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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/feature_ds.cpp Source File

* label_prefix =

);

* label_prefix =

);

* label_prefix =

);

* label_prefix =

);

level,

& title);

* label_prefix =

);

& c_feat = (*iter)->GetFeature();

(

(

, (*c_iter)->GetFeature())) {

has_rna =

;

has_cds =

;

& c_feat = (*iter)->GetFeature();

(!(*iter)->GetChildren().empty()) {

has_rna && !has_cds;

& c_feat = (*iter)->GetFeature();

( (c_feat.

().

() && !(*iter)->GetChildren().empty()) ||

TJobToken token,

max_feat,

& extra_filter)

max_feat, LinkedFeat,

(!extra_filter.empty()) {

(!filter.empty()) filter +=

;

filter += extra_filter;

job->SetFilter(filter);

,

, range, window, token, requests));

,

, lm_feat_sel, m_feat_sel, lm_token,

main_token, landmark_feat, range, window,

, objs,

range, window, token));

&

=

&

(

.object.GetObject());

(

.scope.GetObject(),

);

sid(

);

slabel(

);

, m_FeatLimit(max_feat)

, m_LinkedFeat(LinkedFeatDisplay)

(sortby.empty()) {

found = sortby.find_first_of(

);

(found != string::npos) {

sort_str = sortby.substr(found + 1);

feat_iter(handle, range, sel);

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

feat_iter(handle, range, sel);

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

( ; feature_iter; ++feature_iter) {

(*iter)->GetChildren().clear();

(curr_feats.size() == group->GetChildrenNum()) {

(feat_groups.size() == 1);

objs.swap(group->SetChildren());

(feat_groups.size() == 1);

objs.emplace_back(group.GetPointer());

->GetData(the_map);

annots =

.GetIncludedAnnotsNames();

(

& annot : annots) {

(annot.IsNamed()) {

->m_Desc = annot.GetName();

vector<TSeqRange> ranges;

(

&

: ranges) {

annots =

.GetIncludedAnnotsNames();

(

& annot : annots) {

(annot.IsNamed()) {

->m_Desc = annot.GetName();

glyph_created =

;

(!glyph_created) {

=

(features.size());

->m_ObjectList.swap(objs);

(has_coverage_graph) {

->m_ObjectList.swap(objs);

}

(std::exception& ex) {

passed =

;

CLinkedFeature::TLinkedFeats::iterator p_iter = features.begin();

(p_iter != features.end()) {

is_leaf = (*p_iter)->GetChildren().empty();

filter.

(&(*p_iter)->GetMappedFeature())) {

p_iter = features.erase(p_iter);

feat_groups.clear();

feat_groups.emplace_back(

->GroupIdxToName(grp_iter->first), grp_iter->second);

CLinkedFeature::TLinkedFeats::iterator p_iter = feats.begin();

(p_iter != feats.end()) {

is_leaf = (*p_iter)->GetChildren().empty();

idx =

->GetGroupIdx((*p_iter)->GetMappedFeature());

( !is_leaf &&

->ChildFeatureFirst() ) {

grp_num = child_group_map.

();

p_feat->GetChildren() = grp_iter->second;

group_map[grp_iter->first].push_back(p_feat);

}

(idx > -1 || grp_num == 1) {

idx = child_group_map.

()->first;

group_map[idx].push_back(*p_iter);

p_iter = feats.

(p_iter);

group->SetLevel(Level);

need_group = features.size() > 1;

( !glyph )

;

num_children = (*iter)->GetChildren().size();

(num_children == 0 ) {

group->PushBack(glyph);

group->SetAsMaster(glyph);

(; feature_iter ; ++feature_iter) {

(

& it : glyphs) {

objs.push_back(glyph);

* label_prefix

)

}

(std::exception&) {

(loc_obj.

()) {

loc.

(&loc_obj);

GetCDSFrame = [&]() {

= GetCDSFrame();

(

!= parent_glyph) {

id_num{ 0 };

= GetCDSFrame();

( !

