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CBlastTabularInfo Class Reference

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Class containing information needed for tabular formatting of BLAST results. More...

#include <objtools/align_format/tabular.hpp>

+ Inheritance diagram for CBlastTabularInfo:
+ Collaboration diagram for CBlastTabularInfo:

Public Types

enum  ESeqIdType { eFullId = 0 , eAccession , eAccVersion , eGi }
 In what form should the sequence identifiers be shown? More...
 
enum  EFieldDelimiter { eTab = 0 , eSpace , eComma , eCustom }
 What delimiter to use between fields in each row of the tabular output. More...
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CBlastTabularInfo (CNcbiOstream &ostr, const string &format=kDfltArgTabularOutputFmt, EFieldDelimiter delim=eTab, bool parse_local_ids=false)
 Constructor. More...
 
 ~CBlastTabularInfo ()
 Destructor. More...
 
void SetQueryId (list< CRef< objects::CSeq_id > > &id)
 Set query id from a objects::CSeq_id. More...
 
void SetQueryId (const objects::CBioseq_Handle &bh)
 Set query id from a Bioseq handle. More...
 
const list< CRef< CSeq_id > > & GetQueryId () const
 Get query seqid list. More...
 
void SetSubjectId (list< CRef< objects::CSeq_id > > &id)
 Set subject id from a objects::CSeq_id. More...
 
void SetSubjectId (const objects::CBioseq_Handle &bh)
 Set subject id from a Bioseq handle. More...
 
void SetScores (int score, double bit_score, double evalue)
 Set the HSP scores. More...
 
void SetEndpoints (int q_start, int q_end, int s_start, int s_end)
 Set the HSP endpoints. More...
 
void SetCounts (int num_ident, int length, int gaps, int gap_opens, int positives=0, int query_frame=1, int subject_frame=1)
 Set various counts/lengths. More...
 
void SetBTOP (string btop_string)
 Sets the Blast-traceback-operations string. More...
 
int SetFields (const objects::CSeq_align &sal, objects::CScope &scope, CNcbiMatrix< int > *matrix=0)
 Set all member fields, given a Seq-align. More...
 
void SetCustomDelim (string customDelim)
 
virtual void Print (void)
 Print one line of tabular output. More...
 
void PrintHeader (const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &rid=kEmptyStr, unsigned int iteration=numeric_limits< unsigned int >::max(), const objects::CSeq_align_set *align_set=0, CConstRef< objects::CBioseq > subj_bioseq=CConstRef< objects::CBioseq >())
 Print the tabular output header. More...
 
void PrintNumProcessed (int num_queries)
 Prints number of queries processed. More...
 
list< stringGetAllFieldNames (void)
 Return all field names supported in the format string. More...
 
void SetParseLocalIds (bool val)
 Should local IDs be parsed or not? More...
 
void SetParseSubjectDefline (bool val)
 Should subject deflien be parsed for id or not? More...
 
void SetNoFetch (bool nofetch)
 Avoid fetching sequence (if possible) If the sequence is needed (e.g., will be formatted, it will be fetched) More...
 
bool GetNoFetch ()
 Avoid fetch of sequence if true returned. More...
 
void SetQueryGeneticCode (int q_gc)
 
void SetDbGeneticCode (int db_gc)
 
void SetQueryRange (TSeqRange &q_range)
 Set query range. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Protected Member Functions

bool x_IsFieldRequested (ETabularField field)
 
void x_AddFieldToShow (ETabularField field)
 Add a field to the list of fields to show, if it is not yet present in the list of fields. More...
 
void x_DeleteFieldToShow (ETabularField field)
 Delete a field from the list of fields to show. More...
 
void x_AddDefaultFieldsToShow (void)
 Add a default set of fields to show. More...
 
void x_SetFieldsToShow (const string &format)
 Set fields to show, given an output format string. More...
 
void x_ResetFields (void)
 Reset values of all fields. More...
 
void x_SetFieldDelimiter (EFieldDelimiter delim, string customDelim="")
 Set the tabular fields delimiter. More...
 
void x_PrintFieldNames (void)
 Print the names of all supported fields. More...
 
void x_PrintField (ETabularField field)
 Print the value of a given field. More...
 
void x_PrintQuerySeqId (void) const
 Print query Seq-id. More...
 
void x_PrintQueryGi (void)
 Print query gi. More...
 
void x_PrintQueryAccession (void)
 Print query accession. More...
 
void x_PrintQueryAccessionVersion (void)
 Print query accession.version. More...
 
void x_PrintQueryAndDbNames (const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &rid, unsigned int iteration, CConstRef< objects::CBioseq > subj_bioseq)
 Print query and database names. More...
 
void x_PrintSubjectSeqId (void)
 Print subject Seq-id. More...
 
void x_PrintSubjectAllSeqIds (void)
 Print all Seq-ids associated with this subject, separated by ';'. More...
 
void x_PrintSubjectGi (void)
 Print subject gi. More...
 
void x_PrintSubjectAllGis (void)
 Print all gis associated with this subject, separated by ';'. More...
 
void x_PrintSubjectAccession (void)
 Print subject accession. More...
 
void x_PrintSubjectAccessionVersion (void)
 Print subject accession.version. More...
 
void x_PrintSubjectAllAccessions (void)
 Print all accessions associated with this subject, separated by ';'. More...
 
void x_PrintQuerySeq (void)
 Print aligned part of query sequence. More...
 
void x_PrintSubjectSeq (void)
 Print aligned part of subject sequence. More...
 
void x_PrintQueryStart (void)
 Print query start. More...
 
void x_PrintQueryEnd (void)
 Print query end. More...
 
void x_PrintSubjectStart (void)
 Print subject start. More...
 
void x_PrintSubjectEnd (void)
 Print subject end. More...
 
void x_PrintEvalue (void)
 Print e-value. More...
 
void x_PrintBitScore (void)
 Print bit score. More...
 
void x_PrintScore (void)
 Print raw score. More...
 
void x_PrintAlignmentLength (void)
 Print alignment length. More...
 
void x_PrintPercentIdentical (void)
 Print percent of identical matches. More...
 
void x_PrintNumIdentical (void)
 Print number of identical matches. More...
 
void x_PrintMismatches (void)
 Print number of mismatches. More...
 
void x_PrintNumPositives (void)
 Print number of positive matches. More...
 
void x_PrintGapOpenings (void)
 Print number of gap openings. More...
 
void x_PrintGaps (void)
 Print total number of gaps. More...
 
void x_PrintPercentPositives ()
 Print percent positives. More...
 
void x_PrintFrames ()
 Print frames. More...
 
void x_PrintQueryFrame ()
 
void x_PrintSubjectFrame ()
 
void x_PrintBTOP ()
 
void x_PrintQueryLength ()
 Print the query sequence length. More...
 
void x_PrintSubjectLength ()
 Print the subject sequence length. More...
 
void x_PrintSubjectTaxIds ()
 Print subject tax info. More...
 
