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

objects::CBioseq_Handle handle,

objects::SAnnotSelector& sel,

, m_SmearOverLimit(

)

, m_LinkPair(

)

, m_LoadCoverageGraph(

)

, m_ShowSecondPass(

)

, m_MaxStartTail(maxStartTail)

, m_MaxEndTail(maxEndTail)

objects::CBioseq_Handle handle,

objects::SAnnotSelector& sel,

align_limit,

smear_if_overlimit,

, m_AlignLimit(align_limit)

, m_SmearOverLimit(smear_if_overlimit)

, m_LinkPair(link_pair)

, m_LoadCoverageGraph(

)

, m_ShowSecondPass(

)

, m_MaxStartTail(maxStartTail)

, m_MaxEndTail(maxEndTail)

objects::CBioseq_Handle handle,

objects::SAnnotSelector& sel,

, m_SmearOverLimit(

)

, m_LinkPair(

)

, m_LoadCoverageGraph(

)

, m_ShowSecondPass(

)

, m_MaxStartTail(maxStartTail)

, m_MaxEndTail(maxEndTail)

objects::SAnnotSelector& sel,

sel.SetCollectNames();

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

(sort_by.empty())

;

found = sort_by.find_first_of(

);

(sorter_type.begin(), sorter_type.end(), sorter_type.begin(), ::

);

(found != string::npos) {

sort_str = sort_by.substr(found + 1);

objects::SAnnotSelector& sel,

& has_quality_map,

sel.SetCollectNames(

);

(num_row < 2)

;

& scope = handle.GetScope();

(

= 0;

< num_row; ++

) {

( !row_handle )

;

objects::CSeq_inst::eMol_dna:

objects::CSeq_inst::eMol_rna:

objects::CSeq_inst::eMol_na:

objects::CSeq_inst::eMol_aa:

}

(this_type !=

) {

(

= num_row - 1;

>= 0; --

) {

(graph_iter && graph_iter.

() == 1) {

has_quality_map =

;

(!(*iter)->GetType().IsStr())

id_str =

.GetStr();

& expect_mate_ti =

)

((*iter)->GetType().IsStr() &&

(*iter)->GetType().GetStr() ==

) {

(ti.empty() &&

>=0) {

= ti.size();

mate_ti = ti.substr(0,

- 1) + (ti[

-1] ==

?

:

);

}

(align.

() && !ti.empty()) {

((*iter)->GetType().IsStr() &&

(*iter)->GetType().GetStr() ==

) {

((*iter)->GetType().IsStr() &&

(*iter)->GetType().GetStr() ==

) {

(mate_ti.empty()) {

= ti.size();

last_second_c = ti[

-2];

last_c = ti[

-1];

(last_second_c ==

&& (last_c ==

|| last_c ==

)) {

mate_ti = ti.substr(0,

- 1) + (last_c ==

?

:

);

(mate_ti.empty()) {

(

.IsGeneral() &&

(

.GetGeneral().GetDb() ==

||

.GetGeneral().GetDb() ==

)) {

(

.GetGeneral().GetTag().IsId()) {

ti =

.GetGeneral().GetTag().GetStr();

(!expect_mate_ti.empty() && mate_ti != expect_mate_ti) {

->m_Results.push_back(single_res);

}

(std::exception& ex) {

(upper_limit <= 0) {

(account_for_tails) {

std::unique_ptr<CAlign_CI> extended_align_iter;

extendedRange(ext_from > 0 ? ext_from : 0, ext_to < bs_len ? ext_to : bs_len);

obj_size = (

)extended_align_iter->GetSize();

status =

(objs, *(extended_align_iter.get()),

,

);

seq_loc->

(aligned_seq);

(feat_iter.

() > 0) {

( ; feat_iter; ++feat_iter) {

main_features.push_back(fref);

other_features.push_back(g_glyph);

feature::CFeatTree::eFeatId_by_type,

) ||

(other_features.begin(), other_features.end(),

back_inserter(

));

( !

.empty() ) {

feat =

(mapped_feat, *mapped_loc);

feat =

(mapped_feat, *mapped_loc);

aligned_seq = anchor == 0 ? 1 : 0;

->Assign(aln_mgr.

(aligned_seq));

anchor_loc = aln_mapper_up.

(*lit.GetRangeAsSeq_loc());

(anchor_loc->IsNull())

mapped_loc = aln_mapper_down.

(*anchor_loc);

(mapped_loc->

())

aligned_loc->

(*mapped_loc);

aligned_segment = lit.GetRangeAsSeq_loc();

anchor_loc = aln_mapper_up.

(*aligned_segment);

(anchor_loc->IsNull()) {

prod_loc = prod_mapper.

