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NCBI C++ ToolKit: src/objtools/edit/seq_entry_edit.cpp Source File

<

Key,

Data,

Compare = less<Key>,

Alloc = allocator<pair<const Key,Data> > >

CMapWithOriginalOrderingIteration :

<Key, Data, Compare, Alloc>

m_keysInOriginalOrder.push_back( x.first );

iterator find_iter =

(k);

( find_iter !=

() ) {

find_iter->second;

.first->second;

vector<Key> TKeyVec;

TKeyVec & GetKeysInOriginalOrder(

)

{

( m_keysInOriginalOrder.size() ==

() );

m_keysInOriginalOrder;

TKeyVec m_keysInOriginalOrder;

constexpr

ConstructSortMap()

std::array<unsigned char, CSeqdesc::E_ChoiceStopper::e_MaxChoice> _sorted{};

static_assert(init_seqdesc_sortmap.size() <= _sorted.size());

(

& it: _sorted)

index=0;

(

rec: init_seqdesc_sortmap)

_sorted[rec] = index;

seqdesc_sortmap = ConstructSortMap();

CompareSeqdesc

(c<0 || c>=seqdesc_sortmap.size())

seqdesc_sortmap[c];

mapit(

->Which()) < mapit(

->Which());

((*it)->IsLiteral()) {

= (*it)->GetLiteral().GetLength();

}

((*it)->IsLoc()) {

(

->IsLoc())

;

(

->GetLiteral().CanGetSeq_data() &&

->GetLiteral().GetSeq_data().IsGap()){

(!seq_hl)

;

(!start)

;

(

< (start - 1) )

;

(it.IsInGap())

;

(!seq_hl)

;

(stop >= seq_vec.

() - 1)

;

(

< (stop + 1) )

;

(it.IsInGap())

;

( it->IsSeq() && it->GetSeq().GetInst_Mol() != seq_mol ) {

);

back_inserter(segs));

parts = it->SetSet();

}

( it->IsSeq() &&

master = it->SetSeq();

( !parts || !master ) {

( !target || !insert ) {

}

( target.

() && insert.

() ) {

.MoveTo(nuc_prot);

= 0;

seq->

().push_back(

);

}

( to_mol == add_mol ) {

( it->

() &&

seq.

(nuc_prot, 0);

( !

|| !seq ) {

( !seq_edit || !set_edit ) {

seq_edit.

(set_edit);

(

it:

.Get()) {

(it->Equals(desc)) {

}

(it->IsPub() &&

it->GetPub().GetPub().SameCitation(desc.

().

())) {

seq_descr.

().push_back(d);

(entry.

()) {

}

(entry.

()) {

(entry->

()) {

( ! direct_child_ci ) {

( direct_child_ci ) {

( ; annot_ci; ++annot_ci ) {

vector<CSeq_entry_EditHandle> TBioseqSetsToPromote;

TBioseqSetsToPromote bioseqSetsToPromote;

( ; direct_child_set_ci; ++direct_child_set_ci ) {

++direct_child_direct_child_ci;

( ! direct_child_direct_child_ci );

desc_choices_to_erase );

bioseqSetsToPromote.push_back(

direct_child_direct_child_eh );

( TBioseqSetsToPromote, promoted_set_it, bioseqSetsToPromote ) {

promoted_set_it->GetParentEntry().Remove();

}

( rhs.

() ) {

lhs_asn < rhs_asn;

( asn_text.empty() ) {

stringstream asn_strm;

asn_strm.str().swap( asn_text );

( ! target || ! target.

() ) {

child_became_parent =

;

( ! target_parent_h ) {

target_parent_h = bioseq_set_h;

child_became_parent =

;

vector< CConstRef<CSeqdesc> > TDescRefVec;

TDescRefVec vecDescsToAddToNewBioseqSet;

vector< CConstRef<CSeq_annot> > TAnnotRefVec;

TAnnotRefVec vecAnnotsToAddToNewBioseqSet;

( best_entry_for_bioseq &&

( parent_entry && parent_entry.