void x_PrintSubjectSciNames ()
 
void x_PrintSubjectCommonNames ()
 
void x_PrintSubjectBlastNames ()
 
void x_PrintSubjectSuperKingdoms ()
 
void x_PrintSubjectTaxId ()
 
void x_PrintSubjectSciName ()
 
void x_PrintSubjectCommonName ()
 
void x_PrintSubjectBlastName ()
 
void x_PrintSubjectSuperKingdom ()
 
void x_PrintSubjectTitle ()
 
void x_PrintSubjectAllTitles ()
 
void x_PrintSubjectStrand ()
 
void x_PrintSeqalignCoverage ()
 
void x_PrintSubjectCoverage ()
 
void x_PrintUniqSubjectCoverage ()
 
void x_SetTaxInfo (const objects::CBioseq_Handle &handle, const CRef< objects::CBlast_def_line_set > &bdlRef)
 
void x_SetTaxInfoAll (const objects::CBioseq_Handle &handle, const CRef< objects::CBlast_def_line_set > &bdlRef)
 
void x_SetSubjectIds (const objects::CBioseq_Handle &bh, const CRef< objects::CBlast_def_line_set > &bdlRef)
 
void x_SetQueryCovSubject (const objects::CSeq_align &align)
 
void x_SetQueryCovUniqSubject (const objects::CSeq_align &align)
 
void x_SetQueryCovSeqalign (const CSeq_align &align, int query_len)
 
void x_CheckTaxDB ()
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CNcbiOstreamm_Ostream
 Stream to write output to. More...
 
string m_FieldDelimiter
 Delimiter character for fields to print. More...
 
string m_QuerySeq
 Aligned part of the query sequence. More...
 
string m_SubjectSeq
 Aligned part of the subject sequence. More...
 
int m_QueryStart
 Starting offset in query. More...
 
int m_QueryEnd
 Ending offset in query. More...
 
int m_QueryFrame
 query frame More...
 
int m_SubjectStart
 Starting offset in subject. More...
 
int m_SubjectEnd
 Ending offset in subject. More...
 
int m_SubjectFrame
 subject frame More...
 
bool m_NoFetch
 program as a string More...
 

Private Attributes

list< CRef< objects::CSeq_id > > m_QueryId
 List of query ids for this HSP. More...
 
list< CRef< objects::CSeq_id > > m_SubjectId
 
vector< list< CRef< objects::CSeq_id > > > m_SubjectIds
 All subject sequence ids for this HSP. More...
 
TSeqPos m_QueryLength
 Length of query sequence. More...
 
TSeqPos m_SubjectLength
 Length of subject sequence. More...
 
int m_Score
 Raw score of this HSP. More...
 
string m_BitScore
 Bit score of this HSP, in appropriate format. More...
 
string m_Evalue
 E-value of this HSP, in appropriate format. More...
 
int m_AlignLength
 Alignment length of this HSP. More...
 
int m_NumGaps
 Total number of gaps in this HSP. More...
 
int m_NumGapOpens
 Number of gap openings in this HSP. More...
 
int m_NumIdent
 Number of identities in this HSP. More...
 
int m_NumPositives
 Number of positives in this HSP. More...
 
map< string, ETabularFieldm_FieldMap
 Map of field enum values to field names. More...
 
list< ETabularFieldm_FieldsToShow
 Which fields to show? More...
 
bool m_ParseLocalIds
 Should the query deflines be parsed for local IDs? More...
 
bool m_ParseSubjectDefline
 Parse subejct defline? More...
 
string m_BTOP
 
set< TTaxIdm_SubjectTaxIds
 Blast-traceback-operations. More...
 
vector< stringm_SubjectSciNames
 
vector< stringm_SubjectCommonNames
 
set< stringm_SubjectBlastNames
 
set< stringm_SubjectSuperKingdoms
 
TTaxId m_SubjectTaxId
 
string m_SubjectSciName
 
string m_SubjectCommonName
 
string m_SubjectBlastName
 
string m_SubjectSuperKingdom
 
CRef< CBlast_def_line_setm_SubjectDefline
 
string m_SubjectStrand
 
pair< string, intm_QueryCovSubject
 
pair< string, intm_QueryCovUniqSubject
 
int m_QueryCovSeqalign
 
int m_QueryGeneticCode
 
int m_DbGeneticCode
 
TSeqRange m_QueryRange
 
string m_CustomDelim
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Detailed Description

Class containing information needed for tabular formatting of BLAST results.

Definition at line 54 of file tabular.hpp.

Member Enumeration Documentation

◆ EFieldDelimiter

What delimiter to use between fields in each row of the tabular output.

Enumerator
eTab 

Tab.

eSpace 

Space.

eComma 

Comma.

eCustom 

Custom.

Definition at line 66 of file tabular.hpp.

◆ ESeqIdType

In what form should the sequence identifiers be shown?

Enumerator
eFullId 

Show full seq-id, with multiple ids concatenated.

eAccession 

Show only best accession.

eAccVersion 

Show only best accession.version.

eGi 

Show only gi.

Definition at line 58 of file tabular.hpp.

Constructor & Destructor Documentation

◆ CBlastTabularInfo()

CBlastTabularInfo::CBlastTabularInfo ( CNcbiOstream ostr,
const string format = kDfltArgTabularOutputFmt,
EFieldDelimiter  delim = eTab,
bool  parse_local_ids = false 
)

Constructor.

Parameters
ostrStream to write output to [in]
formatOutput format - what fields to include in the output [in]
delimDelimiter to use between tabular fields [in]
Note
fields that are not recognized will be ignored, if no fields are specified (or left after purging those that are not recognized), the default format is assumed

Definition at line 139 of file tabular.cpp.

References format, m_DbGeneticCode, m_QueryCovSubject, m_QueryCovUniqSubject, m_QueryGeneticCode, NA, SetNoFetch(), SetParseLocalIds(), SetParseSubjectDefline(), x_CheckTaxDB(), x_ResetFields(), x_SetFieldDelimiter(), and x_SetFieldsToShow().

◆ ~CBlastTabularInfo()

CBlastTabularInfo::~CBlastTabularInfo ( )

Destructor.

Definition at line 160 of file tabular.cpp.

References m_Ostream.

Member Function Documentation

◆ GetAllFieldNames()

list< string > CBlastTabularInfo::GetAllFieldNames ( void  )

Return all field names supported in the format string.

Definition at line 1339 of file tabular.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), and m_FieldMap.

◆ GetNoFetch()

bool CBlastTabularInfo::GetNoFetch ( void  )
inline

Avoid fetch of sequence if true returned.

Definition at line 507 of file tabular.hpp.

References m_NoFetch.

Referenced by SetFields().

◆ GetQueryId()

const list<CRef<CSeq_id> >& CBlastTabularInfo::GetQueryId ( void  ) const
inline

Get query seqid list.

Definition at line 94 of file tabular.hpp.

Referenced by CIgBlastTabularInfo::SetAirrFormatData().

◆ Print()

void CBlastTabularInfo::Print ( void  )
virtual

Print one line of tabular output.

Reimplemented in CIgBlastTabularInfo.

Definition at line 1094 of file tabular.cpp.

References ITERATE, m_FieldDelimiter, m_FieldsToShow, m_Ostream, and x_PrintField().

Referenced by BOOST_AUTO_TEST_CASE(), CIgBlastTabularInfo::Print(), and CBlastFormat::x_PrintTabularReport().

◆ PrintHeader()

void CBlastTabularInfo::PrintHeader ( const string program,
const objects::CBioseq &  bioseq,
const string dbname,
const string rid = kEmptyStr,
unsigned int  iteration = numeric_limits<unsigned int>::max(),
const objects::CSeq_align_set *  align_set = 0,
CConstRef< objects::CBioseq >  subj_bioseq = CConstRef<objects::CBioseq>() 
)

Print the tabular output header.