.empty() ) {

<<

);

(std::exception&) {

(loc_obj.

()) {

loc.

(&loc_obj);

GetCDSFrame = [&]() {

vector<CRef<CSeqGlyph>> glyphs;

(

loc_it(*loc); loc_it; ++loc_it) {

copy_loc->

(*loc);

(feat_range != gen_range) {

glyphs.push_back(glyph);

= GetCDSFrame();

(

!= parent_glyph) {

id_num{ 0 };

= GetCDSFrame();

(!

.empty()) {

(

<<

<<

);

(!glyphs.empty()) {

vector<CRef<CSeqGlyph>>::iterator g_it = glyphs.begin();

(g_it != glyphs.end()) {

((*g_it)->GetRange() != range) {

g_it = glyphs.erase(g_it);

* label_prefix

)

& object_type =

.GetUser().GetType().GetStr();

(object_type ==

) {

unique_ptr<CFeatGlyph> feat_glyph;

feat_glyph->SetTopLabelPrefix(label_prefix);

glyph.

(feat_glyph.release());

intervals.push_back((*iter)->GetTotalRange());

& title)

(

&

: features) {

the_map.

(

->GetMappedFeature().GetLocation().GetTotalRange(), 1,

);

(; feat_iter; ++feat_iter) {

& title)

->m_ExtraObj = glyphs.front();

& title)

(; feat_iter ; ++feat_iter) {

(iter == the_maps.

()) {

iter = the_maps.

(

iter->second.AddRange(

( !the_maps.

() ) {

( ; iter; ++iter) {

intervals.push_back(iter.

());

rsite =

;

rsiteRangeFromSet =

;

( ; iter; ++iter) {

(!rsiteRangeFromSet) {

rsiteRangeFromSet =

;

intervals.push_back(rsiteRange);

rsiteRangeFromSet =

;

intervals.push_back(iter.

());

, m_MainFeatSel(m_feat_sel)

, m_MainFeatToken(main_token)

, m_LandmarkFeats(landmark_feat)

( ; feature_iter; ++feature_iter) {

transcripts_filtered =

;

(transcripts_filtered) {

->m_FilterDescr =

;

}

(std::exception& ex) {

((*xit)->IsSetData() && (*xit)->GetData().Which() == choice) {

(

& it : linked_feat.

()) {

(it->GetFeature().GetData().IsCdregion())

(!ext_type.

() || ext_type.

() !=

) {

(!field_label.

() || !field_data.

() || field_label.

() !=

)

& evidence_field = **evidence_iter;

(

& iter : feat.

()) {

(iter->GetQual() ==

&& iter->IsSetVal()) {

&

= iter->GetVal();

(tags.count(

) > 0)

(

);

transcripts_filtered =

;

(skip)

;

vector<CRef<CSeqGlyph>> glyphs;

(glyphs.empty()) {

(!glyph)

;

glyphs.push_back(glyph);

((*iter)->GetChildren().empty()) {

transcripts_filtered =

;

(

& it : glyphs) {

transcripts_filtered =

;

(

& glyph_it : glyphs) {

current_range = glyph->

();

label_prefix;

num_filtered = 0;

vector<CRef<CSeqGlyph>> g_glyphs;

(g_glyphs.empty())

(!g_glyph)

;

g_glyphs.push_back(g_glyph);

(g_glyphs.size() == 1);

exon_group->

(g_glyphs[0]);

rnacds_group->PushBack(g_glyphs[0]);

misc_group->

(g_glyphs[0]);

rnacds_group->PushBack(rna_group);

rna_group->

(g_glyphs[0]);

vector<CRef<CSeqGlyph>> r_glyphs =

((*r_iter)->GetMappedFeature(), current_range, g_glyphs[0].GetPointer(), label_prefix.c_str());

(

& g_it : r_glyphs) {

rna_group->

(g_it.GetNCPointerOrNull());

rnacds_group->PushBack(g_glyphs[0]);

vector<CRef<CSeqGlyph>> r_glyphs =

((*r_iter)->GetMappedFeature(), current_range, g_glyphs[0].GetPointer(), label_prefix.c_str());