() &&

best_entry_for_bioseq = parent_entry;

( ! best_entry_for_bioseq ) {

( ; desc_ci; ++desc_ci ) {

vecDescsToAddToNewBioseqSet.push_back(

( ; annot_ci; ++annot_ci ) {

( ; dest_desc_ci; ++dest_desc_ci ) {

( TDescRefVec, src_seqdesc_ref_it, vecDescsToAddToNewBioseqSet ) {

( descsSeen.

(*src_seqdesc_ref_it) != descsSeen.

() ) {

descsSeen.

( *src_seqdesc_ref_it );

( ; dest_annot_ci; ++dest_annot_ci ) {

( TAnnotRefVec, src_annot_it, vecAnnotsToAddToNewBioseqSet ) {

( annotsSeen.

(*src_annot_it) != annotsSeen.

() ) {

annotsSeen.

( *src_annot_it );

( child_became_parent ) {

vector<CSeq_entry_Handle> siblingVec;

++new_set_sibling_ci;

( ; new_set_sibling_ci; ++new_set_sibling_ci ) {

siblingVec.push_back(*new_set_sibling_ci);

bNeedsNewSet =

;

( vector<CSeq_entry_Handle>, sibling_it, siblingVec ) {

( sibling_it->IsSeq() ) {

bNeedsNewSet =

;

( sibling_it->IsSet() &&

bNeedsNewSet =

;

( bNeedsNewSet ) {

( vector<CSeq_entry_Handle>, sibling_it, siblingVec ) {

( ; parent_descr_ci; ++parent_descr_ci ) {

( ! target || ! target.

() ) {

( ; direct_child_ci; ++direct_child_ci ) {

vecOfSeqEntryHandles.push_back(*direct_child_ci);

bAnyAlignChanged =

;

vector< CConstRef<CDense_diag> > TDenseDiagVec;

TMapEntryToDenseDiags mapEntryToDenseDiags;

pDendiag->IsSetIds() && pDendiag->GetIds().size() == 2 )

bRemoveDendiag =

;

mapDescendentToInputEntry.

(bioseqs_entry) :

mapDescendentToInputEntry.

() );

( find_input_entry_iter == mapDescendentToInputEntry.

() ) {

find_input_entry_iter->second;

(candidate_input_entry);

( ! dest_input_entry ) {

dest_input_entry = candidate_input_entry;

}

( dest_input_entry == candidate_input_entry ) {

bRemoveDendiag =

;

( bRemoveDendiag ) {

bAnyAlignChanged =

;

( dest_input_entry != old_input_entry ) {

bAnyAlignChanged =

;

mapEntryToDenseDiags[dest_input_entry].push_back(pDendiag);

mapEntryToDenseDiags[old_input_entry].push_back(pDendiag);

( mapEntryToDenseDiags.size() == 1 )

mapEntryToDenseDiags.begin()->first;

mapEntryToAlignVec[dest_input_entry].push_back( align.

() );

entry_to_dendiags_iter,

mapEntryToDenseDiags )

entry_to_dendiags_iter->first;

TDenseDiagVec & dendiag_vec = entry_to_dendiags_iter->second;

( ! dendiag_vec.empty() );

pNewAlign->

().SetDendiag();

( TDenseDiagVec, dendiag_vec_it, dendiag_vec ) {

pNewDendiag->Assign( **dendiag_vec_it );

new_dendiag_vec.push_back( pNewDendiag );

mapEntryToAlignVec[dest_input_entry].push_back( pNewAlign );

bAnyAlignChanged =

;

bAnyAlignChanged;

bAnyAlignChanged =

;

vector<CDense_seg::TDim> TRowVec;

TMapInputEntryToDensegRows mapInputEntryToDensegRows;

(

iRow = 0; iRow < ids.size(); ++iRow) {

mapDescendentToInputEntry.