Parameters
programProgram name to show in the header [in]
bioseqQuery Bioseq [in]
dbnameSearch database name [in]
ridthe search RID (if not applicable, it should be empty the string) [in]
iterationIteration number (for PSI-BLAST), use default parameter value when not applicable [in]
align_setAll alignments for this query [in]

Definition at line 1225 of file tabular.cpp.

References dbname(), CSeq_align_set_Base::Get(), m_Ostream, x_PrintFieldNames(), and x_PrintQueryAndDbNames().

Referenced by CBlastFormat::x_PrintTabularReport().

◆ PrintNumProcessed()

void CBlastTabularInfo::PrintNumProcessed ( int  num_queries)

Prints number of queries processed.

Parameters
num_queriesnumber of queries processed [in]

Definition at line 1280 of file tabular.cpp.

References m_Ostream.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastFormat::PrintEpilog().

◆ SetBTOP()

void CBlastTabularInfo::SetBTOP ( string  btop_string)

Sets the Blast-traceback-operations string.

Parameters
btop_stringstring for blast traceback operations [in]

Definition at line 1308 of file tabular.cpp.

References m_BTOP.

Referenced by SetFields().

◆ SetCounts()

void CBlastTabularInfo::SetCounts ( int  num_ident,
int  length,
int  gaps,
int  gap_opens,
int  positives = 0,
int  query_frame = 1,
int  subject_frame = 1 
)

Set various counts/lengths.

Parameters
num_identNumber of identities [in]
lengthAlignment length [in]
gapsTotal number of gaps [in]
gap_opensNumber of gap openings [in]
positivesNumber of positives [in]

Definition at line 1314 of file tabular.cpp.

References m_AlignLength, m_NumGapOpens, m_NumGaps, m_NumIdent, m_NumPositives, m_QueryFrame, and m_SubjectFrame.

Referenced by SetFields().

◆ SetCustomDelim()

void CBlastTabularInfo::SetCustomDelim ( string  customDelim)
inline

Definition at line 135 of file tabular.hpp.

Referenced by CBlastFormat::x_PrintTabularReport().

◆ SetDbGeneticCode()

void CBlastTabularInfo::SetDbGeneticCode ( int  db_gc)
inline

Definition at line 185 of file tabular.hpp.

Referenced by CBlastFormat::x_PrintTabularReport().

◆ SetEndpoints()

void CBlastTabularInfo::SetEndpoints ( int  q_start,
int  q_end,
int  s_start,
int  s_end 
)

Set the HSP endpoints.

Note that if alignment is on opposite strands, the subject offsets must be reversed.

Parameters
q_startStarting offset in query [in]
q_endEnding offset in query [in]
s_startStarting offset in subject [in]
s_endEnding offset in subject [in]

Definition at line 1299 of file tabular.cpp.

References m_QueryEnd, m_QueryStart, m_SubjectEnd, and m_SubjectStart.

Referenced by SetFields().

◆ SetFields()

int CBlastTabularInfo::SetFields ( const objects::CSeq_align &  sal,
objects::CScope &  scope,
CNcbiMatrix< int > *  matrix = 0 
)

Set all member fields, given a Seq-align.

Parameters
salSeq-align to get data from [in]
scopeScope for Bioseq retrieval [in]
matrixMatrix to calculate positives; NULL if not applicable. [in]
Returns
0 on success, 1 if query or subject Bioseq is not found.

Definition at line 743 of file tabular.cpp.

References CDense_seg::Assign(), CAlignFormatUtil::CreateDensegFromDendiag(), CSeq_align::CreateDensegFromStdseg(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CSeq_data_Base::e_Ncbieaa, eAlignmentLength, eBitScore, eBTOP, eEvalue, eFrames, eGapOpenings, eGaps, eMismatches, eNa_strand_minus, eNumIdentical, ePercentIdentical, ePercentPositives, ePositives, eQueryAccession, eQueryAccessionVersion, eQueryCovSeqalign, eQueryCovSubject, eQueryCovUniqSubject, eQueryEnd, eQueryFrame, eQueryGi, eQueryLength, eQuerySeq, eQuerySeqId, eQueryStart, eScore, eSubjAccessionVersion, eSubjectAccession, eSubjectAllAccessions, eSubjectAllGis, eSubjectAllSeqIds, eSubjectAllTitles, eSubjectBlastName, eSubjectBlastNames, eSubjectCommonName, eSubjectCommonNames, eSubjectEnd, eSubjectGi, eSubjectLength, eSubjectSciName, eSubjectSciNames, eSubjectSeq, eSubjectSeqId, eSubjectStart, eSubjectStrand, eSubjectSuperKingdom, eSubjectSuperKingdoms, eSubjectTaxId, eSubjectTaxIds, eSubjectTitle, eSubjFrame, CSeqDB::ExtractBlastDefline(), CAlignFormatUtil::GetAlignLengths(), CAlignFormatUtil::GetAlnScores(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CNcbiMatrix< T >::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CAlignFormatUtil::GetFrame(), GetLength(), COpenRange< Position >::GetLength(), GetNoFetch(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CAlnMap::GetSeqStart(), CAlnMap::GetSeqStop(), CDense_seg::GetSeqStrand(), CScope::GetSequenceType(), CDense_seg_Base::GetStrands(), CAlnVec::GetWholeAlnSeqString(), i, NStr::Int8ToString(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_inst::IsNa(), CDense_seg_Base::IsSetStrands(), CSeq_align_Base::C_Segs::IsStd(), m_DbGeneticCode, m_QueryGeneticCode, m_QueryLength, m_QueryRange, m_QuerySeq, m_SubjectDefline, m_SubjectLength, m_SubjectSeq, m_SubjectStrand, min(), NA, COpenRange< Position >::NotEmpty(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CDense_seg::Reverse(), CAlnVec::SetAaCoding(), SetBTOP(), SetCounts(), SetEndpoints(), CAlnVec::SetGapChar(), CAlnVec::SetGenCode(), SetQueryId(), SetScores(), SetSubjectId(), x_IsFieldRequested(), x_ResetFields(), x_SetQueryCovSeqalign(), x_SetQueryCovSubject(), x_SetQueryCovUniqSubject(), x_SetSubjectIds(), x_SetTaxInfo(), and x_SetTaxInfoAll().

Referenced by BOOST_AUTO_TEST_CASE(), CIgBlastTabularInfo::SetFields(), and CBlastFormat::x_PrintTabularReport().

◆ SetNoFetch()

void CBlastTabularInfo::SetNoFetch ( bool  nofetch)
inline

Avoid fetching sequence (if possible) If the sequence is needed (e.g., will be formatted, it will be fetched)

Parameters
nofetchDo not fetch if true [in]

Definition at line 502 of file tabular.hpp.

References m_NoFetch.

Referenced by CBlastTabularInfo(), and CBlastFormat::x_PrintTabularReport().

◆ SetParseLocalIds()

void CBlastTabularInfo::SetParseLocalIds ( bool  val)
inline

Should local IDs be parsed or not?

Parameters
valvalue to set [in] Returns true if the field was requested in the format specification
fieldWhich field to test [in]

Definition at line 170 of file tabular.hpp.

