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

objects::CBioseq_Handle& handle,

: m_BioseqHandle(handle),

m_AccumSeg(start, stop, window),

m_StrandType(strand_type),

m_CntAligns(0), m_CntMixes(0)

(p_cb) p_cb->

(

);

sel.SetLimitSeqAnnot(

.GetScope().GetSeq_annotHandle

,

(aln->GetSeqStart(aln->GetAnchor()))

,

(aln->GetSeqStop(aln->GetAnchor()))

(

< rhs.

)

;

(rhs.

<

)

;

(

== 0)

;

vector<const objects::CSeq_align*>

;

vector<SAlignSmearSort> aligns_to_smear;

(

ai = 0; align_iter; ++align_iter, ++ai) {

aligns_to_smear.emplace_back(range.

(), range.

(),

);

aln_id_map.push_back(align);

aln_user_options.

(aln_id_map[0][anchor]);

aligns_to_smear.emplace_back(sparse_aln,

);

}

(std::exception&) {

(aligns_to_smear.begin(), aligns_to_smear.end());

vector<SAlignSmearSort>::const_iterator aligns_end = aligns_to_smear.end();

vector<SAlignSmearSort>::const_iterator align_it, last_align = aligns_end;

(align_it = aligns_to_smear.begin();

align_it != aligns_end;

last_align = align_it, ++align_it) {

(last_align != aligns_end &&

last_align->m_Id != align_it->m_Id ) {

(last_align != aligns_end &&

last_align->m_Id == align_it->m_Id &&

last_align->m_End < align_it->m_Start ) {

( !align_it->m_Alignment ) {

pre_stop = (*p_it)->GetAlnRange().GetTo();

(

= 0;

< aln_chunks->size(); ++

) {

start = chunk->GetRange().GetFrom();

stop = chunk->GetRange().GetTo();

(

= 1;

< aln_chunks->size(); ++

) {

start = prev_chunk->GetRange().GetTo();

stop = chunk->GetRange().GetFrom();

(*gap_it > 0 && *seg_it > 0) {

(name ==

||

name ==

) {

(seq_annot.IsSetDesc()) {

seq_annot.GetDesc().Get() ) {

blast_type =

.

();

hist_type =

.

();

( ! annot_name.empty()) {

}

( ! blast_type.empty() ) {

}

( ! hist_type.empty() ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static const string s_HistFieldKey("Hist Seqalign")

static const string s_BlastFieldKey("Blast Type")

CRef< CAnchoredAln > CreateAnchoredAlnFromAln(const _TAlnStats &aln_stats, size_t aln_idx, const CAlnUserOptions &options, objects::CSeq_align::TDim explicit_anchor_row=-1)

Create an anchored alignment from Seq-align using hints.

CRef< CSeq_align > ConvertSeq_align(const CSeq_align &src, CSeq_align::TSegs::E_Choice dst_choice, CSeq_align::TDim anchor_row=-1, CScope *scope=NULL)

Convert source alignment to a new type.

CAlnStats< TAlnIdMap > TAlnStats

Default implementations for alignment stats.

vector< const CSeq_align * > TAlnVector

CAlnIdMap< vector< const CSeq_align * >, TIdExtract > TAlnIdMap

Default implementations of CAlnIdMap.

Container mapping seq-aligns to vectors of participating seq-ids.

const CSeq_id & GetSeqId(TNumrow row) const

TDim GetNumRows(void) const

TSeqPos GetAlnStop(TNumseg seg) const

void SetAnchor(TNumrow anchor)

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

TNumrow GetAnchor(void) const

TSeqPos GetAlnStart(TNumseg seg) const

TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

Options for different alignment manager operations.

void SetAnchorId(const TAlnSeqIdIRef &anchor_id)

Set anchor id.

@ eBothDirections

No filtering: use both direct and reverse sequences.

size_t GetSize(void) const

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

ENa_strand GetSeqStrand(TDim row) const

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

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

TNumrow GetAnchor(void) const

Get anchor row index.

Alignment segment iterator interface.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

Task clients implement this callback interface.

bool operator<(const SAlignSmearSort &rhs) const

SAlignSmearSort(TSeqPos start, TSeqPos end, const TId &id)

CConstRef< CSparseAln > m_Alignment

SAlignSmearSort(CConstRef< CSparseAln > &aln, const TId &id)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void SetTaskName(const string &name)=0

virtual void SetTaskCompleted(int completed)=0

set total finished task number.

void AddAlignment(const CSparseAln &aln)

Add this one alignment to my smear.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

void SetLabel(const string &label)

void AddAnnot(const objects::CSeq_annot &seq_annot, ISeqTaskProgressCallback *p_cb=NULL)

INPUT:

static bool SeparateStrands(const objects::CSeq_annot &seq_annot)

const objects::CBioseq_Handle & m_BioseqHandle

virtual void SetTaskTotal(int total)=0

CAlignmentSmear(const objects::CBioseq_Handle &handle, TSeqPos start, TSeqPos stop, float window=1, EAlignSmearStrand strand_type=eSmearStrand_Both)

unsigned long m_CntAligns

virtual bool StopRequested() const =0

void AddAlignments(const objects::SAnnotSelector &sel, ISeqTaskProgressCallback *p_cb=NULL)

Smear all the alignments matched by this selector on my bioseq.

EAlignSmearStrand m_StrandType

static string x_GetAnnotName(const objects::CSeq_annot &seq_annot)

virtual void AddTaskCompleted(int delta)=0

set to add newly finished task number.

const_iterator end() const

const_iterator begin() const

container_type::iterator iterator

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

@ eSortOrder_None

do not sort annotations for faster retrieval

void Reset(void)

Reset reference object.

position_type GetLength(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetType(void) const

Check if it is safe to call GetType method.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

TBool GetBool(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool CanGetLabel(void) const

Check if it is safe to call GetLabel method.

E_Choice Which(void) const

Which variant is currently selected.

const TDenseg & GetDenseg(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

const TUser & GetUser(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TName & GetName(void) const

Get the variant data.

list< CRef< CAnnotdesc > > Tdata

@ e_Name

a short name for this collection

@ e_User

user defined object

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

#define row(bind, expected)

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