NCBI C++ ToolKit
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Search Toolkit Book for CCmdLineBlastXML2ReportData
Strategy class to gather the data for generating BLAST XML output. More...
#include <algo/blast/format/data4xml2format.hpp>
Public Member Functions | |
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 |
Public Member Functions inherited from IBlastXML2ReportData | |
virtual | ~IBlastXML2ReportData () |
Our virtual destructor. More... | |
Private Member Functions | |
void | x_FillScoreMatrix (const char *matrix_name=BLAST_DEFAULT_MATRIX) |
Initialize the score matrix to be used for formatting (if applicable) More... | |
void | x_InitResults (const blast::CSearchResults &results) |
void | x_InitCommon (const blast::CSearchResults &results, CConstRef< blast::CBlastOptions > opts) |
void | x_InitDB (const vector< align_format::CAlignFormatUtil::SDbInfo > &dbsInfo) |
void | x_InitSubjects (CConstRef< blast::IBlastSeqInfoSrc > subjectsInfo) |
Private Attributes | |
CConstRef< blast::CBlastSearchQuery > | m_Query |
CConstRef< blast::CBlastOptions > | m_Options |
BLAST algorithm options. More... | |
CRef< objects::CScope > | m_Scope |
string | m_DbName |
name of blast database More... | |
Int8 | m_NumSequences |
Number of sequences in all BLAST databases involved in this search. More... | |
Int8 | m_NumBases |
Number of bases in all BLAST databases involved in this search. More... | |
bool | m_TaxDBFound |
bool | m_isBl2seq |
bool | m_isIterative |
vector< CRef< blast::CBlastAncillaryData > > | m_AncillaryData |
ancillary results data More... | |
vector< CConstRef< CSeq_align_set > > | m_Alignments |
the alignments More... | |
vector< string > | m_Errors |
Error messages. More... | |
CBlastFormattingMatrix * | m_Matrix |
Score matrix used to determine neighboring protein residues. More... | |
list< string > | m_SubjectIds |
TMaskedQueryRegions | m_QueryMasks |
Static Private Attributes | |
static const unsigned int | kMatrixCols = 28 |
Number of columns used in score matrices. More... | |
Strategy class to gather the data for generating BLAST XML output.
Definition at line 52 of file data4xml2format.hpp.
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.
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::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.
subjectsInfo | contains bl2seq subjects info [in] |
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.
resultSet | containing results from all iteration [in] |
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.
resultSet | containing results from all iteration [in] |
CCmdLineBlastXML2ReportData::~CCmdLineBlastXML2ReportData | ( | ) |
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Implements IBlastXML2ReportData.
Definition at line 190 of file data4xml2format.hpp.
References m_TaxDBFound.
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Returns a vector continaing set of alignments found for a given query.
Implements IBlastXML2ReportData.
Definition at line 327 of file data4xml2format.cpp.
References eUnknown, m_Alignments, and NCBI_THROW.
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Implements IBlastXML2ReportData.
Definition at line 202 of file data4xml2format.hpp.
References kEmptyStr.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 247 of file data4xml2format.cpp.
References Blast_ProgramNameFromType(), eDeltaBlast, and m_Options.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 101 of file data4xml2format.hpp.
References m_Options.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 200 of file data4xml2format.hpp.
References m_Options.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 106 of file data4xml2format.hpp.
References m_DbName.
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slave genetic code
Implements IBlastXML2ReportData.
Definition at line 352 of file data4xml2format.cpp.
References Blast_SubjectIsTranslated(), and m_Options.
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Returns database length.
Implements IBlastXML2ReportData.
Definition at line 164 of file data4xml2format.hpp.
References m_NumBases.
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Returns number of database sequences.
Implements IBlastXML2ReportData.
Definition at line 160 of file data4xml2format.hpp.
References m_NumSequences.
Returns effective search space for a given query.
Implements IBlastXML2ReportData.
Definition at line 336 of file data4xml2format.cpp.
References eUnknown, m_AncillaryData, and NCBI_THROW.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 205 of file data4xml2format.hpp.
References kEmptyStr.
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Returns Karlin-Altschul H parameter for a given query.
Implements IBlastXML2ReportData.
Definition at line 294 of file data4xml2format.cpp.
References eUnknown, Blast_KarlinBlk::H, m_AncillaryData, and NCBI_THROW.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 109 of file data4xml2format.hpp.
References m_Options.
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Returns filtering option string.
Implements IBlastXML2ReportData.
Definition at line 138 of file data4xml2format.hpp.
References m_Options, NcbiEmptyString, NULL, string, and tmp.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 119 of file data4xml2format.hpp.
References m_Options.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 114 of file data4xml2format.hpp.
References m_Options.
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Returns Karlin-Altschul K parameter for a given query.
Implements IBlastXML2ReportData.
Definition at line 276 of file data4xml2format.cpp.
References eUnknown, Blast_KarlinBlk::K, m_AncillaryData, and NCBI_THROW.
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Returns Karlin-Altschul Lambda parameter for a given query.
Implements IBlastXML2ReportData.
Definition at line 258 of file data4xml2format.cpp.