References val.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastTabularInfo(), CBlastFormat::PrintOneResultSet(), CBlastFormat::x_PrintAirrRearrangement(), CBlastFormat::x_PrintIgTabularReport(), and CBlastFormat::x_PrintTabularReport().

◆ SetParseSubjectDefline()

void CBlastTabularInfo::SetParseSubjectDefline ( bool  val)
inline

Should subject deflien be parsed for id or not?

Parameters
valvalue to set [in]

Definition at line 174 of file tabular.hpp.

References val.

Referenced by CBlastTabularInfo(), and CBlastFormat::x_PrintTabularReport().

◆ SetQueryGeneticCode()

void CBlastTabularInfo::SetQueryGeneticCode ( int  q_gc)
inline

Definition at line 184 of file tabular.hpp.

Referenced by CBlastFormat::x_PrintTabularReport().

◆ SetQueryId() [1/2]

void CBlastTabularInfo::SetQueryId ( const objects::CBioseq_Handle &  bh)

Set query id from a Bioseq handle.

Parameters
bhBioseq handle to get Seq-ids from

◆ SetQueryId() [2/2]

void CBlastTabularInfo::SetQueryId ( list< CRef< objects::CSeq_id > > &  id)

Set query id from a objects::CSeq_id.

Parameters
idList of Seq-ids to use [in]

Referenced by CIgBlastTabularInfo::SetAirrFormatData(), SetFields(), and CIgBlastTabularInfo::SetIgAnnotation().

◆ SetQueryRange()

void CBlastTabularInfo::SetQueryRange ( TSeqRange q_range)
inline

Set query range.

Parameters
queryrange [in]

Definition at line 189 of file tabular.hpp.

Referenced by CBlastFormat::x_PrintTabularReport().

◆ SetScores()

void CBlastTabularInfo::SetScores ( int  score,
double  bit_score,
double  evalue 
)

Set the HSP scores.

Parameters
scoreRaw score [in]
bit_scoreBit score [in]
evalueExpect value [in]

Definition at line 1286 of file tabular.cpp.

References NStr::DoubleToString(), NStr::fDoubleScientific, CAlignFormatUtil::GetScoreString(), m_BitScore, m_Evalue, and m_Score.

Referenced by SetFields().

◆ SetSubjectId() [1/2]

void CBlastTabularInfo::SetSubjectId ( const objects::CBioseq_Handle &  bh)

Set subject id from a Bioseq handle.

Parameters
bhBioseq handle to get Seq-ids from

◆ SetSubjectId() [2/2]

void CBlastTabularInfo::SetSubjectId ( list< CRef< objects::CSeq_id > > &  id)

Set subject id from a objects::CSeq_id.

Parameters
idList of Seq-ids to use [in]

Referenced by SetFields().

◆ x_AddDefaultFieldsToShow()

void CBlastTabularInfo::x_AddDefaultFieldsToShow ( void  )
protected

Add a default set of fields to show.

Definition at line 60 of file tabular.cpp.

References _ASSERT, ITERATE, kDfltArgTabularOutputFmt, and NStr::Split().

Referenced by x_SetFieldsToShow().

◆ x_AddFieldToShow()

void CBlastTabularInfo::x_AddFieldToShow ( ETabularField  field)
protected

Add a field to the list of fields to show, if it is not yet present in the list of fields.

Parameters
fieldWhich field to add? [in]

Definition at line 1351 of file tabular.cpp.

References m_FieldsToShow, and x_IsFieldRequested().

Referenced by CIgBlastTabularInfo::SetMasterFields(), and x_SetFieldsToShow().

◆ x_CheckTaxDB()

void CBlastTabularInfo::x_CheckTaxDB ( )
protected

◆ x_DeleteFieldToShow()

void CBlastTabularInfo::x_DeleteFieldToShow ( ETabularField  field)
protected

Delete a field from the list of fields to show.

Parameters
fieldWhich field to delete? [in]

Definition at line 1359 of file tabular.cpp.

References m_FieldsToShow.

Referenced by CIgBlastTabularInfo::SetMasterFields(), and x_SetFieldsToShow().

◆ x_IsFieldRequested()

bool CBlastTabularInfo::x_IsFieldRequested ( ETabularField  field)
inlineprotected

◆ x_PrintAlignmentLength()

void CBlastTabularInfo::x_PrintAlignmentLength ( void  )
inlineprotected

Print alignment length.

Definition at line 420 of file tabular.hpp.

References m_AlignLength, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintBitScore()

void CBlastTabularInfo::x_PrintBitScore ( void  )
inlineprotected

Print bit score.

Definition at line 410 of file tabular.hpp.

References m_BitScore, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintBTOP()

void CBlastTabularInfo::x_PrintBTOP ( void  )
inlineprotected

Definition at line 454 of file tabular.hpp.

References m_BTOP, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintEvalue()

void CBlastTabularInfo::x_PrintEvalue ( void  )
inlineprotected

Print e-value.

Definition at line 405 of file tabular.hpp.

References m_Evalue, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintField()

void CBlastTabularInfo::x_PrintField ( ETabularField  field)
protected

Print the value of a given field.

Parameters
fieldWhich field to show? [in]

Definition at line 1369 of file tabular.cpp.

References _ASSERT, eAlignmentLength, eBitScore, eBTOP, eEvalue, eFrames, eGapOpenings, eGaps, eMismatches, eNumIdentical, ePercentIdentical, ePercentPositives, ePositives, eQueryAccession, eQueryAccessionVersion, eQueryCovSeqalign, eQueryCovSubject, eQueryCovUniqSubject, eQueryEnd, eQueryFrame, eQueryGi, eQueryLength, eQuerySeq, eQuerySeqId, eQueryStart, eScore, eSubjAccessionVersion, eSubjectAccession, eSubjectAllAccessions, eSubjectAllGis, eSubjectAllSeqIds, eSubjectAllTitles, eSubjectBlastName, eSubjectBlastNames, eSubjectCommonName, eSubjectCommonNames, eSubjectEnd, eSubjectGi, eSubjectLength, eSubjectSciName, eSubjectSciNames, eSubjectSeq, eSubjectSeqId, eSubjectStart, eSubjectStrand, eSubjectSuperKingdom, eSubjectSuperKingdoms, eSubjectTaxId, eSubjectTaxIds, eSubjectTitle, eSubjFrame, x_PrintAlignmentLength(), x_PrintBitScore(), x_PrintBTOP(), x_PrintEvalue(), x_PrintFrames(), x_PrintGapOpenings(), x_PrintGaps(), x_PrintMismatches(), x_PrintNumIdentical(), x_PrintNumPositives(), x_PrintPercentIdentical(), x_PrintPercentPositives(), x_PrintQueryAccession(), x_PrintQueryAccessionVersion(), x_PrintQueryEnd(), x_PrintQueryFrame(), x_PrintQueryGi(), x_PrintQueryLength(), x_PrintQuerySeq(), x_PrintQuerySeqId(), x_PrintQueryStart(), x_PrintScore(), x_PrintSeqalignCoverage(), x_PrintSubjectAccession(), x_PrintSubjectAccessionVersion(), x_PrintSubjectAllAccessions(), x_PrintSubjectAllGis(), x_PrintSubjectAllSeqIds(), x_PrintSubjectAllTitles(), x_PrintSubjectBlastName(), x_PrintSubjectBlastNames(), x_PrintSubjectCommonName(), x_PrintSubjectCommonNames(), x_PrintSubjectCoverage(), x_PrintSubjectEnd(), x_PrintSubjectFrame(), x_PrintSubjectGi(), x_PrintSubjectLength(), x_PrintSubjectSciName(), x_PrintSubjectSciNames(), x_PrintSubjectSeq(), x_PrintSubjectSeqId(), x_PrintSubjectStart(), x_PrintSubjectStrand(), x_PrintSubjectSuperKingdom(), x_PrintSubjectSuperKingdoms(), x_PrintSubjectTaxId(), x_PrintSubjectTaxIds(), x_PrintSubjectTitle(), and x_PrintUniqSubjectCoverage().