(

& g_it : r_glyphs) {

rnacds_group->PushBack(g_it.GetNCPointerOrNull());

rnacds_group->PushBack(r_glyph);

transcripts_filtered =

;

is_filtered = (num_filtered > 0 && num_filtered == (*iter)->GetChildren().size());

objs.emplace_back(group);

group->PushBack(misc_group);

(!rnacds_group->GetChildren().empty()) {

(rnacds_group->GetChildren().size() == 1 ||

group->Append(rnacds_group->SetChildren());

group->PushBack(rnacds_group);

group->PushBack(exon_group);

((*iter)->GetChildren().empty()) {

objs.push_back(glyph);

vector<CRef<CSeqGlyph>> r_glyphs;

(

& g_it : r_glyphs) {

group->PushBack(g_it.GetNCPointerOrNull());

group->PushBack(r_glyph);

(; feature_iter ; ++feature_iter) {

objs.push_back(glyph);

( ; feature_iter; ++feature_iter) {

features.push_back(fref);

feature::CFeatTree::eFeatId_by_type,

) ) {

( !(*iter)->GetFeature().GetData().IsGene() )

;

(skip)

;

objs.push_back(glyph);

;

*obj_stream >> gbl_reply;

(

.CanGetGenes()) {

(

<<

<< gi <<

<< e.

());

vector<SLandmarkFeat> landmark_feats;

(m_StopRequested) {

score = (float)range.

();

score /= s.length();

landmark_feats.push_back(

);

vector<int> gene_uids;

(m_StopRequested) {

(gene_tag && gene_tag->

().

()) {

gene_uids.push_back(gene_tag->

().

());

TScoreMap gene_scores;

CEntrezCache& cache = CEntrezCache::GetInstance();

vector<int>::iterator iter = gene_uids.begin();

db(

);

( ; iter != gene_uids.end(); ) {

gene_scores[ds->GetUid()] =

s_GetGeneDocsumWeight(*ds);

iter = gene_uids.erase(iter);

(gene_uids.size()) {

(ds && ds->IsSetList()) {

cache.Put(

, *ds);

gene_scores[(*iter)->GetUid()] =

s_GetGeneDocsumWeight(**iter);

(m_StopRequested) {

(gene_tag && gene_tag->

().

()) {

TScoreMap::iterator it = gene_scores.find(uid);

(it != gene_scores.end()) {

landmark_feats.push_back(

);

(idh && idh.

() > 0) {

(number_genes > 0) {

(gene_weights.

()) {

score /= s.length();

(

->GetTag().IsId()) {

(g_iter != gene_weights.

()) {

score = (float)g_iter->second;

landmark_feats.push_back(

);

(landmark_feats.empty())

;

(landmark_feats.begin(), landmark_feats.end(),

*

(landmark_feats.front().obj.GetPointer());

(vector<SLandmarkFeat>, iter, landmark_feats) {

range = iter->obj->GetRange();

= landmark_feats.size() - 1;

vector<SLandmarkFeat>::iterator

=

vector<SLandmarkFeat>::iterator s_iter =

;

vector<SLandmarkFeat>::iterator end = landmark_feats.end();

landmark_feats.erase(s_iter, end);

(highlight_num > 40) {

}

(highlight_num < 10) {

s_iter = landmark_feats.begin();

(highlight_num > 0 && s_iter != landmark_feats.end()) {

s_iter->obj->SetHighlighted(

);

s_iter = landmark_feats.begin();

(highlight_num > 0 && s_iter != landmark_feats.end()) {

comment_objs.push_back(glyph);

(landmark_feats.begin(), landmark_feats.end(),

(vector<SLandmarkFeat>, l_iter, landmark_feats) {

objs.push_back(l_iter->obj);