(*aligned_segment);

(prod_loc->IsNull()) {

prod_range = prod_loc->GetTotalRange();

prod_from = prod_range.GetFrom();

prod_to = prod_range.GetTo();

gen_loc = aln_mapper_down.

(*anchor_loc);

(offset_from > 0) {

(offset_from == 2) {

(offset_to == 1) {

prod_mapped = prod_mapper_up->Map(*prod_loc);

(prod_mapped->IsNull()) {

diff_loc = prod_mapped->Subtract(*aligned_segment, 0,

,

);

(g_l.

().

() > aligned_segment->GetTotalRange().GetTo())

(g_l.

().

() < aligned_segment->GetTotalRange().GetFrom())

(g_l.

().

() < aligned_segment->GetTotalRange().GetFrom())

(g_l.

().

() > aligned_segment->GetTotalRange().GetTo())

(offset_from > 0) {

(offset_from == 2) {

prod_to -= offset_from;

prod_range.SetTo(prod_range.GetTo() - 1);

prod_from += offset_from;

prod_range.SetFrom(prod_range.GetFrom() + 1);

prod_to -= offset_from;

prod_from += offset_from;

prod_from -= offset_to;

prod_to += offset_to;

prod_int->

(prod_range.GetFrom());

prod_int->

(prod_range.GetTo());

prod_int->

(prod_loc->GetStrand());

prod_int->

().Assign(*prod_loc->GetId());

gen_int->

(aligned_segment->GetTotalRange().GetFrom());

gen_int->

(aligned_segment->GetTotalRange().GetTo());

gen_int->

(aligned_segment->GetStrand());

gen_int->

(*

);

anchor_loc->GetTotalRange(),

(prod_from, prod_to)));

( ; iter; ++iter) {

intervals.push_back(iter.

());

( !glyph )

;

(*iter)->GetFeature().GetData().GetSubtype();

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

( !global_exon_group ) {

global_exon_group->

(glyph);

objs.push_back(glyph);

( !c_glyph )

;

subtype = (*c_iter)->GetFeature().GetData().GetSubtype();

(global_exon_group) {

(objs.size() == 1 &&

*

(objs.front().GetPointer())) {

(global_exon_group->

().size() == 1) {

group->Append(global_exon_group->

());

group->PushBack(global_exon_group.

());

(global_exon_group->

().size() == 1) {

objs.push_back(global_exon_group->

().front());

objs.emplace_back(smear_glyph.

());

objs.emplace_back(smear_glyph.

());

match_id =

;

(aln_annot && aln_annot->

()) {

(objects::CAnnot_descr::Tdata, descrIter, aln_annot->

().

())

((*descrIter)->IsUser() &&

(*descrIter)->GetUser().GetType().IsStr() &&

(*descrIter)->GetUser().GetType().GetStr() ==

) {

(*descrIter)->GetUser().

(

);

reciprocity = 0;

align.

(

, reciprocity) && reciprocity != 3;

match_id =

;

synonyms =

.GetSynonyms();

(; align_iter; ++align_iter) {

vector<CSeq_align::TDim> anchors;

(objs, align, align_handle, aln_datasources, mated_aligns, match_id, flag, filterResults);

(!iter->second.first) {

& ti = iter->first;

mate_ti = iter->second.second;

(mate_iter == mated_aligns.

()) {

id(

+ mate_ti);

(; second_mate_iter; ++second_mate_iter) {

temp, mate_ti, ti)) {

vector<CSeq_align::TDim> anchors;

(!aln_datasources.empty()) {

aln_datasources.front().first, orig_align, align,

}

(!mate_iter->second.first) {

second_mate = mate_iter->second.first;

mate_iter->second.first.

();

als.emplace_back(&first_mate);

als.emplace_back(second_mate.

());

(!objs_to_remove.

()) {

return objs_to_remove.count(glyph.GetPointer()) > 0;

objs.erase(remove_begin, objs.end());

move(mated_objs.begin(), mated_objs.end(), back_inserter(objs));

TAlignGroupMap sorted_aligns;

sorted_aligns[idx].push_back(*iter);

(sorted_aligns.size() > 1) {

(

& group : sorted_aligns) {

sorted_groups[

->GroupIdxToName(group.first)] = group.first;

(

& group : sorted_groups) {

(

& o : objs) {

o->SetLeft(range.