Referenced by Print().

◆ x_PrintFieldNames()

void CBlastTabularInfo::x_PrintFieldNames ( void  )
protected

◆ x_PrintFrames()

void CBlastTabularInfo::x_PrintFrames ( void  )
inlineprotected

Print frames.

Definition at line 439 of file tabular.hpp.

References m_Ostream, m_QueryFrame, and m_SubjectFrame.

Referenced by x_PrintField().

◆ x_PrintGapOpenings()

void CBlastTabularInfo::x_PrintGapOpenings ( void  )
inlineprotected

Print number of gap openings.

Definition at line 483 of file tabular.hpp.

References m_NumGapOpens, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintGaps()

void CBlastTabularInfo::x_PrintGaps ( void  )
inlineprotected

Print total number of gaps.

Definition at line 488 of file tabular.hpp.

References m_NumGaps, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintMismatches()

void CBlastTabularInfo::x_PrintMismatches ( void  )
inlineprotected

Print number of mismatches.

Definition at line 464 of file tabular.hpp.

References m_AlignLength, m_NumGaps, m_NumIdent, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintNumIdentical()

void CBlastTabularInfo::x_PrintNumIdentical ( void  )
inlineprotected

Print number of identical matches.

Definition at line 459 of file tabular.hpp.

References m_NumIdent, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintNumPositives()

void CBlastTabularInfo::x_PrintNumPositives ( void  )
inlineprotected

Print number of positive matches.

Definition at line 470 of file tabular.hpp.

References m_NumPositives, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintPercentIdentical()

void CBlastTabularInfo::x_PrintPercentIdentical ( void  )
inlineprotected

Print percent of identical matches.

Definition at line 425 of file tabular.hpp.

References NStr::DoubleToString(), m_AlignLength, m_NumIdent, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintPercentPositives()

void CBlastTabularInfo::x_PrintPercentPositives ( void  )
inlineprotected

Print percent positives.

Definition at line 432 of file tabular.hpp.

References NStr::DoubleToString(), m_AlignLength, m_NumPositives, and m_Ostream.

Referenced by x_PrintField().

◆ x_PrintQueryAccession()

void CBlastTabularInfo::x_PrintQueryAccession ( void  )
protected

Print query accession.

Definition at line 209 of file tabular.cpp.

References eAccession, m_Ostream, m_QueryId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintQueryAccessionVersion()

void CBlastTabularInfo::x_PrintQueryAccessionVersion ( void  )
protected

Print query accession.version.

Definition at line 214 of file tabular.cpp.

References eAccVersion, m_Ostream, m_QueryId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintQueryAndDbNames()

void CBlastTabularInfo::x_PrintQueryAndDbNames ( const string program,
const objects::CBioseq &  bioseq,
const string dbname,
const string rid,
unsigned int  iteration,
CConstRef< objects::CBioseq >  subj_bioseq 
)
protected

◆ x_PrintQueryEnd()

void CBlastTabularInfo::x_PrintQueryEnd ( void  )
inlineprotected

Print query end.

Definition at line 390 of file tabular.hpp.

References m_Ostream, and m_QueryEnd.

Referenced by x_PrintField().

◆ x_PrintQueryFrame()

void CBlastTabularInfo::x_PrintQueryFrame ( void  )
inlineprotected

Definition at line 444 of file tabular.hpp.

References m_Ostream, and m_QueryFrame.

Referenced by x_PrintField().

◆ x_PrintQueryGi()

void CBlastTabularInfo::x_PrintQueryGi ( void  )
protected

Print query gi.

Definition at line 204 of file tabular.cpp.

References eGi, m_Ostream, m_QueryId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintQueryLength()

void CBlastTabularInfo::x_PrintQueryLength ( void  )
inlineprotected

Print the query sequence length.

Definition at line 492 of file tabular.hpp.

References m_Ostream, and m_QueryLength.

Referenced by x_PrintField().

◆ x_PrintQuerySeq()

void CBlastTabularInfo::x_PrintQuerySeq ( void  )
inlineprotected

Print aligned part of query sequence.

Definition at line 375 of file tabular.hpp.

References m_Ostream, and m_QuerySeq.

Referenced by x_PrintField().

◆ x_PrintQuerySeqId()

void CBlastTabularInfo::x_PrintQuerySeqId ( void  ) const
protected

Print query Seq-id.

Definition at line 199 of file tabular.cpp.

References eFullId, m_Ostream, m_QueryId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintQueryStart()

void CBlastTabularInfo::x_PrintQueryStart ( void  )
inlineprotected

Print query start.

Definition at line 385 of file tabular.hpp.

References m_Ostream, and m_QueryStart.

Referenced by x_PrintField().

◆ x_PrintScore()

void CBlastTabularInfo::x_PrintScore ( void  )
inlineprotected

Print raw score.

Definition at line 415 of file tabular.hpp.

References m_Ostream, and m_Score.

Referenced by x_PrintField().

◆ x_PrintSeqalignCoverage()

void CBlastTabularInfo::x_PrintSeqalignCoverage ( void  )
protected

Definition at line 460 of file tabular.cpp.

References NStr::IntToString(), m_Ostream, m_QueryCovSeqalign, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectAccession()

void CBlastTabularInfo::x_PrintSubjectAccession ( void  )
protected

Print subject accession.

Definition at line 247 of file tabular.cpp.

References eAccession, m_Ostream, m_SubjectId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectAccessionVersion()

void CBlastTabularInfo::x_PrintSubjectAccessionVersion ( void  )
protected

Print subject accession.version.

Definition at line 252 of file tabular.cpp.

References eAccVersion, m_Ostream, m_SubjectId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectAllAccessions()

void CBlastTabularInfo::x_PrintSubjectAllAccessions ( void  )
protected

Print all accessions associated with this subject, separated by ';'.

Definition at line 257 of file tabular.cpp.

References eAccession, ITERATE, m_Ostream, m_SubjectIds, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectAllGis()

void CBlastTabularInfo::x_PrintSubjectAllGis ( void  )
protected

Print all gis associated with this subject, separated by ';'.

Definition at line 238 of file tabular.cpp.

References eGi, ITERATE, m_Ostream, m_SubjectIds, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectAllSeqIds()

void CBlastTabularInfo::x_PrintSubjectAllSeqIds ( void  )
protected

Print all Seq-ids associated with this subject, separated by ';'.

Definition at line 224 of file tabular.cpp.