& filter)

vector<string> filters;

feat_iter(handle, range, sel);

filters.push_back(filter);

feat_iter(handle, range, sel);

filters.push_back(filter);

feat_iter(handle, range, sel);

filters.push_back(filter);

feat_iter(handle, range, sel);

(; feat_iter; ++feat_iter) {

features.push_back(fref);

feature::CFeatTree::eFeatId_by_type,

);

filters.push_back(filter);

feat_iter(handle, range, sel);

(; feat_iter; ++feat_iter) {

features.push_back(fref);

feature::CFeatTree::eFeatId_by_type,

);

filters.push_back(filter);

}

( !filter.empty() ) {

, m_Requests(requests)

->m_Results.push_back(single_res);

}

(std::exception& ex) {

(align_iter && !mapper) {

packed = feat_iter &&

( ; feat_iter; ++feat_iter) {

}

(

> 0) {

( ; feat_iter; ++feat_iter) {

(dmap)

->m_ExtraObj.Reset(dmap);

( !

.empty() )

->m_ObjectList.swap(

);

->m_ExtraObj.Reset(dmap);

}

(std::exception& ex) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Seq-loc and seq-align mapper exceptions.

const TAnnotNames & GetAnnotNames(void) const

size_t GetSize(void) const

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CBatchFeatJob: a job class for loading annotated features from a given a set of sequences within the ...

virtual CRef< CSGJobResult > x_LoadFeatProducts(CRef< CFeatGlyph > feat, const SAnnotSelector &sel)

virtual EJobState x_Execute()

method truly doing the job.

TFeatBatchJobRequests m_Requests

CBatchFeatJob(const string &desc, CBioseq_Handle handle, const TSeqRange &range, TModelUnit window, TJobToken token, const TFeatBatchJobRequests &requests)

CBatchFeatJob.

CBatchJobResult – the data structure holding the seqgraphic job results for a batch job processing.

CCloneConcordancySorter is a feature sorter used to sort clone features based on clone concordancy.

static const string & GetID()

CClonePlacementGlyph is similar to CFeatureGlyph, but with different rendering style and settings.

TIntervals & SetIntervals()

CClonePlacementGlyph inline implementations.

This stream exchanges data with an HTTP server located at the URL: http[s]://host[:port]/path[?...

CDbvarClinicalAsstSorter is a feature sorter used to sort variant features based on variant quality.

static const string & GetID()

CDbvarPilotSorter is a feature sorter used to sort variant features based on variant pilot number.

static const string & GetID()

CDbvarQualitySorter is a feature sorter used to sort variant features based on variant quality.

static const string & GetID()

CDbvarSamplesetTypeSorter is a feature sorter used to sort variant features based on variant quality.

static const string & GetID()

CDbvarValidationSorter is a feature sorter used to sort variant features based on variant quality.

static const string & GetID()

CRef< CEntrez2_docsum_list > GetDocsums(const vector< TUid > &uids, const string &db)

Retrieve the docsums for a set of UIDs.

void SetMappingInfo(const TMappingInfo &info)

TIntervals & SetIntervals()

CFeatGlyph inline implementations.

const TMappingInfo & GetMappingInfo() const

virtual const objects::CSeq_loc & GetLocation(void) const

access the position of this object.

void SetTopLabelPrefix(const char *prefix)

Set prefix to prepend to labels on top.

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

static size_t GetCustomColorIdx(const objects::CSeq_feat &feat)

Get the customized color idx for a given feature.

void GetLabel(string &label, CLabel::ELabelType type) const

retrieve feature label for a given type

static const string & GetID()

bool NeedFiltering() const

bool Pass(const objects::CMappedFeat *feat)

void Init(const string &filter)

CGRCStatusSorter is a feature sorter used to sort GRC issue features based on resolving status stored...

static const string & GetID()

CGeneGroup is a subclass of CLayoutGroup contains gene, RNA, cds, and Exon features.

bool m_CCDSOnly

Show only CCDS variants.

