmdLineBlastXML2ReportData Class Reference

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

#include <algo/blast/format/data4xml2format.hpp>

  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. More...
    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. More...
    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. More...
    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. More...
    ~CCmdLineBlastXML2ReportData ()   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   Returns pattern string, for PHI BLAST search only. More...
  string  GetFilterString (void) const   Returns filtering option string. More...
  string  GetMatrixName (void) const   Returns matrix name. More...
  CBlastFormattingMatrix *  GetMatrix (void) const   Returns a 256x256 ASCII-alphabet matrix, needed for formatting. More...
  CConstRef< objects::CSeq_loc >  GetQuerySeqLoc (void) const   const TMaskedQueryRegions &  GetMaskLocations (void) const   Returns list of mask locations for a given query. More...
  Int8  GetDbNumSeqs (void) const   Returns number of database sequences. More...
  Int8  GetDbLength (void) const   Returns database length. More...
  int  GetLengthAdjustment (int num) const   Returns length adjustment for a given query. More...
  Int8  GetEffectiveSearchSpace (int num) const   Returns effective search space for a given query. More...
  double  GetLambda (int num) const   Returns Karlin-Altschul Lambda parameter for a given query. More...
  double  GetKappa (int num) const   Returns Karlin-Altschul K parameter for a given query. More...
  double  GetEntropy (int num) const   Returns Karlin-Altschul H parameter for a given query. More...
  CRef< objects::CScope >  GetScope () const   Returns scope . More...
  CConstRef< CSeq_align_set >  GetAlignmentSet (int num) const   Returns a vector continaing set of alignments found for a given query. More...
  int  GetQueryGeneticCode () const   master genetic code More...
  int  GetDbGeneticCode () const   slave genetic code More...
  string  GetMessages (int num) const   Get error messages. More...
  bool  CanGetTaxInfo (void) const   bool  IsBl2seq (void) const   int  GetNumOfSearchResults (void) const   list< string >  GetSubjectIds (void) const   bool  IsGappedSearch (void) const   int  GetCompositionBasedStats (void) const   string  GetBl2seqMode (void) const   bool  IsIterativeSearch (void) const   string  GetEntrezQuery (void) const   virtual  ~IBlastXML2ReportData ()   Our virtual destructor. More...
 

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

Definition at line 52 of file data4xml2format.hpp.

◆ CCmdLineBlastXML2ReportData() [1/4] CCmdLineBlastXML2ReportData::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.

Parameters
query Query sequences [in] results results set containing one query per element or one opts Blast options container [in] scope scope containing query and subject seqs [in] dbsInfo vector of SDbInfo containing db names and type [in]
◆ CCmdLineBlastXML2ReportData() [2/4] CCmdLineBlastXML2ReportData::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.

Parameters
subjectsInfo contains bl2seq subjects info [in]
◆ CCmdLineBlastXML2ReportData() [3/4] CCmdLineBlastXML2ReportData::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.

Parameters
resultSet containing results from all iteration [in]
◆ CCmdLineBlastXML2ReportData() [4/4] CCmdLineBlastXML2ReportData::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.

Parameters
resultSet containing results from all iteration [in]
◆ ~CCmdLineBlastXML2ReportData() CCmdLineBlastXML2ReportData::~CCmdLineBlastXML2ReportData ( ) ◆ CanGetTaxInfo() bool CCmdLineBlastXML2ReportData::CanGetTaxInfo ( void  ) const inlinevirtual ◆ GetAlignmentSet() ◆ GetBl2seqMode() string CCmdLineBlastXML2ReportData::GetBl2seqMode ( void  ) const inlinevirtual ◆ GetBlastProgramName() string CCmdLineBlastXML2ReportData::GetBlastProgramName ( void  ) const virtual ◆ GetBlastTask() ◆ GetCompositionBasedStats() int CCmdLineBlastXML2ReportData::GetCompositionBasedStats ( void  ) const inlinevirtual ◆ GetDatabaseName() string CCmdLineBlastXML2ReportData::GetDatabaseName ( void  ) const inlinevirtual ◆ GetDbGeneticCode() int CCmdLineBlastXML2ReportData::GetDbGeneticCode ( ) const virtual ◆ GetDbLength() Int8 CCmdLineBlastXML2ReportData::GetDbLength ( void  ) const inlinevirtual ◆ GetDbNumSeqs() Int8 CCmdLineBlastXML2ReportData::GetDbNumSeqs ( void  ) const inlinevirtual ◆ GetEffectiveSearchSpace() Int8 CCmdLineBlastXML2ReportData::GetEffectiveSearchSpace ( int  num ) const virtual ◆ GetEntrezQuery() string CCmdLineBlastXML2ReportData::GetEntrezQuery ( void  ) const inlinevirtual ◆ GetEntropy() double CCmdLineBlastXML2ReportData::GetEntropy ( int  num ) const virtual ◆ GetEvalueThreshold() double CCmdLineBlastXML2ReportData::GetEvalueThreshold ( void  ) const inlinevirtual ◆ GetFilterString() string CCmdLineBlastXML2ReportData::GetFilterString ( void  ) const inlinevirtual ◆ GetGapExtensionCost() int CCmdLineBlastXML2ReportData::GetGapExtensionCost ( void  ) const inlinevirtual ◆ GetGapOpeningCost() int CCmdLineBlastXML2ReportData::GetGapOpeningCost ( void  ) const inlinevirtual ◆ GetKappa() double CCmdLineBlastXML2ReportData::GetKappa ( int  num ) const virtual ◆ GetLambda() double CCmdLineBlastXML2ReportData::GetLambda ( int  num ) const virtual ◆ GetLengthAdjustment() int CCmdLineBlastXML2ReportData::GetLengthAdjustment ( int  num ) const virtual ◆ GetMaskLocations() ◆ GetMatchReward() int CCmdLineBlastXML2ReportData::GetMatchReward ( void  ) const inlinevirtual ◆ GetMatrix() ◆ GetMatrixName() string CCmdLineBlastXML2ReportData::GetMatrixName ( void  ) const inlinevirtual ◆ GetMessages() string CCmdLineBlastXML2ReportData::GetMessages ( int  num ) const inlinevirtual ◆ GetMismatchPenalty() int CCmdLineBlastXML2ReportData::GetMismatchPenalty ( void  ) const inlinevirtual ◆ GetNumOfSearchResults() int CCmdLineBlastXML2ReportData::GetNumOfSearchResults ( void  ) const inlinevirtual ◆ GetPHIPattern() string CCmdLineBlastXML2ReportData::GetPHIPattern ( void  ) const inlinevirtual ◆ GetQueryGeneticCode() int CCmdLineBlastXML2ReportData::GetQueryGeneticCode ( ) const virtual ◆ GetQuerySeqLoc() CConstRef<objects::CSeq_loc> CCmdLineBlastXML2ReportData::GetQuerySeqLoc ( void  ) const inlinevirtual ◆ GetScope() CRef<objects::CScope> CCmdLineBlastXML2ReportData::GetScope ( ) const inlinevirtual ◆ GetSubjectIds() list<string> CCmdLineBlastXML2ReportData::GetSubjectIds ( void  ) const inlinevirtual ◆ IsBl2seq() bool CCmdLineBlastXML2ReportData::IsBl2seq ( void  ) const inlinevirtual ◆ IsGappedSearch() bool CCmdLineBlastXML2ReportData::IsGappedSearch ( void  ) const inlinevirtual ◆ IsIterativeSearch() bool CCmdLineBlastXML2ReportData::IsIterativeSearch ( void  ) const inlinevirtual ◆ x_FillScoreMatrix()

