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NCBI C++ ToolKit: src/gui/widgets/aln_table/annot_compare_ds.cpp Source File

ref->GetNormDone();

identical_locs = 0;

identical_seqs = 0;

identical_prods = 0;

identical_locs_seqs = 0;

identical_locs_prods = 0;

identical_seqs_prods = 0;

identical_locs_seqs_prods = 0;

TFeatCountMap feat_counts;

TCountNotFound count_not_found;

subtype = iter->feat1->GetData().GetKey();

}

(iter->feat2) {

subtype = iter->feat2->GetData().GetKey();

TFeatCountMap::iterator it =

feat_counts.insert(make_pair(subtype, TCountMap())).first;

TCountMap::iterator count_it = it->second.insert(elt).first;

++identical_seqs_prods;

++identical_locs_seqs_prods;

++identical_locs_seqs;

++identical_locs_prods;

iter->feat1 ? iter->feat1_seq : iter->feat2_seq;

iter->feat1 ? *iter->feat1 : *iter->feat2;

TCountNotFound::iterator i1 = count_not_found.insert(v1).first;

TFeatCountMap::iterator i2 = i1->second.insert(

).first;

TCountMap::iterator i3 = i2->second.insert(v3).first;

ostr <<

<<

.size() <<

;

ostr << setw(10) << identical_locs <<

;

ostr << setw(10) << identical_seqs <<

;

ostr << setw(10) << identical_prods <<

;

ostr << setw(10) << identical_locs_seqs <<

;

ostr << setw(10) << identical_locs_prods <<

;

ostr << setw(10) << identical_seqs_prods <<

;

ostr << setw(10) << identical_locs_seqs_prods <<

;

ostr <<

;

ostr <<

;

(TCountNotFound, iter, count_not_found) {

total_feats = 0;

(TFeatCountMap, it, iter->second) {

(TCountMap,

, it->second) {

total_feats +=

->second;

ostr << setw(10) << total_feats <<

<< s <<

;

(TFeatCountMap, it, iter->second) {

(TCountMap,

, it->second) {

ostr << setw(14) <<

<<

<< it->first;

ostr <<

;

ostr <<

;

ostr <<

;

(TFeatCountMap, iter, feat_counts) {

total_feats = 0;

(TCountMap, it, iter->second) {

total_feats += it->second;

ostr << setw(10) << total_feats <<

<< iter->first;

(total_feats != 1) {

(TCountMap, it, iter->second) {

ostr << setw(14) << it->second <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

<< e.GetMsg());

(e.GetErrCode()) {

<< e);

x_OnAppJobNotification(evt);

(

);

, m_Align(&alignment)

list<CSeq_id_Handle> ids;

(

= 0;

< rows; ++

) {

TFeats& feats = fmap[sih];

( ; feat_iter; ++feat_iter) {

feats[ref] = *feat_iter;

(list<CSeq_id_Handle>, idh_iter1, ids) {

(list<CSeq_id_Handle>, idh_iter2, ids) {

(idh_iter1 == idh_iter2) {

do_swap = (*idh_iter2 < *idh_iter1);

TFeats& feat_set1 = (do_swap ? fmap[sih2] : fmap[sih1]);

TFeats& feat_set2 = (do_swap ? fmap[sih1] : fmap[sih2]);

(TFeats, fiter1, feat_set1) {

( ; iter; ++iter) {

TFeats::iterator fi2 = feat_set2.find(ref2);

(fi2 != feat_set2.end()) {

feat_set2.erase(fi2);

(TCompMap, cmiter, comp_map) {

.feat2.Reset(&cmiter->second.GetOriginalFeature());

.feat2_loc.Reset(&cmiter->second.GetLocation());

.loc_state = cmiter->first;

.feat2_loc = mapped_loc;

(

.feat1 && !

.feat1_loc ) {

.feat1_loc.Reset(&

.feat1->GetLocation());

(

.feat2 && !

.feat2_loc ) {

.feat2_loc.Reset(&

.feat2->GetLocation());

(

.feat1_loc) {

(

.feat2_loc) {

back_inserter(m_Alignments));

align_set.