EMergeStyle m_MergeStyle

the way on how to merge CDSs and RNAs.

bool m_SelectOnly

Show only Select/MANE variants.

bool m_HideNonCoding

Hide transcripts without associated CDS.

bool m_ShowHistogram

show gene distribution histogram.

@ eMerge_OneLine

merge into one line

@ eMerge_Pairs

merge each transcript and CDS pair

@ eMerge_No

show all feature individually

bool m_HideModels

Hide Model RefSeqs.

CGeneModelFeatJob: a job class for loading annotated main features, including genes,...

static vector< string > GetFilters(const CBioseq_Handle &handle, const TSeqRange &range, SAnnotSelector &sel, const string &filter)

static bool x_IsncRNA(const CLinkedFeature &linked_feat)

static bool x_IsDbref(const string &db, const CSeq_feat &feat)

virtual CRef< CSeqGlyph > x_CreateFeature2(const CMappedFeat &feat, const CSeq_loc &loc, const char *label_prefix=NULL)

overridable creator.

IAppJob::EJobState x_CreateFeaturesWithFilter(CFeat_CI &feature_iter, CSeqGlyph::TObjects &objs, TFilterType filter)

create features when there is a filter set up.

static bool x_IsnpcGene(const CLinkedFeature &linked_feat)

static TFilterType x_FilterStrToValue(const string &filter)

static bool x_IsCCDS(const CLinkedFeature &linked_feat)

static bool x_IsDbref(const string &db, const CLinkedFeature &linked_feat)

bool x_IsTranscriptAcceptable(const CLinkedFeature &feat)

Check if transcript passes Config filters.

IAppJob::EJobState x_CreateGeneModels(CLinkedFeature::TLinkedFeats &feats, CSeqGlyph::TObjects &objs, bool &transcripts_filtered)

Link features into a hierarchical list.

SAnnotSelector m_MainFeatSel

annotation selector for all main features.

EJobState x_ProcessLandMarkFeatures(CSeqGlyph::TObjects &objs, CRef< CSeqGlyph > &hist_obj, CSeqGlyph::TObjects &comment_objs)

TJobToken m_MainFeatToken

Job token for loading main features.

CGeneModelConfig m_Config

CGeneModelFeatJob(const string &desc, CBioseq_Handle handle, const SAnnotSelector &lm_feat_sel, const SAnnotSelector &m_feat_sel, TJobToken lm_token, TJobToken main_token, bool landmark_feat, const TSeqRange &range, TModelUnit window, const CGeneModelConfig &conf, ICoordMapper *mapper)

CGeneModelFeatJob.

@ eFilter_dbref

one specific dbref

@ eFilter_dbref_all

any dbref

@ eFilter_CCDS

genes with Consensus CDS

bool m_LandmarkFeats

is overview mode?

static bool x_IsPseudoGene(const CSeq_feat &feat)

virtual EJobState x_Execute()

method truly doing the job.

CRef< TData > GetData(const string &data_key)

Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instan...

static CGraphCache & GetInstance()

CRef< TData > GetCachedData(const string &data_key)

Retrieves TData from in-memory cache.

static int GetNearestLevel(const set< int > &levels, double zoom)

CLayoutGroup is a container of CSeqGlyphs (layout objects).

void PushBack(CSeqGlyph *obj)

Append a layout object to the end.

TObjectList & SetChildren()

const TObjectList & GetChildren() const

CLayoutGroup inline methods.

void SetAsMaster(CRef< CSeqGlyph > master)

master glyph has some special meaning (e.g.

ILayoutPolicy::TObjectList TObjectList

CLinkedFeatsGroup is a container class contains related features.

