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NCBI C++ ToolKit: src/gui/objutils/table_data_aln_summary.cpp Source File

& obj = *iter->object;

type_info&

=

(obj);

num_rows = (*aix)->CheckNumRows();

total = prev_total + num_rows -1;

*iter->second;

sum->m_SStop = align.

(seqrow+1) + 1;

coverage = 0.0;

identity = 0.0;

gap_bases = 0;

(align_length < 1000000) {

identity = identities * 100.0 / align_length;

sum->m_PctCoverage = coverage;

sum->m_PctIdentity = identity;

sum->m_Mismatches = mismatches;

sum->m_GappedBases = gap_bases;

sum->m_Score = score;

e_value = 0.0;

sum->m_EValue = e_value;

sequence::CDeflineGenerator

;

sum->m_QDefline =

.GenerateDefline(bsh);

sum->m_QDefline = sum->m_Query;

sum->m_SDefline =

.GenerateDefline(bsh);

sum->m_SDefline = sum->m_Subject;

;

TSeqPos GetAlignLength(const CSeq_align &align, bool ungapped=false)

Compute the length of the alignment (= length of all segments, gaps + aligned)

int GetGapCount(const CSeq_align &align)

Compute the number of gaps in the alignment.

double GetPercentCoverage(CScope &scope, const CSeq_align &align, unsigned query=0)

Compute percent coverage of the query (sequence 0) (range 0-100)

int GetMismatchCount(CScope &scope, const CSeq_align &align)

Compute the number of mismatches in the alignment.

int GetGapBaseCount(const CSeq_align &align)

Compute the number of gap bases in the alignment (= length of all gap segments)

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

objects::ENa_strand m_QStrand

objects::ENa_strand m_SStrand

virtual long GetIntValue(size_t row, size_t col) const

virtual ColumnType GetColumnType(size_t col) const

virtual string GetColumnLabel(size_t col) const

virtual double GetRealValue(size_t row, size_t col) const

virtual SConstScopedObject GetObjectValue(size_t row, size_t col) const

virtual size_t GetRowsCount() const

CRef< objects::CScope > m_Scope

CTableDataAlnSummary(TConstScopedObjects &objects)

vector< CConstRef< objects::CSeq_align > > m_Aligns

virtual SConstScopedObject GetRowObject(size_t row) const

const CAlnSummary & x_GetAlnSummary(size_t row) const

virtual void GetStringValue(size_t row, size_t col, string &value) const

TAlnSummary m_CachedSummary

virtual size_t GetColsCount() const

string x_StrandToStr(objects::ENa_strand strand) const

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

API (CDeflineGenerator) for computing sequences' titles ("definitions").

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

vector< SConstScopedObject > TConstScopedObjects

CConstRef< CSeq_id > GetSeqId(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const Tdata & Get(void) const

Get the member data.

ENa_strand

strand of nucleic acid

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

list< CRef< CSeq_align > > TAlign

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const GenericPointer< typename T::ValueType > T2 value

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

#define row(bind, expected)

static const string s_ColNames[CTableDataAlnSummary::eMaxColNum]

static ITableData::ColumnType s_ColTypes[CTableDataAlnSummary::eMaxColNum]

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