(id_bioseq_entry) :

mapDescendentToInputEntry.

() );

( find_input_entry_iter == mapDescendentToInputEntry.

() ) {

bAnyAlignChanged =

;

find_input_entry_iter->second;

( id_input_entry != old_input_entry ) {

bAnyAlignChanged =

;

mapInputEntryToDensegRows[id_input_entry].push_back(iRow);

( ! bAnyAlignChanged ) {

mapEntryToAlignVec[old_input_entry].push_back( align.

() );

(TMapInputEntryToDensegRows,

input_entry_to_denseg_it,

mapInputEntryToDensegRows)

input_entry_to_denseg_it->first;

TRowVec & rowVec = input_entry_to_denseg_it->second;

pNewSeqAlign->

().SetDenseg( *pNewDenseg );

mapEntryToAlignVec[dest_input_entry].push_back( pNewSeqAlign );

bAnyAlignChanged =

;

bAnyAlignChanged;

( ! annot_h.

() ) {

bAnyAlignNeedsChange =

;

( ; align_ci; ++align_ci) {

align, mapDescendentToInputEntry, mapEntryToAlignVec) )

bAnyAlignNeedsChange =

;

align, mapDescendentToInputEntry, mapEntryToAlignVec) )

bAnyAlignNeedsChange =

;

mapEntryToAlignVec[old_input_entry].push_back(align.

());

( ! bAnyAlignNeedsChange ) {

pOldAnnotWithNoAligns->

().SetAlign().clear();

( TMapEntryToAlignVec::TKeyVec,

entry_to_aligns_iter,

mapEntryToAlignVec.GetKeysInOriginalOrder() )

mapEntryToAlignVec.find(dest_input_entry)->second;

pNewAnnot->

(*pOldAnnotWithNoAligns);

pNewAnnot->

().SetAlign();

( new_aligns.empty() );

pNewAlign->

( **align_it );

new_aligns.push_back( pNewAlign );

mapSeqAnnotToDest[pNewAnnot] = dest_input_entry;

vecOfSeqAnnotToErase.push_back(annot_h);

mapDescendentToInputEntry[*input_entry_iter] = *input_entry_iter;

(; descendent_entry_iter; ++descendent_entry_iter ) {

mapDescendentToInputEntry[*descendent_entry_iter] = *input_entry_iter;

( ; annot_ci; ++annot_ci ) {

mapDescendentToInputEntry,

vecOfSeqAnnotsToErase );

(TMapSeqAnnotToDest::TKeyVec,

mapSeqAnnotToDest.GetKeysInOriginalOrder() )

& dest_entry_h = mapSeqAnnotToDest.find(pAnnot)->second;

( dest_entry_h ) {

pAnnotCopy->

(*pAnnot);

input_entry_iter->GetEditHandle().AttachAnnot(*pAnnotCopy);

annot_iter->GetEditHandle().Remove();

(

.IsEmptySeq_set()) {

((*it)->IsSetDescr()) {

(!(*d)->IsTitle() && !(*d)->IsMolinfo() && !(*d)->IsSource()) {

master->

().push_back(cpy);

CSeq_descr::Tdata::iterator d = master->

().begin();

(d != master->

().end()) {

found =

;

((*d)->Equals(**s)) {

d = master->

().erase(d);

(master->

() && !master->

().empty()) {

((*it)->IsSeq()) {

CBioseq::TDescr::Tdata::iterator di = bse.

().Set().begin();

(di != bse.

().Set().end() && !(*di)->Equals(**d)) {

(di != bse.

().Set().end()) {

}

((*it)->IsSet()) {

CBioseq_set::TDescr::Tdata::iterator di = bsse.

().Set().begin();

(di != bsse.

().Set().end() && !(*di)->Equals(**d)) {

(di != bsse.