References eUnknown, Blast_KarlinBlk::Lambda, m_AncillaryData, and NCBI_THROW.
Returns length adjustment for a given query.
Implements IBlastXML2ReportData.
Definition at line 318 of file data4xml2format.cpp.
References eUnknown, m_AncillaryData, and NCBI_THROW.
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Returns list of mask locations for a given query.
Implements IBlastXML2ReportData.
Definition at line 156 of file data4xml2format.hpp.
References m_QueryMasks.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 124 of file data4xml2format.hpp.
References m_Options.
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Returns a 256x256 ASCII-alphabet matrix, needed for formatting.
Implements IBlastXML2ReportData.
Definition at line 312 of file data4xml2format.cpp.
References m_Matrix.
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Returns matrix name.
Implements IBlastXML2ReportData.
Definition at line 144 of file data4xml2format.hpp.
Get error messages.
Implements IBlastXML2ReportData.
Definition at line 188 of file data4xml2format.hpp.
References m_Errors.
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@inheritDoc
Implements IBlastXML2ReportData.
Definition at line 129 of file data4xml2format.hpp.
References m_Options.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 194 of file data4xml2format.hpp.
References m_Alignments.
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Returns pattern string, for PHI BLAST search only.
Implements IBlastXML2ReportData.
Definition at line 133 of file data4xml2format.hpp.
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master genetic code
Implements IBlastXML2ReportData.
Definition at line 344 of file data4xml2format.cpp.
References Blast_QueryIsTranslated(), and m_Options.
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Implements IBlastXML2ReportData.
Definition at line 151 of file data4xml2format.hpp.
References m_Query.
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Returns scope .
Implements IBlastXML2ReportData.
Definition at line 178 of file data4xml2format.hpp.
References m_Scope.
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Implements IBlastXML2ReportData.
Definition at line 196 of file data4xml2format.hpp.
References m_SubjectIds.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 192 of file data4xml2format.hpp.
References m_isBl2seq.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 198 of file data4xml2format.hpp.
References m_Options.
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inlinevirtual |
Implements IBlastXML2ReportData.
Definition at line 204 of file data4xml2format.hpp.
References m_isIterative.
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Initialize the score matrix to be used for formatting (if applicable)
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().
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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().
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Definition at line 157 of file data4xml2format.cpp.
References eUnknown, i, ITERATE, m_DbName, m_NumBases, m_NumSequences, and NCBI_THROW.
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Definition at line 114 of file data4xml2format.cpp.
References CSearchResults::GetAncillaryData(), CSearchResults::GetErrorStrings(), CSearchResults::GetSeqAlign(), CSearchResults::GetWarningStrings(), CSearchResults::HasAlignments(), CSearchResults::HasWarnings(), kEmptyStr, m_Alignments, m_AncillaryData, and m_Errors.
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Definition at line 174 of file data4xml2format.cpp.
References eUnknown, CAlignFormatUtil::GetSeqIdString(), i, m_SubjectIds, and NCBI_THROW.
Number of columns used in score matrices.
Definition at line 231 of file data4xml2format.hpp.
Referenced by x_FillScoreMatrix().
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the alignments
Definition at line 226 of file data4xml2format.hpp.
Referenced by GetAlignmentSet(), GetNumOfSearchResults(), and x_InitResults().
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ancillary results data
Definition at line 224 of file data4xml2format.hpp.
Referenced by GetEffectiveSearchSpace(), GetEntropy(), GetKappa(), GetLambda(), GetLengthAdjustment(), and x_InitResults().
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name of blast database
Definition at line 213 of file data4xml2format.hpp.
Referenced by GetDatabaseName(), and x_InitDB().
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Error messages.
Definition at line 228 of file data4xml2format.hpp.
Referenced by GetMessages(), and x_InitResults().
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Definition at line 219 of file data4xml2format.hpp.
Referenced by IsBl2seq().
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Definition at line 220 of file data4xml2format.hpp.
Referenced by IsIterativeSearch(), and x_InitCommon().
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Score matrix used to determine neighboring protein residues.
Definition at line 234 of file data4xml2format.hpp.
Referenced by GetMatrix(), x_FillScoreMatrix(), and ~CCmdLineBlastXML2ReportData().
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Number of bases in all BLAST databases involved in this search.
Definition at line 217 of file data4xml2format.hpp.
Referenced by GetDbLength(), and x_InitDB().
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Number of sequences in all BLAST databases involved in this search.
Definition at line 215 of file data4xml2format.hpp.
Referenced by GetDbNumSeqs(), and x_InitDB().
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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().
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Definition at line 209 of file data4xml2format.hpp.
Referenced by GetQuerySeqLoc().
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Definition at line 238 of file data4xml2format.hpp.
Referenced by GetMaskLocations().
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Definition at line 212 of file data4xml2format.hpp.
Referenced by GetScope(), and x_InitCommon().
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Definition at line 236 of file data4xml2format.hpp.
Referenced by GetSubjectIds(), and x_InitSubjects().
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Definition at line 218 of file data4xml2format.hpp.
Referenced by CanGetTaxInfo(), and x_InitCommon().