());

group.SetChildren().swap(objs);

group.SetChildren().swap(objs);

return !glyph->GetVisible();

objs.erase(remove_begin, objs.end());

vector<CSeq_align::TDim> anchors;

synonyms =

.GetSynonyms();

retry =

;

vector<CSeq_align::TDim> anchors;

synonyms =

.GetSynonyms();

(

& exon_it : const_exons) {

exon_rng = exon_it->GetRowSeq_range(anchors[0],

);

(!ranges_str.empty()) {

ranges_str +=

;

ranges_str +=

;

(

& exon_it : const_exons) {

exon_rng = exon_it->GetRowSeq_range(anchors[0],

);

& exons = new_align->

().SetSpliced().SetExons();

& exon = **iter;

exon_range(exon.GetGenomic_start(), exon.GetGenomic_end());

(exon_range != exon_rng) {

(

& it : align_ds) {

it.first->SetCrossOrigin(

);

it.first->SetCrossOriginRange(ranges_str);

(objs, *new_align, align_handle, align_ds, mated_aligns, match_id, flag, filterResults);

(

= 0;

< aln_datasources.size(); ++

) {

anchor = aln_datasources[

].second;

& aln_datasource = aln_datasources[

].first;

(filterResults) {

aln_range = aln_datasource->GetAlnRangeWithTails();

align_glyph =

(

(aln_datasource, align_handle, align, anchor));

objs.emplace_back(align_glyph.GetPointer());

mated_aligns.emplace(ti, make_pair(align_glyph, mate_ti));

->m_ObjectList.swap(glyphs);

, m_AlnScoreMap(scores)

(

);

( !score->HasScores() ) {

score->CalculateScores();

objects::CBioseq_Handle handle,

objects::SAnnotSelector& aln_sel,

objects::SAnnotSelector& graph_sel,

& cache_key)

, m_GraphSel(graph_sel)

, m_CacheKey(cache_key)

(iter != sm_GraphTitleMap.end()) {

(

)iter->second;

(iter = sm_GraphTitleMap.begin(); iter != sm_GraphTitleMap.end(); ++iter) {

((

)iter->second == idx) {

vector<unsigned char> ref_bases;

seq_vector.

(start, stop, seq_str);

ref_len = seq_str.length();

(ref_len < stop - start) {

stop = start +

(ref_len);

ref_bases.resize(ref_len);

(

= 0;

< ref_len; ++

) {

loc->

().SetFrom(start);

loc->

().SetTo(stop - 1);

range.

(start, stop - 1);

loc->

(*seq_id);

vector<CRef<CSeq_graph>> graphs;

->SetGraph().SetInt().SetValues().resize(ref_bases.size(), 0);

anchor_start =

(anchor_start, start);

anchor_stop =

(anchor_stop, stop - 1);

((*iter)->IsSimplified()) {

vector<int>& match_vals =

(anchor_start < start) anchor_start = start;

(anchor_stop > stop) anchor_stop = stop;

(anchor_start <= anchor_stop) {

curr_pos = anchor_start - start;

vector<int>& ref_vals =

graphs[ref_bases[curr_pos]]->SetGraph().SetInt().SetValues();

ref_vals[curr_pos]++;

match_vals[curr_pos]++;

(aln_r_e < aln_r_s)

(aln_r_s, aln_r_e);

unique_ptr<IAlnSegmentIterator> p_it(

(curr_aln_r.

())

(curr_seq_from > curr_seq_to)

(curr_seq_from, curr_seq_to);

(curr_seq_from < start) {

pos = start - curr_seq_from;

off = curr_seq_from - start;

curr_pos = off;

0,

(aln_seq.length()), tmp_seq);

(tmp_seq, aln_seq);

(pos < seg_len && curr_pos < ref_len) {

(pos < aln_seq.size()) {

graphs[base_type]->SetGraph().SetInt().SetValues();

vals[curr_pos] += 1;

(base_type == ref_bases[curr_pos])) {

vector<int>& m_vals =

m_vals[curr_pos] += 1;

(pos < aln_seq.size()) {

vals[curr_pos] += 1;

vals[curr_pos] += 1;

(

& gr : graphs) {

graphs_out.emplace_back(gr.GetPointer());

.reserve(batch_size);

vector<CPileUpGraph::TValType>

;

val_num = (size_t)(stop - start);

match_graph =

;

(; graph_iter; ++graph_iter) {

(g_idx == (

)-1)

it = groups.

(range);

(it == groups.

())

it->second[g_idx] = &gr;

match_graph =

;

(groups.

()) {

(!graphs.empty())

groups.emplace(range, graphs);

match_graph =

;

(groups.

())

window = stat_collector.

();

(window < 1.0) window = 1.0;

pix_num = (size_t)ceil(val_num / window);

(graph.

