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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cigar__formatter_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/format/cigar_formatter.hpp Source File

1 #ifndef OBJTOOLS_FORMAT___CIGAR_FORMATTER__HPP 2 #define OBJTOOLS_FORMAT___CIGAR_FORMATTER__HPP 57

fCIGAR_GffForFlybase = 1 << 0,

70 void

FormatByReferenceId(

const CSeq_id

& ref_id);

71 void

FormatByTargetId(

const CSeq_id

& target_id);

73 void

FormatByReferenceRow(

TNumrow

ref_row);

74 void

FormatByTargetRow(

TNumrow

target_row);

86 virtual void AddRow

(

const string

) {}

88 virtual void

AddSegment(ostream& cigar,

97 const CSeq_align

& GetCurrentSeq_align(

void

)

const

;

126

TNumrow x_GetRowById(

const CSeq_id

id

);

128 void

x_FormatAlignmentRows(

void

);

129 void

x_FormatAlignmentRows(

const CSeq_align

& sa,

130 bool

width_inverted);

131 void

x_FormatDensegRows(

const CDense_seg

& ds,

132 bool

width_inverted);

133 void

x_FormatLine(

bool

width_inverted);

static CRef< CScope > m_Scope

The base class for alignment formatters which use CIGAR format.

unsigned int TSeqPos

Type for sequence locations and lengths.

TNumrow GetRefRow(void) const

virtual void EndSubAlignment(void)

TSeqPos GetRefWidth(void) const

CScope * GetScope(void) const

const CSeq_align & m_Align

bool IsFirstSubalign(void) const

CConstRef< CSeq_id > m_TargetId

const TRange & GetTargetRange(void) const

TNumrow GetTargetRow(void) const

virtual void EndRows(void)

const CSeq_align & GetSeq_align(void) const

const CSeq_align * m_CurAlign

virtual void StartRow(void)

CConstRef< CSeq_id > m_RefId

int GetTargetSign(void) const

const TRange & GetRefRange(void) const

virtual void StartSubAlignment(void)

int GetRefSign(void) const

virtual void AdjustSeqIdType(CConstRef< CSeq_id > &)

const CSeq_align & GetCurrentSeq_align(void) const

bool IsSetFlag(ECIGARFlags flag) const

TSeqPos GetTargetWidth(void) const

virtual void StartRows(void)

const CDense_seg & GetDense_seg(void) const

const CSeq_id & GetRefId(void) const

char GetLastType(void) const

virtual void EndAlignment(void)

virtual void StartAlignment(void)

bool IsTrivial(void) const

CConstRef< CDense_seg > m_DenseSeg

virtual void AddRow(const string &)

const CAlnMap & GetAlnMap(void) const

virtual void EndRow(void)

const CSeq_id & GetTargetId(void) const

CAlnMap::TSignedRange TRange

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_FORMAT_EXPORT

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