CLayoutGroup & SetGroup()

void PushBack(CSeqGlyph *obj)

CTitleGroup is a layout group with a title.

objects::SAnnotSelector m_Sel

our annotation selector

objects::CScope & GetScope(void) const

CSGAnnotJob inline methods.

int GetGraphLevel() const

TSeqRange m_Range

target range

objects::CBioseq_Handle m_Handle

target sequence

IAppJob::EJobState x_LoadCoverageGraph(CSeqGlyph::TObjects &glyphs, int level, TModelUnit window, const string &title, bool fixed_scale, const TAxisLimits &y_limits)

TSeqRange m_Range

target range

TModelUnit m_Window

current window for smear bars

EJobState x_CalcFeatHistRecursive(CRef< CSeqGlyph > obj, CDensityMap< float > &the_map)

CSGCalcFeatHistJob(const string &desc, const CSeqGlyph::TObjects &objs, const TSeqRange &range, TModelUnit window, TJobToken token)

const CSeqGlyph::TObjects & m_Objects

virtual EJobState x_Execute()

CSGCalcFeatHistJob.

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool IsSharable() const

check if the data source can be shared.

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

CSGFeatureDS(objects::CScope &scope, const objects::CSeq_id &id)

CSGFeatureDS.

void LoadGeneModelFeatures(objects::SAnnotSelector &lm_feat_sel, objects::SAnnotSelector &m_feat_sel, TJobToken lm_token, TJobToken main_token, bool landmark_feat, const TSeqRange &range, TModelUnit window, const CRef< CGeneModelConfig > &conf)

load features for gene model.

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

void CalcFeatHistogram(const CSeqGlyph::TObjects &objs, const TSeqRange &range, TModelUnit window, TJobToken token=-1)

virtual void LoadFeatures(objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token=-1, int max_feat=-1, ELinkedFeatDisplay LinkedFeatDisplay=ELinkedFeatDisplay::eLFD_Default, const string &extra_filter="")

void GetAnnotNames_var(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

vector< string > GetFilters(const string &annot_name, const TSeqRange &range) const

CSGFeatureJob: a job class for loading annotated features from a given sequence and visible range.

CRef< CSeqGlyph > x_CreateCloneFeature(const CMappedFeat &feat, const CSeq_loc &loc)

bool x_FilterFeature_recursive(CLinkedFeature::TLinkedFeats &features, CFeatureFilter &filter)

void x_GetLinkedFeatures(CFeat_CI &feature_iter, CLinkedFeature::TLinkedFeats &features)

IAppJob::EJobState x_CreateFeatSmear(CFeat_CI &feat_iter, CSGJobResult *result, const string &title)

int m_FeatLimit

the maximum number of features allowed.

void SetVcfCacheKey(const string &cache_key)

void x_SortFeatures(CLinkedFeature::TLinkedFeats &feats, TFeatGroups &feat_groups)

bool x_ProcessCachedVcfTabix()

IAppJob::EJobState x_LinkFeatures(CLinkedFeature::TLinkedFeats &feats, CSeqGlyph::TObjects &objs)

bool x_ProcessCachedBigBed()

void x_CalcIntervals(CFeatGlyph &feat)

CSGFeatureJob(const string &desc, CBioseq_Handle handle, const SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token)

vector< TSortedFeats > TFeatGroups

EJobState x_CreateFeatHist(CLinkedFeature::TLinkedFeats &features, CSGJobResult *result, const string &title)

CRef< CSeqGlyph > x_CreateFeature1(const CMappedFeat &feat, CSeqGlyph *parent_glyph=NULL, const char *label_prefix=NULL)

CIRef< ICoordMapper > m_Mapper

void x_SortFeature_recursive(CLinkedFeature::TLinkedFeats &feats, TFeatGroupMap &group_map)

ELinkedFeatDisplay m_LinkedFeat

controls creation of parent or child features

TModelUnit m_Window

current window for smear bars

vector< CRef< CSeqGlyph > > x_CreateCrossOriginGlyphs(const CMappedFeat &feat, CSeqGlyph *parent_glyph=nullptr, const char *label_prefix=nullptr)

static void GetAnnotNames_var(const CBioseq_Handle &handle, const TSeqRange &range, SAnnotSelector &sel, TAnnotNameTitleMap &names)

IAppJob::EJobState x_CreateFeature_Recursive(CLinkedFeature::TLinkedFeats &features, CLayoutGroup *group, int Level)