().Set().end()) {

vector<CSeqdesc::E_Choice> &choices_to_delete )

( ! bioseq_set_h ) {

stable_sort( sorted_choices_to_delete.begin(),

sorted_choices_to_delete.end() );

( ; desc_ci; ++desc_ci ) {

( ! binary_search( sorted_choices_to_delete.begin(),

sorted_choices_to_delete.end(), desc_ci->

() ) )

pSeqDescrWithChosenDescs->

().push_back(

pSeqDescrToCopy = pSeqDescrWithChosenDescs;

( ; direct_child_ci; ++direct_child_ci ) {

(

.Which()) {

(

.GetLocal().IsStr()) {

=

.GetLocal().GetStr();

}

(

.GetLocal().IsId()) {

=

.AsFastaString();

(entry.

()) {

need_object =

;

need_object =

;

obj->

().push_back(field);

seq.

().Set().push_back(desc);

found =

;

any_type =

;

found_mismatch =

;

((*id_it)->Which() == choice) {

found_mismatch =

;

found_mismatch =

;

found_mismatch =

;

found_mismatch =

;

(!found && (any_type || found_mismatch)) {

(

it: user.

()) {

(entry.

()) {

(entry.

()) {

((*desc_it)->IsUser() && (*desc_it)->GetUser().GetObjectType() ==

) {

((*desc_it)->IsUser() && (*desc_it)->GetUser().GetObjectType() ==

) {

ds->SetLiteral().SetSeq_data().SetIupacna().Set(element);

ds->SetLiteral().SetLength(

(element.length()));

inst.

().SetDelta().Set().push_back(ds);

(is_assembly_gap)

gap->SetLiteral().SetSeq_data().SetGap();

gap->SetLiteral().SetSeq_data().SetGap().SetType(gap_type);

gap->SetLiteral().SetSeq_data().SetGap().SetLinkage(linkage);

(linkage_evidence >= 0)

link_ev->SetType(linkage_evidence);

gap->SetLiteral().SetSeq_data().SetGap().SetLinkage_evidence().push_back(link_ev);

gap->SetLiteral().SetLength(n_len);

inst.

().SetDelta().Set().push_back(gap);

min_unknown,

max_unknown,

min_known,

max_known,

is_assembly_gap,

gap_type,

linkage,

linkage_evidence )

(

, it, iupacna) {

((*it) ==

) {

is_unknown =

;

is_known =

;

(n_len >= min_unknown && (max_unknown < 0 || n_len <= max_unknown)) {

}

(n_len >= min_known && (max_known < 0 || n_len <= max_known)) {

(is_unknown || is_known) {

(element.length() > n_len) {

element = element.substr(0, element.length() - n_len);

(inst, n_len, is_unknown, is_assembly_gap, gap_type, linkage, linkage_evidence);

is_unknown =

;

is_known =

;

(n_len >= min_unknown && (max_unknown < 0 || n_len <= max_unknown)) {

}

(n_len >= min_known && (max_known < 0 || n_len <= max_known)) {

(is_unknown || is_known) {

(element.length() > n_len) {

element = element.substr(0, element.length() - n_len);

(inst, n_len, is_unknown, is_assembly_gap, gap_type, linkage, linkage_evidence);

((*it)->IsLiteral()) {

((*it)->GetLiteral().IsSetLength()) {

orig_len = (*it)->GetLiteral().GetLength();

((*it)->GetLiteral().IsSetFuzz()

&& orig_len != unknown_length

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

diff = unknown_length - orig_len;

(*it)->SetLiteral().SetLength(unknown_length);

}

((*it)->IsLoc()) {

orig_len = (*it)->GetLoc().GetTotalRange().GetLength();

min_unknown,

max_unknown,

min_known,

max_known,

is_assembly_gap,

gap_type,

linkage,

linkage_evidence )

(*inst, min_unknown, max_unknown, min_known, max_known, is_assembly_gap, gap_type, linkage, linkage_evidence);

(changes.size() > 0) {

cpy->

(*(

->GetSeq_feat()));