()) {

= vals[curr_idx];

= (

)(

)(vals[curr_idx]);

curr_start, curr_idx, num_vals, ref_idx, stat_idx, end_idx;

(

& group : groups) {

& range = group.first;

& graphs = group.second;

curr_start = max<int>(main_range.

(), range.GetFrom());

curr_idx = curr_start - range.GetFrom();

num_vals = range.GetLength();

stat_collector.

(

(num_vals));

seq_vector.

(

(curr_start),

(curr_start + num_vals), ref_seq_str);

graph_off = (

)range.GetFrom() - (

)main_range.

();

curr_pos = (double)(curr_start - main_range.

());

stat_idx = (size_t)floor(curr_pos / window);

(; stat_idx < pix_num && curr_idx < num_vals; ++stat_idx) {

end_idx = min<size_t>(floor(curr_pos + 0.5) - graph_off, num_vals);

(; curr_idx < end_idx; ++curr_idx, ++ref_idx) {

matches = (match_graph && graphs[g_idx]) ?

l_GetVal(graphs[g_idx]->GetGraph(),

(curr_idx)) : 0;

(ref_idx < ref_seq_str.size()) {

matches = tmp_stat.

[base_type];

(tmp_stat.

[base_type] == 0) {

tmp_stat.

[base_type] = matches;

}

(graphs[g_idx]) {

tmp_stat.

[g_idx] = l_GetVal(graphs[g_idx]->GetGraph(),

(curr_idx));

stat_collector.

(stat_idx, tmp_stat);

vector<TSeqRange> missing_ranges;

->GetMissingRegions(

, missing_ranges);

update_data = !missing_ranges.empty();

(!

->IsCacheGood()) {

vector<future<void>>

;

mutex data_handle_lock;

(

& range : missing_ranges) {

.emplace_back(async(launch::async, [&](){

lock_guard<mutex> guard(data_handle_lock);

->m_DataHandle = tse_handle;

num_reads =

->GetNumberOfReads(

);

(num_reads == 0) {

->m_DataHandle = tse_handle;

(num_reads != 0) {

err_msg =

diag.Print(

, err_msg);

(

<<

<< err_msg);

stat_glyph->ShowIntrons();

}

(exception& e) {

.resize(pix_num);

stat_glyph->ShowIntrons();

->m_DataHandle = tse_handle;

(align_iter.

() == 0)

(

);

synonyms =

.GetSynonyms();

( ; align_iter; ++align_iter) {

vector<CSeq_align::TDim> anchors;

(

= 0;

< aln_datasources.size(); ++

) {

& aln_datasource = aln_datasources[

].first;

.push_back(aln_datasource);

& ids = handle.

();

(

= 0;

< num_row; ++

) {

(

&

: ids) {

(

.

()->Match(row_id)) {

anchors.push_back(

);

(anchors.empty() && synonyms) {

(

level = 0; level <= 5 && anchors.empty(); ++level) {

(

= 0;

< num_row; ++

) {

anchors.push_back(

);

(aln_set.empty())

(!aln_set.front()->GetSegs().IsDenseg())

& new_ds = new_sa->SetSegs().SetDenseg();

dim = aln_set.front()->

();

new_ds.

() = aln_set.front()->GetSegs().GetDenseg().GetIds();

(

j = 0; j < aln_set.size(); ++j) {

(

= 0;

< dim; ++

) {

new_ds.

().push_back(aln_set.front()->GetSeqStrand(

));

vector<int> prev_start(dim, -1);

(

it : aln_set) {

= it->GetSeqRange(anchor_row).GetLength();

(

= 0;

< dim; ++

) {

= it->GetSeqRange(

);

from = max<int>(prev_start[

],

.GetFrom());

prev_start[

] = from +

;

new_sa->Validate(

);

}

(exception& e) {

new_sa.Reset(

);

vector<CSeq_align::TDim>& anchors,

data_sources.clear();

(anchors.empty())

self_alignment =

;

(num_row == (

)anchors.size()) {

self_alignment =

;

exact_self_aligned =

;

exact_self_aligned =

;

(exact_self_aligned) {

anchors.push_back(0);

(align.