().end(),

back_inserter(m_Alignments));

( ; feat_iter; ++feat_iter) {

( ; feat_iter2; ++feat_iter2) {

}

(annot_name.empty()) {

(comp_map.size()) {

(TCompMap, cmiter, comp_map) {

.feat2.Reset(&cmiter->second.GetOriginalFeature());

.feat2_loc.Reset(&cmiter->second.GetLocation());

.loc_state = cmiter->first;

static CRef< CScope > m_Scope

ON_EVENT(CAppJobNotification, CAppJobNotification::eStateChanged, &CAnnotCompareDS::OnAJNotification) void CAnnotCompareDS

void Add(const CDense_seg &ds, TAddFlags flags=0)

void Merge(TMergeFlags flags=0)

const CSeq_align & GetSeqAlign(void) const

objects::CScope & GetScope() const

CAppJobDispatcher::TJobID m_ActiveJob

control of background loading

size_t GetRows(void) const

void RegisterListener(CEventHandler *listener)

register a listener to respond to background job completion events

CEventHandler * m_Listener

const SRow & GetRow(size_t row_idx) const

CRef< objects::CScope > m_Scope

virtual void x_OnAppJobNotification(CEvent *evt)

float GetProgress() const

return progress indicator

void DumpTextReport(CNcbiOstream &ostr) const

dump a text report of the comparisons

const TRows & GetData() const

void x_BackgroundJob(IAppJob *job)

CAnnotCompare_AlignDS(objects::CScope &scope, const objects::CSeq_annot &annot)

list< CConstRef< objects::CSeq_align > > m_Alignments

our original alignments

CConstRef< objects::CSeq_align > m_Align

merged alignment from the above

CConstRef< objects::CSeq_loc > m_Loc

CAnnotCompare_LocationDS(objects::CScope &scope, const objects::CSeq_loc &loc)

~CAnnotCompare_LocationDS()

TCompareFlags CompareFeats(const CSeq_feat &feat1, CScope &scope1, const CSeq_feat &feat2, CScope &scope2, vector< ECompareFlags > *complex_flags, list< string > *comments)

compare two different features, possibly living in different scopes.

@ eLocation_3PrimeExtraExon

@ eLocation_RegionOverlap

locations exhibit a non-shared-exon overlap of total range

@ eLocation_MissingExon

missing an exon, either 5', 3', or internal

@ eLocation_5PrimeExtension

5', 3' extended exon

@ eLocation_Overlap

locations overlap without sharing exon boundaries

@ eSequence_SameSeq

sequence categories (genomic and product)

@ eLocation_Complex

complex relation - results may be returned as a set of the above

@ eLocationMask

masks for the above

@ eLocation_Subset

one location is a subset of another

@ eLocation_DifferentStrand

locations annotated on different strands

@ eLocation_3PrimeExtension

@ eSequence_SameProduct

locations have the same product sequence

@ eLocation_Missing

genomic location categories

@ eLocation_Same

no difference in lcoation

@ eLocation_5PrimeExtraExon

5', 3' extra exons

size_t GetSize(void) const

IAppJobListener Interface for components that need to be notified about changes in Jobs.

CAppJobNotification Notification send by CAppJobEventTranslator.

CAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message an...

CEvent - generic event implementation TODO TODO - Attachments.

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

CFeatCompareJob_Align(CScope &scope, const CSeq_align &alignment)

CConstRef< CSeq_align > m_Align

Annotation Comparison by location alone This is done by checking a few constraints.

CFeatCompareJob_Location(CScope &scope, const CSeq_loc &loc)

CConstRef< CSeq_loc > m_Loc

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

Alignment-based data source.

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

CFeatCompareJob(CScope &scope)

CRef< CAppJobError > m_Error

size_t m_TotalComparisons

for status reporting

virtual CRef< CObject > GetResult()

Returns the Job Result.

CRef< CFeatCompare_Result > m_Result

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

size_t m_CompletedComparisons

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

AppJobs for background loading and preparation.

CAnnotCompareDS::TRows m_Rows

row represents a pair of compared features

Base class to build jobs with cancel functionality.

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) 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).

namespace ncbi::objects::

@ eWidgetDataChanged

notification from child to parent that the underlying data has changed

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

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

request an annotation selector for a given type

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

static CAppJobDispatcher & GetInstance()

CRef< CObject > GetResult() const

returns non-null pointer only if Completed or Running and has temporary results available

virtual bool IsCanceled() const override

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

EJobState

Job states (describe FSM)

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

CConstIRef< IAppJobProgress > GetJobProgress(TJobID job_id)

TJobState GetState() const

virtual bool Send(CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Sends an event synchronously.

void SetNormDone(float done)

@ eEngine_UnknownJob

the job is not registered in the Engine

@ eUnknownJob

Job record lost.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeqFeatData & GetData(void) const

const string & GetName(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

const Tdata & Get(void) const

Get the member data.

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

double value_type

The numeric datatype used by the parser.

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

#define row(bind, expected)

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