TLocAdjustmentVector::reverse_iterator it = changes.rbegin();

trimmed =

;

(it != changes.rend() && !cut) {

(it->second < 0) {

((*it)->IsLiteral()

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

& gap = (*it)->SetLiteral().SetSeq_data().SetGap();

((*it)->IsLiteral()

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

& gap = (*it)->SetLiteral().SetSeq_data().SetGap();

((*it)->IsLiteral()

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

& gap = (*it)->SetLiteral().SetSeq_data().SetGap();

((*it)->IsLiteral()

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

& gap = (*it)->SetLiteral().SetSeq_data().SetGap();

((*it)->IsLiteral()

&& (!(*it)->GetLiteral().IsSetSeq_data() || (*it)->GetLiteral().GetSeq_data().IsGap())) {

& gap = (*it)->SetLiteral().SetSeq_data().SetGap();

ss <<

<< nuc_len;

TCuts::const_iterator cit;

(cit = cuts.begin(); cit != cuts.end(); ++cit) {

& cut = *cit;

(cut_from < 0 || cut_to < 0 || cut_from >= nuc_len || cut_to >= nuc_len) {

ss <<

<< cut_from <<

<< cut_to <<

;

num_cuts = sorted_merged_cuts.size();

(num_cuts==1 || num_cuts==2);

& first_cut = sorted_merged_cuts[0];

(num_cuts == 1) {

(first_cut.GetFrom() == 0) {

range.

(first_cut.GetTo()+1);

range.

(seqLength-1);

range.

(first_cut.GetFrom()-1);

(first_cut.GetFrom() > 0);

range.

(first_cut.GetFrom()-1);

range.

(sorted_merged_cuts[1].GetTo()+1);

(bsh, cuts, sorted_cuts, internal_cut_conversion);

(; feat_ci; ++feat_ci) {

bFeatureDeleted =

;

bFeatureTrimmed =

;

isPartialStart =

;

isPartialStop =

;

(copy_feat, sorted_cuts, bFeatureDeleted, bFeatureTrimmed, isPartialStart, isPartialStop);

(bFeatureDeleted) {

}

(bFeatureTrimmed) {

new_frame = sequence::CFeatTrim::GetCdsFrame(original_feat, retainedRange);

copy_feat->

().SetCdregion().SetFrame(new_frame);

(bsh, isPartialStart, isPartialStop, copy_inst, copy_feat, sorted_cuts);

feat_eh.

(*copy_feat);

(; align_ci; ++align_ci) {

(; graph_ci; ++graph_ci) {

(it = sorted_cuts.begin(); it != sorted_cuts.end(); ) {

( it+1 != sorted_cuts.end() ) {

& next_cut = *(it+1);

( next_from <= (to + 1) ) {

cut.

(next_to);

sorted_cuts.erase(it+1);

(TCuts::size_type ii = 0; ii < cuts.size(); ++ii) {

(from != 0 && to != seq_length-1) {

(from - 0 < seq_length-1 - to) {

cut.

(seq_length-1);

cut.

(seq_length-1);

& sorted_cuts,

(TCuts::size_type ii = 0; ii < cuts.size(); ++ii) {

& cut = cuts[ii];

sorted_cuts.push_back(cut);

(sorted_cuts.begin(), sorted_cuts.end(), asc);

internal_cut_conversion);

(sorted_cuts.begin(), sorted_cuts.end(), descend);

(seqmap_ci.

()) {

(pOriginalGapSeqLiteral) {

pNewGapLiteral->Assign(*pOriginalGapSeqLiteral);

(!bIsLengthKnown) {

pNewGapLiteral->SetLength(uGapLength);

pDeltaSeq->SetLiteral(*pNewGapLiteral);

pDeltaExt->

().push_back(

(&*pDeltaSeq));

new_length += uGapLength;

pDeltaSeq->SetLiteral().SetLength(seqmap_ci.