() == 2 && (anchors.size() == 1 || self_alignment)) {

(vector<CSeq_align::TDim>, row_iter, anchors) {

vector< CRef< CSeq_loc > >& locs =

(locs[0]->IsInt() && locs[1]->IsInt()) {

len1 = locs[0]->GetTotalRange().GetLength();

len2 = locs[1]->GetTotalRange().GetLength();

(len1 != len2 && len1 != 3 * len2 && len2 != 3 * len1) {

& new_aln_list = new_aln_set->Set();

is_minus = orig_aln_list.front()->GetSeqStrand(anchor_row) ==

;

<void(

*)> add_to_front = [&new_aln_list](

* aln) { new_aln_list.emplace_front(aln); };

<void(

*)> add_to_back = [&new_aln_list](

* aln) { new_aln_list.emplace_back(aln); };

add_to_list = is_minus ? add_to_front : add_to_back;

= aln->GetSeqRange(anchor_row);

seq_align =

*

(aln.GetPointer());

(

.GetTo() < range->

()) {

add_to_list(

);

add_to_list(seq_align);

(

.GetFrom() > range->

()) {

add_to_list(

);

add_to_list(seq_align);

all_of(orig_aln_list.rbegin(), orig_aln_list.rend(), splice_alignment);

all_of(orig_aln_list.begin(), orig_aln_list.end(), splice_alignment);

prev_size = new_aln_list.size();

(prev_size > 300) {

(compressed_aln) {

(!new_aln_list.empty() && new_aln_list.size() < orig_aln_list.size()) {

(new_align->SetSegs().SetDisc().Set(), new_aln_set->Set());

align_ref.

(&*new_align);

( !data_sources.empty() )

report_overlaps =

;

(vector<CSeq_align::TDim>, row_iter, anchors) {

vector<const objects::CSeq_align*>

;

aln_container.

(*align_ref);

(

aln_idx = 0; aln_idx < aln_stats.

(); ++aln_idx) {

( anchored_aln ) {

anchored_aln_vec.push_back(anchored_aln);

anchored_aln->

() += rng_it->GetLength();

(self_alignment) {

(anchored_aln_vec, *out_aln, aln_user_options);

anchored_aln_vec.clear();

anchored_aln_vec.push_back(out_aln);

has_overlaps =

;

& anchored_aln = **a_iter;

(anchored_aln.GetDim() > 1);

(anchored_aln.GetDim() < 2) {

<<

);

report_overlaps =

;

(has_overlaps || anchored_aln.GetPairwiseAlns()[0]->GetSecondBaseWidth() == -1) {

(sparse_aln->

() < 2) {

<<

);

mix.

(*align_ref);

(report_overlaps) {

(

<<

);

for_each(data_sources.begin(), data_sources.end(), [&alignment_partiality](

& dsa){

dsa.first->SetPartialFlags(alignment_partiality);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

static void s_ObjectIdToStr(const CObject_id &id, string &id_str)

static const double kDetailsZoomLevel

Scale at which align details are made visible Align details: unaligned tails, mate pairs.

static const TGraphTitle s_GraphTitles[]

SStaticPair< const char *, CAlnStatConfig::EStatType > TGraphTitle

layout style to layout display name

static const int kMaxAlignmentLoaded

maximal number of alignments allowed to load to avoid potential memery and performance problem.

void GetAnchors(CBioseq_Handle &handle, const CSynonymsSet *synonyms, const CSeq_align &align, vector< CSeq_align::TDim > &anchors)

const string & s_GraphIndexToTitle(size_t idx)

static CRef< CSeq_align > s_CompressDiscToDenseq(list< CRef< CSeq_align >> &aln_set, int anchor_row)

static bool s_IsMatchById(CConstRef< CSeq_annot > aln_annot)

size_t s_GraphTitleToIndex(const string &title)

static bool s_IsSecondPassAlignment(const CSeq_align &align)

DEFINE_STATIC_ARRAY_MAP(TGraphTitleMap, sm_GraphTitleMap, s_GraphTitles)

CStaticArrayMap< string, CAlnStatConfig::EStatType > TGraphTitleMap

void BuildAlignDataSource(CBioseq_Handle &handle, vector< CSeq_align::TDim > &anchors, const CSeq_align &align, bool sparseAln, TModelUnit window, TAlnDataSources &data_sources, CRange< TSeqPos > *range)

static bool s_CheckTraceMateAlign(bool match_id, bool is_bam_align, const CSeq_align &align, string &ti, string &mate_ti, const string &expect_mate_ti="")

static const double kSequenceZoomLevel

always show individual alignments when zoom level is below this threshold.

pair< CRef< IAlnGraphicDataSource >, int > TAlnDS_Anchor

CSGAlignmentJob.

vector< TAlnDS_Anchor > TAlnDataSources

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

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.