References eFullId, ITERATE, m_Ostream, m_SubjectIds, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectAllTitles()

void CBlastTabularInfo::x_PrintSubjectAllTitles ( )
protected

◆ x_PrintSubjectBlastName()

void CBlastTabularInfo::x_PrintSubjectBlastName ( )
protected

Definition at line 289 of file tabular.cpp.

References kEmptyStr, m_Ostream, m_SubjectBlastName, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectBlastNames()

void CBlastTabularInfo::x_PrintSubjectBlastNames ( )
protected

◆ x_PrintSubjectCommonName()

void CBlastTabularInfo::x_PrintSubjectCommonName ( )
protected

Definition at line 358 of file tabular.cpp.

References kEmptyStr, m_Ostream, m_SubjectCommonName, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectCommonNames()

void CBlastTabularInfo::x_PrintSubjectCommonNames ( )
protected

Definition at line 367 of file tabular.cpp.

References ITERATE, m_Ostream, m_SubjectCommonNames, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectCoverage()

void CBlastTabularInfo::x_PrintSubjectCoverage ( void  )
protected

Definition at line 444 of file tabular.cpp.

References NStr::IntToString(), m_Ostream, m_QueryCovSubject, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectEnd()

void CBlastTabularInfo::x_PrintSubjectEnd ( void  )
inlineprotected

Print subject end.

Definition at line 400 of file tabular.hpp.

References m_Ostream, and m_SubjectEnd.

Referenced by x_PrintField().

◆ x_PrintSubjectFrame()

void CBlastTabularInfo::x_PrintSubjectFrame ( void  )
inlineprotected

Definition at line 449 of file tabular.hpp.

References m_Ostream, and m_SubjectFrame.

Referenced by x_PrintField().

◆ x_PrintSubjectGi()

void CBlastTabularInfo::x_PrintSubjectGi ( void  )
protected

Print subject gi.

Definition at line 233 of file tabular.cpp.

References eGi, m_Ostream, m_SubjectId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectLength()

void CBlastTabularInfo::x_PrintSubjectLength ( void  )
inlineprotected

Print the subject sequence length.

Definition at line 497 of file tabular.hpp.

References m_Ostream, and m_SubjectLength.

Referenced by x_PrintField().

◆ x_PrintSubjectSciName()

void CBlastTabularInfo::x_PrintSubjectSciName ( )
protected

Definition at line 335 of file tabular.cpp.

References kEmptyStr, m_Ostream, m_SubjectSciName, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectSciNames()

void CBlastTabularInfo::x_PrintSubjectSciNames ( )
protected

Definition at line 344 of file tabular.cpp.

References ITERATE, m_Ostream, m_SubjectSciNames, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectSeq()

void CBlastTabularInfo::x_PrintSubjectSeq ( void  )
inlineprotected

Print aligned part of subject sequence.

Definition at line 380 of file tabular.hpp.

References m_Ostream, and m_SubjectSeq.

Referenced by x_PrintField().

◆ x_PrintSubjectSeqId()

void CBlastTabularInfo::x_PrintSubjectSeqId ( void  )
protected

Print subject Seq-id.

Definition at line 219 of file tabular.cpp.

References eFullId, m_Ostream, m_SubjectId, and s_GetSeqIdListString().

Referenced by x_PrintField().

◆ x_PrintSubjectStart()

void CBlastTabularInfo::x_PrintSubjectStart ( void  )
inlineprotected

Print subject start.

Definition at line 395 of file tabular.hpp.

References m_Ostream, and m_SubjectStart.

Referenced by x_PrintField().

◆ x_PrintSubjectStrand()

void CBlastTabularInfo::x_PrintSubjectStrand ( )
protected

Definition at line 436 of file tabular.cpp.

References m_Ostream, m_SubjectStrand, NA, and NcbiEmptyString.

Referenced by x_PrintField().

◆ x_PrintSubjectSuperKingdom()

void CBlastTabularInfo::x_PrintSubjectSuperKingdom ( )
protected

Definition at line 312 of file tabular.cpp.

References kEmptyStr, m_Ostream, m_SubjectSuperKingdom, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectSuperKingdoms()

void CBlastTabularInfo::x_PrintSubjectSuperKingdoms ( )
protected

◆ x_PrintSubjectTaxId()

void CBlastTabularInfo::x_PrintSubjectTaxId ( )
protected

Definition at line 266 of file tabular.cpp.

References m_Ostream, m_SubjectTaxId, NA, and ZERO_TAX_ID.

Referenced by x_PrintField().

◆ x_PrintSubjectTaxIds()

void CBlastTabularInfo::x_PrintSubjectTaxIds ( )
protected

Print subject tax info.

Definition at line 275 of file tabular.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::empty(), ITERATE, m_Ostream, m_SubjectTaxIds, and NA.

Referenced by x_PrintField().

◆ x_PrintSubjectTitle()

void CBlastTabularInfo::x_PrintSubjectTitle ( )
protected

◆ x_PrintUniqSubjectCoverage()

void CBlastTabularInfo::x_PrintUniqSubjectCoverage ( void  )
protected

Definition at line 452 of file tabular.cpp.

References NStr::IntToString(), m_Ostream, m_QueryCovUniqSubject, and NA.

Referenced by x_PrintField().

◆ x_ResetFields()

void CBlastTabularInfo::x_ResetFields ( void  )
protected

◆ x_SetFieldDelimiter()

void CBlastTabularInfo::x_SetFieldDelimiter ( EFieldDelimiter  delim,
string  customDelim = "" 
)
protected

Set the tabular fields delimiter.

Parameters
delimWhich delimiter to use

Definition at line 116 of file tabular.cpp.

References eComma, eCustom, eSpace, and m_FieldDelimiter.

Referenced by CBlastTabularInfo().

◆ x_SetFieldsToShow()

void CBlastTabularInfo::x_SetFieldsToShow ( const string format)
protected

Set fields to show, given an output format string.

Parameters
formatOutput format [in]

Definition at line 70 of file tabular.cpp.

References format, i, map_checker< Container >::insert(), ITERATE, kDfltArgTabularOutputFmtTag, kNumTabularOutputFormatSpecifiers, m_FieldMap, m_FieldsToShow, sc_FormatSpecifiers, NStr::Split(), x_AddDefaultFieldsToShow(), x_AddFieldToShow(), and x_DeleteFieldToShow().

Referenced by CBlastTabularInfo().

◆ x_SetQueryCovSeqalign()

void CBlastTabularInfo::x_SetQueryCovSeqalign ( const CSeq_align align,
int  query_len 
)
protected

◆ x_SetQueryCovSubject()

void CBlastTabularInfo::x_SetQueryCovSubject ( const objects::CSeq_align &  align)
protected

◆ x_SetQueryCovUniqSubject()

void CBlastTabularInfo::x_SetQueryCovUniqSubject ( const objects::CSeq_align &  align)
protected

◆ x_SetSubjectIds()

void CBlastTabularInfo::x_SetSubjectIds ( const objects::CBioseq_Handle &  bh,
const CRef< objects::CBlast_def_line_set > &  bdlRef 
)
protected

◆ x_SetTaxInfo()

void CBlastTabularInfo::x_SetTaxInfo ( const objects::CBioseq_Handle &  handle,
const CRef< objects::CBlast_def_line_set > &  bdlRef 
)
protected

◆ x_SetTaxInfoAll()

void CBlastTabularInfo::x_SetTaxInfoAll ( const objects::CBioseq_Handle &  handle,
const CRef< objects::CBlast_def_line_set > &  bdlRef 
)
protected

Member Data Documentation

◆ m_AlignLength

int CBlastTabularInfo::m_AlignLength
private

Alignment length of this HSP.