());

pDeltaSeq->SetLiteral().SetSeq_data(*pSeqData);

pDeltaExt->

().push_back(

(&*pDeltaSeq));

& sorted_cuts)

(

& cut : sorted_cuts) {

(cut.GetTo() == right_pos) {

right_pos = cut.GetFrom() - 1;

(cut.GetFrom() == left_pos) {

left_pos = cut.GetTo() + 1;

1 + (right_pos - left_pos),

(; seqmap_ci; ++seqmap_ci) {

(! seqmap_ci_first)

seqmap_ci_first = seqmap_ci;

seqmap_ci_last = seqmap_ci;

(seqmap_ci = seqmap_ci_first; seqmap_ci && seqmap_ci != seqmap_ci_last; ++seqmap_ci) {

(seqmap_ci_last) {

(pDeltaExt, complete_bsh, seqmap_ci_last, new_length);

(pDeltaExt->

().size() == 1) {

& seq_data = pDeltaSeq->SetLiteral().SetSeq_data();

inst->

().SetDelta(*pDeltaExt);

& sorted_cuts,

(TCuts::size_type ii = 0; ii < sorted_cuts.size(); ++ii) {

& cut = sorted_cuts[ii];

( trim_start <= to ) {

trim_start = to + 1;

( trim_stop >= from ) {

trim_stop = from - 1;

& bCompleteCut,

cut_size = cut_to - cut_from + 1;

(feat_to < cut_from)

(feat_from >= cut_from && feat_to <= cut_to)

bCompleteCut =

;

(feat_from > cut_to)

feat_from -= cut_size;

feat_to -= cut_size;

interval->

(feat_from);

interval->

(feat_to);

(feat_to > cut_to) {

feat_to -= cut_size;

feat_to = cut_from - 1;

(feat_from >= cut_from) {

feat_from = cut_to + 1;

feat_from -= cut_size;

interval->

(feat_from);

interval->

(feat_to);

& bCompleteCut,

bCompleteCut =

;

(loc->

())

loc->

(*interval);

(intervals->CanGet()) {

(

it = intervals->Set().begin();

it != intervals->Set().end(); )

bDeleted =

;

bCurrentTrimmed =

;

it = intervals->Set().erase(it);

(bCurrentTrimmed) {

(intervals->Get().empty()) {

bCompleteCut =

;

mix->Assign(loc->

());

(mix->CanGet()) {

(

it = mix->Set().begin();

it != mix->Set().end(); )

bDeleted =

;

bCurrentTrimmed =

;

it = mix->Set().erase(it);

(bCurrentTrimmed) {

(mix->Get().empty()) {

bCompleteCut =

;

& sorted_cuts)

(TCuts::size_type ii = 0; ii < sorted_cuts.size(); ++ii) {

& cut = sorted_cuts[ii];

new_loc->Assign(graph->

());

bDeleted =

;

bTrimmed =

;

graph->

(*new_loc);

& sorted_cuts)

copy_start = graph_start;

(trim_start > graph_start) {

copy_start = trim_start;

copy_stop = graph_stop;

(trim_stop < graph_stop) {

copy_stop = trim_stop;

(dst_data.

()) {

copy_start -= graph_start;

copy_stop -= graph_start;

graph->

(copy_stop - copy_start + 1);

(seg = 0; seg < denseg.

(); ++seg) {

(pos >= start && pos < start +

) {

(pos == seg_start) {

first_len, second_len;

first_len = pos - seg_start;

second_len = denseg.

()[foundseg] - first_len;

second_len = pos - seg_start;

first_len = denseg.

()[foundseg] - second_len;

(denseg.

()[index] == -1) {

new_denseg->

().push_back(-1);

new_denseg->

().push_back(first_len);

(denseg.

()[index] == -1) {

new_denseg->

().push_back(-1);

new_denseg->

().push_back(second_len);

align->

().SetDenseg(*new_denseg);

& sorted_cuts)

(CDense_seg::TIds::size_type rr = 0; rr < ids.size(); ++rr) {

(ids[rr]->Match( *(bsh.