CIRef< IFeatSorter > m_Sorter

map< int, CLinkedFeature::TLinkedFeats > TFeatGroupMap

void SetBigBedCacheKey(const string &cache_key)

vector< CRef< CSeqGlyph > > x_CreateAndFilterCrossOriginGlyphs(const CMappedFeat &feat, const TSeqRange &range, CSeqGlyph *parent_glyph=nullptr, const char *label_prefix=nullptr)

IAppJob::EJobState x_CreateFeatures(CFeat_CI &feature_iter, CSeqGlyph::TObjects &objs)

static void GetAnnotNames(const CBioseq_Handle &handle, const TSeqRange &range, SAnnotSelector &sel, TAnnotNameTitleMap &names)

EJobState x_CreateFeatHistFromGraph(CSGJobResult *result, int level, const string &title)

pair< string, CLinkedFeature::TLinkedFeats > TSortedFeats

void SetSortBy(const string &sortby)

virtual EJobState x_Execute()

method truly doing the job.

virtual CRef< CSeqGlyph > x_CreateFeature2(const CMappedFeat &feat, const CSeq_loc &loc, const char *label_prefix=NULL)

overridable creator.

void SetFilter(const string &filter)

CIRef< ICoordMapper > m_Mapper

coordinate mapper between mapped features coord. and sequence coord.

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

bool m_Adaptive

adaptive/exact annot selector

int m_Depth

annotation resolving depth

TGraphLevels m_GraphLevels

Existing coverage graph levels.

objects::CBioseq_Handle m_Handle

CSGJobResult – the data structure holding the seqgraphic job results.

ESubtype GetSubtype(void) const

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

void SetTearlineText(const string &sTearlineText)

tearline text – if set, is appended to the glyph name (does not naffect processing otherwise)

list< CRef< CSeqGlyph > > TObjects

CSeqGraphicJob – the base class of seqgraphic job for handling the job status such as reporting the p...

virtual void SetTaskTotal(int total)

map< string, string > TAnnotNameTitleMap

List of annotations with the corresponding titles.

virtual void SetTaskName(const string &name)

virtual void SetTaskCompleted(int completed)

set total finished task number.

void SetToken(TJobToken token)

CSeqGraphicJob inline methods.

virtual void AddTaskCompleted(int delta)

set to add newly finished task number.

TJobToken m_Token

Job token recognizable by job listener.

CRef< CAppJobError > m_Error

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

ICoordMapper interface for converting location between two coordinate systems.

vector< TSeqRange > TIntervals

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

static bool s_HasCDS(const CLinkedFeature &linked_feat)

static bool s_HasFeatXref(const CSeq_feat &feat, CSeqFeatData_Base::E_Choice choice)

static const char * kGeneByLocUrl

static bool s_IsGnomonModel(const CSeq_feat &feat)

static const float kMinScaleForMapping

static const char * kUnsortedGroupName

static bool s_HasTag(const CSeq_feat &feat, const set< string > &tags)

static bool s_IsSelect(const CLinkedFeature &feat)

static const size_t kMaxChildNum

static const int kMaxObjNum

static bool s_IsCCDS(const CLinkedFeature &linked_feat)

bool s_GetGeneWeight(TId2Wt &genes, TGi gi, const TSeqRange &r, size_t retmax)

static const float kSeqZoomLevel

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#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.

@ fHTTP_AutoReconnect

See HTTP_CreateConnectorEx()

#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.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static TMappingInfo GetMappingInfoFromLocation(const objects::CSeq_loc &feat_loc, const objects::CSeq_id &product_id, const int feat_offset=0)

static TMappingInfo GetRnaMappingInfo(const objects::CSeq_loc &feat_loc, const objects::CMappedFeat &feat, const objects::CBioseq_Handle &handle)

Helper function to generate mapping info between the specified product sequence and genomic sequence ...

const objects::CSeq_feat & GetFeature() const

static bool LinkFeatures(CLinkedFeature::TLinkedFeats &feats, TFeatLinkingMode mode=1, ISeqTaskProgressCallback *p_cb=NULL)

Link features into a hierarchical list.