CAlnStats< TAlnIdMap > TAlnStats

Default implementations for alignment stats.

vector< const CSeq_align * > TAlnVector

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

Default implementations of CAlnIdMap.

void remove_if(Container &c, Predicate *__pred)

void transform(Container &c, UnaryFunction *op)

Checksum and hash calculation classes.

bool IsSet(int flags) const

static IAlignSorter * CreateAlignSorter(std::string const &sort_by, std::string const &sort_str)

const_iterator insert(const CSeq_align &seq_align)

Insert new CSeq_align into the list.

size_type size(void) const

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

void push_back(const CSeq_align &aln)

Adding an alignment.

void SetAnchor(TNumrow anchor)

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

void Merge(TMergeFlags flags=0)

const CDense_seg & GetDenseg(void) const

static int GetRefSeqIdex(char base)

@ eStat_Intron

intron (for mRNA-to-genome alignments)

@ eStat_Mismatch

mismatches (A+G+T+C - matches)

@ eStat_Total

total alignment count at this base (A+G+T+C+Gap)

vector< SStatStruct > TStatVec

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

size_t GetAlnCount(void) const

How many alignments do we have?

Options for different alignment manager operations.

@ ePreserveRows

Preserve all rows as they were in the input (e.g.

@ eBothDirections

No filtering: use both direct and reverse sequences.

CAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for CAlnVec-based alignments.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

TDim GetDim(void) const

How many rows.

void SetScore(int score)

Set the total score.

Seq-loc and seq-align mapper exceptions.

const TAnnotNames & GetAnnotNames(void) const

size_t GetSize(void) const

CSeq_annot_Handle GetAnnot(void) const

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

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

TNumseg CheckNumSegs(void) const

bool IsSetWidths(void) const

This class is intended to be used for pairwised dense-seg seq-align to replace CSparseAlnGraphicDataS...

void SetColoringAvailable(bool v=true)

TIntervals & SetIntervals()

CFeatGlyph inline implementations.

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

access the position of this object.

void SetProjectedMappingInfo(const CProjectedMappingInfo &info)

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

void SaveData(CRef< TData > data)

Clones TData, puts it into Save Queue for asynchroneous storage operation.

void RemoveData(const string &data_key)

Removes Data from in-memory cache.

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()

CAlnStatGlyph::TStatVec & m_Stats

CGraphStatCollector_Glyph(double window, CAlnStatGlyph::TStatVec &stats)

virtual void AddStat(size_t index, CAlnStatGlyph::SStatStruct &stat) override

virtual void UpdateGroup(size_t offset) override

virtual bool ComputePileUp() override

virtual void NewGroup(int batch_size) override

vector< CPileUpGraph::TValType > matches

vector< CPileUpGraph::TValType > mismatches

virtual void AddStat(size_t index, CAlnStatGlyph::SStatStruct &stat) override

CGraphStatCollector_Graph(double window, CPileUpGraph &data)

vector< CPileUpGraph::TValType > introns

vector< CPileUpGraph::TValType > gaps

virtual void ClearRange(const TSeqRange &range) override

CGraphStatCollector Helper class to use with CSGAlignStatJob::x_CollectAlignStats x_CollectAlignStats...

virtual bool ComputePileUp()

virtual void ClearRange(const TSeqRange &range)

virtual void AddStat(size_t index, CAlnStatGlyph::SStatStruct &stat)=0

virtual void UpdateGroup(size_t offset)

virtual void NewGroup(int batch_size)

CJobResultBase – the basic job result class holding a token.

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 Append(TObjectList &objs)

vector< CRef< CAlignGlyph > > TAlignList

CTitleGroup is a layout group with a title.

A pairwise aln is a collection of ranges for a pair of rows.

void SetAlignmentDataSource(const IAlnGraphicDataSource &align_ds)

CProjectedMappingInfo inline methods.

CSGAlignScoringJob(const string &desc, const TAlnScoreMap &scores)

CSGAlignScoringJob.

virtual EJobState x_Execute()

method truly doing the job.

TAlnScoreMap m_AlnScoreMap

EJobState x_LoadAlignments(objects::CTSE_Handle &tse_handle)

EJobState x_CollectAlignStats(const TSeqRange &main_range, objects::CTSE_Handle &tse_handle, CGraphStatCollector &stat_collector)

vector< CConstRef< IAlnGraphicDataSource > > TAlnMgrVec

objects::SAnnotSelector m_GraphSel

pileup graph selector

string m_CacheKey

Graph cache key calculated by alignment ds.

TModelUnit m_Window

current zoom scale

CSGAlignStatJob(const string &desc, objects::CBioseq_Handle handle, const objects::SAnnotSelector &aln_sel, const objects::SAnnotSelector &graph_sel, const TSeqRange &range, const TAlnMgrVec &aligns, TModelUnit scale, const string &cache_key)

CSGAlignStatJob.

