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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cigar__formatter_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/cigar_formatter.cpp Source File

m_CurAlign(

),

m_IsFirstSubalign(

),

m_FormatBy(eFormatBy_NotSet)

);

(1,

<<

.AsFastaString());

);

frameshift = +(ref_piece.

()%width);

);

last_count +=

;

last_frameshift += frameshift;

(last_frameshift) {

(last_frameshift < 0 ?

:

),

(last_frameshift));

last_frameshift = frameshift;

cigar_string = cigar.str();

(width_inverted) {

ds_no_widths.

(ds);

ds_for_alnmix = &ds_no_widths;

cigar << seg_len << seg_type;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Base class for CIGAR formatters.

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

TDim GetNumRows(void) const

unsigned int TSegTypeFlags

TSignedRange GetRange(TNumrow row, TNumseg seg, int offset=0) const

int StrandSign(TNumrow row) const

TNumseg GetNumSegs(void) const

The base class for alignment formatters which use CIGAR format.

void Assign(const CSerialObject &obj, ESerialRecursionMode how=eRecursive)

overloaded Assign()

const TWidths & GetWidths(void) const

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

CRef< CSeq_align > AsDiscSeg() const

Convert this alignment to a discontinuous segment.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define STD_CATCH_ALL_X(err_subcode, message)

Standard handling of "exception"-derived exceptions; catches non-standard exceptions and generates "u...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void EndSubAlignment(void)

CScope * GetScope(void) const

TNumrow x_GetRowById(const CSeq_id &id)

void FormatByReferenceRow(TNumrow ref_row)

CConstRef< CSeq_id > m_TargetId

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

void x_FormatLine(bool width_inverted)

void x_FormatAlignmentRows(void)

virtual void StartSubAlignment(void)

virtual void AdjustSeqIdType(CConstRef< CSeq_id > &)

bool IsSetFlag(ECIGARFlags flag) const

virtual void StartRows(void)

void FormatByReferenceId(const CSeq_id &ref_id)

void FormatByTargetId(const CSeq_id &target_id)

virtual void EndAlignment(void)

void x_FormatDensegRows(const CDense_seg &ds, bool width_inverted)

virtual void StartAlignment(void)

CConstRef< CDense_seg > m_DenseSeg

virtual void AddSegment(ostream &cigar, char seg_type, TSeqPos seg_len)

virtual void AddRow(const string &)

void FormatByTargetRow(TNumrow target_row)

virtual void EndRow(void)

virtual ~CCIGAR_Formatter(void)

@ fCIGAR_GffForFlybase

Flybase flavour of GFF3.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

position_type GetLength(void) const

static TThisType GetEmpty(void)

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

TScore & SetScore(void)

Assign a value to Score data member.

E_Choice Which(void) const

Which variant is currently selected.

const TSpliced & GetSpliced(void) const

Get the variant data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

#define row(bind, expected)

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