Definition at line 335 of file tabular.hpp.

Referenced by SetCounts(), x_PrintAlignmentLength(), x_PrintMismatches(), x_PrintPercentIdentical(), x_PrintPercentPositives(), and x_ResetFields().

◆ m_BitScore

string CBlastTabularInfo::m_BitScore
private

Bit score of this HSP, in appropriate format.

Definition at line 333 of file tabular.hpp.

Referenced by SetScores(), x_PrintBitScore(), and x_ResetFields().

◆ m_BTOP

string CBlastTabularInfo::m_BTOP
private

Definition at line 347 of file tabular.hpp.

Referenced by SetBTOP(), x_PrintBTOP(), and x_ResetFields().

◆ m_CustomDelim

string CBlastTabularInfo::m_CustomDelim
private

Definition at line 371 of file tabular.hpp.

◆ m_DbGeneticCode

int CBlastTabularInfo::m_DbGeneticCode
private

Definition at line 368 of file tabular.hpp.

Referenced by CBlastTabularInfo(), and SetFields().

◆ m_Evalue

string CBlastTabularInfo::m_Evalue
private

E-value of this HSP, in appropriate format.

Definition at line 334 of file tabular.hpp.

Referenced by SetScores(), x_PrintEvalue(), and x_ResetFields().

◆ m_FieldDelimiter

string CBlastTabularInfo::m_FieldDelimiter
protected

◆ m_FieldMap

map<string, ETabularField> CBlastTabularInfo::m_FieldMap
private

Map of field enum values to field names.

Definition at line 341 of file tabular.hpp.

Referenced by GetAllFieldNames(), and x_SetFieldsToShow().

◆ m_FieldsToShow

list<ETabularField> CBlastTabularInfo::m_FieldsToShow
private

Which fields to show?

Definition at line 342 of file tabular.hpp.

Referenced by Print(), x_AddFieldToShow(), x_DeleteFieldToShow(), x_IsFieldRequested(), x_PrintFieldNames(), and x_SetFieldsToShow().

◆ m_NoFetch

bool CBlastTabularInfo::m_NoFetch
protected

program as a string

Definition at line 322 of file tabular.hpp.

Referenced by GetNoFetch(), and SetNoFetch().

◆ m_NumGapOpens

int CBlastTabularInfo::m_NumGapOpens
private

Number of gap openings in this HSP.

Definition at line 337 of file tabular.hpp.

Referenced by SetCounts(), x_PrintGapOpenings(), and x_ResetFields().

◆ m_NumGaps

int CBlastTabularInfo::m_NumGaps
private

Total number of gaps in this HSP.

Definition at line 336 of file tabular.hpp.

Referenced by SetCounts(), x_PrintGaps(), x_PrintMismatches(), and x_ResetFields().

◆ m_NumIdent

int CBlastTabularInfo::m_NumIdent
private

Number of identities in this HSP.

Definition at line 338 of file tabular.hpp.

Referenced by SetCounts(), x_PrintMismatches(), x_PrintNumIdentical(), x_PrintPercentIdentical(), and x_ResetFields().

◆ m_NumPositives

int CBlastTabularInfo::m_NumPositives
private

Number of positives in this HSP.

Definition at line 339 of file tabular.hpp.

Referenced by SetCounts(), x_PrintNumPositives(), x_PrintPercentPositives(), and x_ResetFields().

◆ m_Ostream

CNcbiOstream& CBlastTabularInfo::m_Ostream
protected

Stream to write output to.

Definition at line 312 of file tabular.hpp.

Referenced by Print(), CIgBlastTabularInfo::Print(), CIgBlastTabularInfo::PrintAirrRearrangement(), CIgBlastTabularInfo::PrintHeader(), PrintHeader(), CIgBlastTabularInfo::PrintHtmlSummary(), CIgBlastTabularInfo::PrintMasterAlign(), PrintNumProcessed(), x_PrintAlignmentLength(), x_PrintBitScore(), x_PrintBTOP(), x_PrintEvalue(), x_PrintFieldNames(), x_PrintFrames(), x_PrintGapOpenings(), x_PrintGaps(), CIgBlastTabularInfo::x_PrintIgDomain(), CIgBlastTabularInfo::x_PrintIgDomainHtml(), CIgBlastTabularInfo::x_PrintIgGenes(), x_PrintMismatches(), x_PrintNumIdentical(), x_PrintNumPositives(), CIgBlastTabularInfo::x_PrintPartialQuery(), x_PrintPercentIdentical(), x_PrintPercentPositives(), x_PrintQueryAccession(), x_PrintQueryAccessionVersion(), x_PrintQueryAndDbNames(), x_PrintQueryEnd(), x_PrintQueryFrame(), x_PrintQueryGi(), x_PrintQueryLength(), x_PrintQuerySeq(), x_PrintQuerySeqId(), x_PrintQueryStart(), x_PrintScore(), x_PrintSeqalignCoverage(), x_PrintSubjectAccession(), x_PrintSubjectAccessionVersion(), x_PrintSubjectAllAccessions(), x_PrintSubjectAllGis(), x_PrintSubjectAllSeqIds(), x_PrintSubjectAllTitles(), x_PrintSubjectBlastName(), x_PrintSubjectBlastNames(), x_PrintSubjectCommonName(), x_PrintSubjectCommonNames(), x_PrintSubjectCoverage(), x_PrintSubjectEnd(), x_PrintSubjectFrame(), x_PrintSubjectGi(), x_PrintSubjectLength(), x_PrintSubjectSciName(), x_PrintSubjectSciNames(), x_PrintSubjectSeq(), x_PrintSubjectSeqId(), x_PrintSubjectStart(), x_PrintSubjectStrand(), x_PrintSubjectSuperKingdom(), x_PrintSubjectSuperKingdoms(), x_PrintSubjectTaxId(), x_PrintSubjectTaxIds(), x_PrintSubjectTitle(), x_PrintUniqSubjectCoverage(), and ~CBlastTabularInfo().

◆ m_ParseLocalIds

bool CBlastTabularInfo::m_ParseLocalIds
private

Should the query deflines be parsed for local IDs?

Definition at line 344 of file tabular.hpp.

Referenced by x_PrintQueryAndDbNames(), and x_SetSubjectIds().

◆ m_ParseSubjectDefline

bool CBlastTabularInfo::m_ParseSubjectDefline
private

Parse subejct defline?

Definition at line 346 of file tabular.hpp.

◆ m_QueryCovSeqalign

int CBlastTabularInfo::m_QueryCovSeqalign
private

Definition at line 365 of file tabular.hpp.

Referenced by x_PrintSeqalignCoverage(), x_ResetFields(), and x_SetQueryCovSeqalign().

◆ m_QueryCovSubject

pair<string, int> CBlastTabularInfo::m_QueryCovSubject
private

Definition at line 363 of file tabular.hpp.

Referenced by CBlastTabularInfo(), x_PrintSubjectCoverage(), and x_SetQueryCovSubject().