IAlnGraphicDataSource::TNumrow TNumrow

vector< CConstRef< objects::CSeq_graph > > TGraphs

virtual EJobState x_Execute()

method truly doing the job.

void x_CreatePileUpGraphs(TSeqRange &range, TGraphs &graphs)

void x_UpdateMaxTails(const IAlnGraphicDataSource &aln_datasource)

CIRef< ILayoutPolicy > m_LayoutPolicy

CAlignmentConfig::EUnalignedTailsMode m_UnalignedTailsMode

Flag, indicating whether and how to display unaligned tails.

void x_CreateCAlignGlyph(CSeqGlyph::TObjects &objs, const objects::CSeq_align &align, const objects::CSeq_align_Handle &align_handle, const TAlnDataSources &aln_datasources, TMatedAlignments &mated_aligns, bool match_id, CSGAlignmentJob::EAlignFlags flag, bool filterResults)

EJobState x_LoadAlignments()

CRef< CSGJobResult > x_LoadAlignmentFeats(CAlignGlyph &align)

CAlignmentConfig::EHideSraAlignments m_HideSra

Flag, indicating whether to hide duplicates and/or bad reads.

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

int m_AlignLimit

max number of alignments to load.

bool x_CreateGeneModels(objects::CSeq_loc_Mapper &mapper, CLinkedFeature::TLinkedFeats &feats, CSeqGlyph::TObjects &objs, CAlignGlyph &align) const

IAppJob::EJobState x_GetAlignments(CSeqGlyph::TObjects &objs, objects::CAlign_CI &align_iter, bool sparseAln, bool filterResults=false)

EAlignFlags

Request a list of alignments from a bioseq.

static IAlnExplorer::EAlignType GetAlignType(const objects::CBioseq_Handle &handle, objects::SAnnotSelector &sel, bool &has_quality_map, bool isFastConfig=false)

when isFastConfig set to true, it indicates that that the call is used by seqconfig this means that s...

IAppJob::EJobState x_GetCoverageGraph()

IAppJob::EJobState x_GetAlignSmear(CSeqGlyph::TObjects &objs, objects::CAlign_CI &align_iter)

void SetSortBy(const string &sort_by)

TModelUnit m_Window

current window for smear bars

CSGAlignmentJob(const string &desc, objects::CBioseq_Handle handle, const objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TSignedSeqPos &maxStartTail, TSignedSeqPos &maxEndTail)

constructor for loading coverage graph.

void x_BuildAlignDataSource(const objects::CSeq_align &align, TAlnDataSources &align_ds, bool sparseAln)

TSignedSeqPos & m_MaxEndTail

Max length of unaligned tail at the end of the sequence.

vector< CRef< CAlignGlyph > > m_Aligns

alignments feature retrieval

bool FilterDuplicatesAndBadReads(const objects::CSeq_align &mapped_align)

virtual EJobState x_Execute()

method truly doing the job.

void x_CreateAlignGlyphsForCrossOriginAlign(CSeqGlyph::TObjects &objs, const objects::CSeq_align &align, const objects::CSeq_align_Handle &align_handle, bool sparseAln, TMatedAlignments &mated_aligns, bool match_id, CSGAlignmentJob::EAlignFlags flag, bool filterResults)

CRef< CSeqGlyph > x_CreateFeatGlyph(objects::CSeq_loc_Mapper &mapper, const objects::CMappedFeat &mapped_feat, CAlignGlyph &align) const

CIRef< IAlignSorter > m_Sorter

bool m_SmearOverLimit

flag indicating if smear is needed

bool m_LinkPair

link mate pair aligns

TSignedSeqPos & m_MaxStartTail

> Flag to show second-pass alignments (relevant to assembly to assembly alignments)

objects::SAnnotSelector m_Sel

our annotation selector

objects::CScope & GetScope(void) const

CSGAnnotJob inline methods.

TSeqRange m_Range

target range

IAppJob::EJobState x_CreateHistFromGraph(CSeqGlyph::TObjects &glyphs, const objects::SAnnotSelector &sel, TModelUnit window, bool fixed_scale, const TAxisLimits &y_limits)

objects::CBioseq_Handle m_Handle

target sequence

CSGJobResult – the data structure holding the seqgraphic job results.

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)

virtual void SetTaskName(const string &name)

virtual void SetTaskCompleted(int completed)

set total finished task number.

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

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

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...

CRef< CSeq_loc > CreateRowSeq_loc(TDim row) const

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

bool GetNamedScore(const string &id, int &score) const

Get score.

void Validate(bool full_test=false) const

void SetPartialStart(bool val, ESeqLocExtremes ext)

void SetPartialStop(bool val, ESeqLocExtremes ext)

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

This class is intended to be used for optimized version of pairwise seq-align to replace CSparseAlnGr...

void SetRegularity(bool f)

TDim GetDim(void) const

Alignment dimension (number of sequence rows in the alignment)

void Update(const TSeqRange &range, const TUpdateMap &update)

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Return a field reference representing the tokenized key, or a NULL reference if the key doesn't exist...