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

Parameters
matrix_name Name of score matrix. NULL defaults to BLOSUM62 [in]

Definition at line 194 of file data4xml2format.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, util::strcmp(), and tmp.

Referenced by x_InitCommon().

◆ x_InitCommon() void CCmdLineBlastXML2ReportData::x_InitCommon ( const blast::CSearchResults &  results, CConstRef< blast::CBlastOptions >  opts  ) private

Definition at line 134 of file data4xml2format.cpp.

References CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), eUnknown, CBlastOptions::IsIterativeSearch(), m_isIterative, m_Options, m_Scope, m_TaxDBFound, NCBI_THROW, SeqDB_ResolveDbPath(), and x_FillScoreMatrix().

◆ x_InitDB() void CCmdLineBlastXML2ReportData::x_InitDB ( const vector< align_format::CAlignFormatUtil::SDbInfo > &  dbsInfo ) private ◆ x_InitResults() void CCmdLineBlastXML2ReportData::x_InitResults ( const blast::CSearchResults &  results ) private ◆ x_InitSubjects() void CCmdLineBlastXML2ReportData::x_InitSubjects ( CConstRef< blast::IBlastSeqInfoSrc >  subjectsInfo ) private ◆ kMatrixCols const unsigned int CCmdLineBlastXML2ReportData::kMatrixCols = 28 staticprivate ◆ m_Alignments ◆ m_AncillaryData vector<CRef<blast::CBlastAncillaryData> > CCmdLineBlastXML2ReportData::m_AncillaryData private ◆ m_DbName string CCmdLineBlastXML2ReportData::m_DbName private ◆ m_Errors vector<string> CCmdLineBlastXML2ReportData::m_Errors private ◆ m_isBl2seq bool CCmdLineBlastXML2ReportData::m_isBl2seq private ◆ m_isIterative bool CCmdLineBlastXML2ReportData::m_isIterative private ◆ m_Matrix ◆ m_NumBases Int8 CCmdLineBlastXML2ReportData::m_NumBases private ◆ m_NumSequences Int8 CCmdLineBlastXML2ReportData::m_NumSequences private ◆ m_Options CConstRef<blast::CBlastOptions> CCmdLineBlastXML2ReportData::m_Options private

BLAST algorithm options.

Definition at line 211 of file data4xml2format.hpp.

Referenced by GetBlastProgramName(), GetBlastTask(), GetCompositionBasedStats(), GetDbGeneticCode(), GetEvalueThreshold(), GetFilterString(), GetGapExtensionCost(), GetGapOpeningCost(), GetMatchReward(), GetMatrixName(), GetMismatchPenalty(), GetPHIPattern(), GetQueryGeneticCode(), IsGappedSearch(), x_FillScoreMatrix(), and x_InitCommon().

◆ m_Query CConstRef<blast::CBlastSearchQuery> CCmdLineBlastXML2ReportData::m_Query private ◆ m_QueryMasks ◆ m_Scope CRef<objects::CScope> CCmdLineBlastXML2ReportData::m_Scope private ◆ m_SubjectIds list<string> CCmdLineBlastXML2ReportData::m_SubjectIds private ◆ m_TaxDBFound bool CCmdLineBlastXML2ReportData::m_TaxDBFound private

The documentation for this class was generated from the following files:

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