()) )) {

(TCuts::size_type ii = 0; ii < sorted_cuts.size(); ++ii) {

& cut = sorted_cuts[ii];

cut_len = cut_to - cut_from + 1;

(cut_to < cut_from) {

cut_len = cut_from - cut_to + 1;

(seg_start < 0) {

}

(

(seg_start) < cut_from) {

}

(

(seg_start) >= cut_from &&

(seg_start) + denseg.

()[curseg] <= cut_from + cut_len) {

align->

().SetDenseg().SetStarts()[index] = -1;

align->

().SetDenseg().SetStarts()[index] -= cut_len;

(partial_start, partial_stop);

(partial_start) {

(partial_start || partial_stop) {

(

& cut : sorted_cuts) {

partial_start =

;

partial_stop =

;

(new_location, from, to, bFeatureDeleted, bFeatureTrimmed);

(bFeatureTrimmed) {

(bFeatureDeleted) {

bProdDeleted =

;

bProdTrimmed =

;

(new_product, from, to, bProdDeleted, bProdTrimmed);

& sorted_cuts)

bIsPartialStart =

;

(TCuts::size_type ii = 0; ii < sorted_cuts.size(); ++ii) {

& cut = sorted_cuts[ii];

to == original_nuc_len - 1 &&

old_frame = new_cdregion->GetFrame();

(old_frame == 0) {

new_frame = old_frame - ((to - from + 1) % 3);

(new_frame < 1) {

cds->

().SetCdregion(*new_cdregion);

(!new_protein_bioseq) {

new_protein_bioseq;

isPartialStart,

& sorted_cuts)

bseh.

(*trimmed_nuc_inst);

( !new_protein_bioseq ) {

(partial5 && partial3) {

found =

;

CBioseq::TDescr::Tdata::iterator it;

(it = prot_eh.

().Set().begin(); it != prot_eh.

().Set().end(); ++it) {

((*it)->IsMolinfo()) {

(*it)->SetMolinfo().SetCompleteness(completeness);

(*it)->SetMolinfo().SetCompleteness(completeness);

prot_eh.

().Set().push_back(desc);

prot_feat_ci(prot_bsh, sel);

( ; prot_feat_ci; ++prot_feat_ci ) {

prot_feat_eh.

(*new_feat);

(it->IsUser() && it->GetUser().IsUnverifiedOrganism()) {

(it->IsUser() && it->GetUser().IsUnverifiedFeature()) {

(it->IsUser() && it->GetUser().IsUnverifiedMisassembled()) {

(it->IsUser() && it->GetUser().IsUnverifiedContaminant()) {

descr.

().sort(CompareSeqdesc());

(entry.

())

(

.IsSetName() &&

.GetName().size() > 0) {

.GetName().front();

.GetRnaProductName();

(

it : feat.

()) {

(it->IsSetQual() &&

(it->GetQual(),

) && it->IsSetVal()) {

(pos != string::npos) {

tln = tln.substr(pos + 1);

(gene_for_feat) {

(

&& !quit) {

(

->GetData().Which()) {

found =

;

((*it)->IsUser() &&

(*it)->SetUser().Assign(*new_obj);

bh.

().Set().push_back(new_desc);

vector<string> tokens1;

vector<string> tokens2;

t1_match_start = string::npos;

t1_match_end = 0;

(vector<string>, it1, tokens1){

(vector<string>, it2, tokens2) {

t1_match_start = t1_pos;

t1_match_end = t1_pos;

(it1 != tokens1.end() && it2 != tokens2.end() &&

(*it1, *it2)) {

(t1_match_start != string::npos) {

(t1_match_start == string::npos) {

start_pos = 0;

string::const_iterator s = tls1.begin();

(s != tls1.end() && (*s ==

|| *s ==

|| *s ==

)) {

(

< t1_match_start) {

start_pos += tokens1[

].length();