◆ m_QueryCovUniqSubject

pair<string, int> CBlastTabularInfo::m_QueryCovUniqSubject
private

◆ m_QueryEnd

int CBlastTabularInfo::m_QueryEnd
protected

Ending offset in query.

Definition at line 317 of file tabular.hpp.

Referenced by SetEndpoints(), x_PrintQueryEnd(), and x_ResetFields().

◆ m_QueryFrame

int CBlastTabularInfo::m_QueryFrame
protected

query frame

Definition at line 318 of file tabular.hpp.

Referenced by SetCounts(), x_PrintFrames(), x_PrintQueryFrame(), and x_ResetFields().

◆ m_QueryGeneticCode

int CBlastTabularInfo::m_QueryGeneticCode
private

Definition at line 367 of file tabular.hpp.

Referenced by CBlastTabularInfo(), and SetFields().

◆ m_QueryId

list<CRef<objects::CSeq_id> > CBlastTabularInfo::m_QueryId
private

List of query ids for this HSP.

Definition at line 326 of file tabular.hpp.

Referenced by x_PrintQueryAccession(), x_PrintQueryAccessionVersion(), x_PrintQueryGi(), and x_PrintQuerySeqId().

◆ m_QueryLength

TSeqPos CBlastTabularInfo::m_QueryLength
private

Length of query sequence.

Definition at line 330 of file tabular.hpp.

Referenced by SetFields(), x_PrintQueryLength(), and x_ResetFields().

◆ m_QueryRange

TSeqRange CBlastTabularInfo::m_QueryRange
private

Definition at line 370 of file tabular.hpp.

Referenced by SetFields().

◆ m_QuerySeq

string CBlastTabularInfo::m_QuerySeq
protected

Aligned part of the query sequence.

Definition at line 314 of file tabular.hpp.

Referenced by SetFields(), x_PrintQuerySeq(), and x_ResetFields().

◆ m_QueryStart

int CBlastTabularInfo::m_QueryStart
protected

Starting offset in query.

Definition at line 316 of file tabular.hpp.

Referenced by SetEndpoints(), x_PrintQueryStart(), and x_ResetFields().

◆ m_Score

int CBlastTabularInfo::m_Score
private

Raw score of this HSP.

Definition at line 332 of file tabular.hpp.

Referenced by SetScores(), x_PrintScore(), and x_ResetFields().

◆ m_SubjectBlastName

string CBlastTabularInfo::m_SubjectBlastName
private

Definition at line 358 of file tabular.hpp.

Referenced by x_PrintSubjectBlastName(), and x_SetTaxInfo().

◆ m_SubjectBlastNames

set<string> CBlastTabularInfo::m_SubjectBlastNames
private

Definition at line 353 of file tabular.hpp.

Referenced by x_PrintSubjectBlastNames(), and x_SetTaxInfoAll().

◆ m_SubjectCommonName

string CBlastTabularInfo::m_SubjectCommonName
private

Definition at line 357 of file tabular.hpp.

Referenced by x_PrintSubjectCommonName(), and x_SetTaxInfo().

◆ m_SubjectCommonNames

vector<string> CBlastTabularInfo::m_SubjectCommonNames
private

Definition at line 352 of file tabular.hpp.

Referenced by x_PrintSubjectCommonNames(), and x_SetTaxInfoAll().

◆ m_SubjectDefline

CRef<CBlast_def_line_set> CBlastTabularInfo::m_SubjectDefline
private

Definition at line 360 of file tabular.hpp.

Referenced by SetFields(), x_PrintSubjectAllTitles(), and x_PrintSubjectTitle().

◆ m_SubjectEnd

int CBlastTabularInfo::m_SubjectEnd
protected

Ending offset in subject.

Definition at line 320 of file tabular.hpp.

Referenced by SetEndpoints(), x_PrintSubjectEnd(), and x_ResetFields().

◆ m_SubjectFrame

int CBlastTabularInfo::m_SubjectFrame
protected

subject frame

Definition at line 321 of file tabular.hpp.

Referenced by SetCounts(), x_PrintFrames(), x_PrintSubjectFrame(), and x_ResetFields().

◆ m_SubjectId

list<CRef<objects::CSeq_id> > CBlastTabularInfo::m_SubjectId
private

◆ m_SubjectIds

vector<list<CRef<objects::CSeq_id> > > CBlastTabularInfo::m_SubjectIds
private

All subject sequence ids for this HSP.

Definition at line 329 of file tabular.hpp.

Referenced by x_PrintSubjectAllAccessions(), x_PrintSubjectAllGis(), x_PrintSubjectAllSeqIds(), and x_SetSubjectIds().

◆ m_SubjectLength

TSeqPos CBlastTabularInfo::m_SubjectLength
private

Length of subject sequence.

Definition at line 331 of file tabular.hpp.

Referenced by SetFields(), x_PrintSubjectLength(), and x_ResetFields().

◆ m_SubjectSciName

string CBlastTabularInfo::m_SubjectSciName
private

Definition at line 356 of file tabular.hpp.

Referenced by x_PrintSubjectSciName(), and x_SetTaxInfo().

◆ m_SubjectSciNames

vector<string> CBlastTabularInfo::m_SubjectSciNames
private

Definition at line 351 of file tabular.hpp.

Referenced by x_PrintSubjectSciNames(), and x_SetTaxInfoAll().

◆ m_SubjectSeq

string CBlastTabularInfo::m_SubjectSeq
protected

Aligned part of the subject sequence.

Definition at line 315 of file tabular.hpp.

Referenced by SetFields(), CIgBlastTabularInfo::x_ComputeIgDomain(), x_PrintSubjectSeq(), and x_ResetFields().

◆ m_SubjectStart

int CBlastTabularInfo::m_SubjectStart
protected

Starting offset in subject.

Definition at line 319 of file tabular.hpp.

Referenced by SetEndpoints(), x_PrintSubjectStart(), and x_ResetFields().

◆ m_SubjectStrand

string CBlastTabularInfo::m_SubjectStrand
private

Definition at line 362 of file tabular.hpp.

Referenced by SetFields(), x_PrintSubjectStrand(), and x_ResetFields().

◆ m_SubjectSuperKingdom

string CBlastTabularInfo::m_SubjectSuperKingdom
private

Definition at line 359 of file tabular.hpp.

Referenced by x_PrintSubjectSuperKingdom(), and x_SetTaxInfo().

◆ m_SubjectSuperKingdoms

set<string> CBlastTabularInfo::m_SubjectSuperKingdoms
private

Definition at line 354 of file tabular.hpp.

Referenced by x_PrintSubjectSuperKingdoms(), and x_SetTaxInfoAll().

◆ m_SubjectTaxId

TTaxId CBlastTabularInfo::m_SubjectTaxId
private

Definition at line 355 of file tabular.hpp.

Referenced by x_PrintSubjectTaxId(), and x_SetTaxInfo().

◆ m_SubjectTaxIds

set<TTaxId> CBlastTabularInfo::m_SubjectTaxIds
private

Blast-traceback-operations.

Definition at line 350 of file tabular.hpp.

Referenced by x_PrintSubjectTaxIds(), and x_SetTaxInfoAll().


The documentation for this class was generated from the following files:
Modified on Tue May 21 10:57:26 2024 by modify_doxy.py rev. 669887