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

IAlnGraphicDataSource - interface to a data source representing an abstract alignment used in graphic...

virtual void GetUnalignedTails(TSignedSeqPos &start_tail, TSignedSeqPos &end_tail, bool clipped=true) const

virtual IAlnExplorer::EAlignType GetAlignType() const

virtual TSeqPos GetSeqStart(TNumrow row) const =0

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const =0

virtual string & GetSeqString(string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const

Get sequence string for a given row in sequence range.

virtual bool IsPositiveStrand(TNumrow row) const =0

virtual TSeqPos GetSeqStop(TNumrow row) const =0

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

Alignment segment iterator interface.

@ eAllSegments

Iterate all segments.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fAligned

Aligned segment.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

vector< TSeqRange > TIntervals

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(IAlnExplorer::TNumrow, const IAlnExplorer::TSignedRange &, IAlnSegmentIterator::EFlags) const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(IAlnExplorer::TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

container_type::iterator iterator

const_iterator end() const

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const struct name_t names[]

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

NetSchedule worker node application.

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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.

void Warning(CExceptionArgs_Base &args)

void Fatal(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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 bool IsCrossOrigin(const objects::CSeq_loc &loc)

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

int GetOrigAnchor(void) const

const IAlnGraphicDataSource & GetAlignMgr(void) const

Inline methods.

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static bool IsGeneModelFeature(int type, int subtype)

Does feature belong to gene model track Gene, RNA, cdregion, exon, C_region, and VDJ segments.

const objects::CSeq_align_Handle & GetOrigAlignment(void) const

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

access the position of this object.

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

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

const objects::CSeq_align & GetAlignment(void) const

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

void SetId(CSeq_id &id)

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

TRange GetTotalRange(void) const

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

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.

ENa_strand GetStrand(void) const

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,...

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_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

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.

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const CTSE_Handle & GetTSE_Handle(void) const

const CSeqFeatData & GetData(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

bool ContainsSegment(const CSeq_id &id, size_t resolve_depth=kMax_Int, EFindSegment limit_flag=eFindSegment_NoLimit) const

Check if the seq-id describes a segment of the bioseq.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

const TId & GetId(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const string & GetTitle(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_graph & GetMappedGraph(void) const

Graph mapped to the master sequence.

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

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

bool IntersectingWith(const TThisType &r) const

position_type GetToOpen(void) const

TThisType & Set(position_type from, position_type to)

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

static TThisType GetWhole(void)

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

Convert int to 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.

@ fWithCommas

Use commas as thousands separator.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

const TTag & GetTag(void) const

Get the Tag member data.

const TData & GetData(void) const

Get the Data member data.

TBool GetBool(void) const

Get the variant data.

bool IsInt(void) const

Check if variant Int is selected.

bool IsStr(void) const

Check if variant Str is selected.

TInt GetInt(void) const

Get the variant data.

bool IsBool(void) const

Check if variant Bool is selected.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

list< CRef< CUser_object > > TExt

vector< CRef< CSeq_id > > TIds

const TSpliced & GetSpliced(void) const

Get the variant data.

TDim GetDim(void) const

Get the Dim member data.

const TStd & GetStd(void) const

Get the variant data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsDisc(void) const

Check if variant Disc is selected.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

TIds & SetIds(void)

Assign a value to Ids data member.

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.

@ eType_disc

discontinuous alignment

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

void SetTo(TTo value)

Assign a value to To data member.

bool IsEmpty(void) const

Check if variant Empty is selected.

void SetId(TId &value)

Assign a value to Id data member.

bool IsGeneral(void) const

Check if variant General is selected.

void SetFrom(TFrom value)

Assign a value to From data member.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TInt & GetInt(void) const

Get the variant data.

bool IsInt(void) const

Check if variant Int is selected.

const TValues & GetValues(void) const

Get the Values member data.

const TByte & GetByte(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

const TLoc & GetLoc(void) const

Get the Loc member data.

const Tdata & Get(void) const

Get the member data.

const TInst & GetInst(void) const

Get the Inst member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

TMol GetMol(void) const

Get the Mol member data.

unsigned int

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

double value_type

The numeric datatype used by the parser.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Useful/utility classes and methods.

T bound(T x_, T xlo_, T xhi_)

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

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

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

struct named_group named_group

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Reader-writer based streams.

#define row(bind, expected)

int m_Data[CAlnStatConfig::eStat_Total+1]

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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