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

request an annotation selector for a given type

list< CRef< CLinkedFeature > > TLinkedFeats

static TMappingInfo GetCdsMappingInfoFromRna(const TMappingInfo &rna_mapping_info, const objects::CSeq_feat &rna_feat, const objects::CMappedFeat &mapped_cds_feat, const objects::CSeq_loc &feat_loc, objects::CScope &scope, const int feat_offset=0)

Derive the CDS feature mapping information based on its parent RNA feature mapping info.

static bool IsCrossOrigin(const objects::CSeq_loc &loc)

static string GetAnnotName(const objects::CSeq_annot_Handle &annot_handle)

static CRef< objects::CSeq_loc > MixLocToLoc(const objects::CSeq_loc &mix_loc, const objects::CBioseq_Handle &handle)

Create a new seq-loc with a unique seq-id from a "mixed" loc.

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static bool IsSameStrands(const objects::CSeq_loc &loc)

static void SetAnnot(objects::SAnnotSelector &sel, const string &annot)

help function for setting up an annotation.

vector< TMappedInt > TMappingInfo

const TLinkedFeats & GetChildren() const

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

CGlPoint< TModelUnit > TModelPoint

virtual bool IsCanceled() const override

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

EJobState

Job states (describe FSM)

@ eSerial_AsnBinary

ASN.1 binary.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

string GetLabel(const CSeq_id &id)

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void Delete(void)

Delete current element, and make iterator to point to the next element.

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TRange GetTotalRange(void) const

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TRange GetRange(void) const

Get the range.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

@ fFGL_Content

Include its content if there is any.

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,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ fComparePositional

Use positional coordinates (ignore strands) when looking for abutting locations.

@ eNoOverlap

CSeq_locs do not overlap or abut.

@ eGetId_ForceGi

return only a gi-based seq-id

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeqFeatData & GetData(void) const

bool IsSetProduct(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

vector< CAnnotName > TAnnotsNames

Object manager recognizes several fields of Seq-annot as annot name.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void)

Get object.

position_type GetLength(void) const

TThisType & IntersectWith(const TThisType &r)

TThisType & SetToOpen(position_type toOpen)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Convert int to string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another 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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

unsigned int usec

microseconds (modulo 1,000,000)

static const char label[]

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.

list< CRef< CEntrez2_docsum > > TList

const TStr & GetStr(void) const

Get the variant data.

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

bool IsLim(void) const

Check if variant Lim is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

TLim GetLim(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TObject & GetObject(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsObject(void) const

Check if variant Object is selected.

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

vector< CRef< CUser_field > > TData

TId GetId(void) const

Get the variant data.

@ eLim_tl

space to left of position

list< CRef< CGBL_Gene > > TGenes

const TData & GetData(void) const

Get the variant data.

bool IsError(void) const

Check if variant Error is selected.

const TError & GetError(void) const

Get the variant data.

vector< CRef< CDbtag > > TDbxref

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TQual & GetQual(void) const

Get the Qual member data.

E_Choice

Choice variants.

bool IsGene(void) const

Check if variant Gene is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetFrame(void) const

Check if a value has been assigned to Frame data member.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

list< CRef< CSeq_loc > > Tdata

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

bool CanGetFuzz(void) const

Check if it is safe to call GetFuzz method.

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

@ e_Empty

to NULL one Seq-id in a collection

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

struct named_group named_group

vector< SFeatBatchJobRequest > TFeatBatchJobRequests

#define row(bind, expected)

CSGFeatureJob implementation.

bool operator()(const CSGFeatureJob::SLandmarkFeat &f1, const CSGFeatureJob::SLandmarkFeat &f2) const

bool operator()(const CSGFeatureJob::SLandmarkFeat &f1, const CSGFeatureJob::SLandmarkFeat &f2) const

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