(

k = 0; k < tokens1[

].length(); k++) {

(s != tls1.end() && (*s ==

|| *s ==

|| *s ==

)) {

match_len = tokens1[

].length();

(

k = 0; k < tokens1[

].length(); k++) {

(

<= t1_match_end) {

(s != tls1.end() && (*s ==

|| *s ==

|| *s ==

)) {

match_len += tokens1[

].length();

(

k = 0; k < tokens1[

].length(); k++) {

consensus = tls1.substr(start_pos, match_len);

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< CUser_object > MakeUserObject() const

void InitFromUserObject(const CUser_object &obj)

void SetTargetedLocusName(const string &tls)

void Set(T *object)

Initialize with an existing object.

CBioseq_set_EditHandle –.

TSeqPos GetLength(void) const

CRef< CDense_seg > ExtractRows(const vector< TDim > &rows) const

Extract specified rows of the alignment, in specified order.

@RNA_ref.hpp User-defined methods of the data storage class.

Helper functor to compare cuts during sorting.

bool operator()(const TRange &a1, const TRange &a2)

CRangeCmp(ESortOrder sortorder=eAscending)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

ESubtype GetSubtype(void) const

@ eSubtype_mobile_element

@Seq_descr.hpp User-defined methods of the data storage class.

void SetDescr(CSeq_descr &value)

void ReassignConflictingIds(void)

bool IsSetDescr(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

bool AddLinkageEvidence(CLinkage_evidence::TType evidence_type)

void ChangeType(TType linkage_type)

void SetLinkageTypeLinkedRepeat(CLinkage_evidence::TType evidence_type)

void SetLinkageTypeScaffold(CLinkage_evidence::TType evidence_type)

bool IsEntrys(void) const

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

void SetObjectType(EObjectType obj_type)

@ eObjectType_AutodefOptions

container_type::const_iterator const_iterator

container_type::iterator iterator

container_type::mapped_type & operator[](const key_type &key)

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

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char si[8][64]

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char * expected[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define 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)

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

const TPrim & Get(void) const

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

void SetPacked_int(TPacked_int &v)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

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,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CBioseq_Handle > TBioseqHandles

CBioseq_set_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TSeq ConvertSetToSeq(void) const

Do the same as CollapseSet() when sub-entry is of type bioseq.

bool IsNucleotide(void) const

void SetDescr(TDescr &v) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

void SetDescr(TDescr &v) const

CBioseq_EditHandle MoveTo(const CSeq_entry_EditHandle &entry, int index=-1) const

Move current bioseq into seq-entry.

void SetClass(TClass v) const

void AddDescr(TDescr &v) const

void SetInst_Mol(TInst_Mol v) const

void ResetDescr(void) const

bool IsEmptySeq_set(void) const

Check if the bioseq set is empty.

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeqFeatData & GetData(void) const

bool CanGetInst(void) const

TSeqPos GetBioseqLength(void) const

void Replace(const CSeq_align &new_obj) const

Replace the Seq-align with new Seq-align object.

bool AddSeqdesc(CSeqdesc &d) const

CSeq_entry_EditHandle TakeEntry(const CSeq_entry_EditHandle &entry, int index=-1) const

Remove seq-entry from its location and attach to current one.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

TSet ConvertSeqToSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the entry from Bioseq to Bioseq-set.

void TakeAllAnnots(const CSeq_entry_EditHandle &src_entry) const

Remove all the annotation from seq-entry and attach to current one.

void AddSeq_descr(TDescr &v) const

void SetInst_Length(TInst_Length v) const

void Remove(void) const

Remove the feature from Seq-annot.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

TInst_Mol GetInst_Mol(void) const

const CSeq_align::TSegs & GetSegs(void) const

bool IsSetProduct(void) const

CConstRef< CSeq_align > GetSeq_align(void) const

Get const reference to current seq-align.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

void SetInst(TInst &v) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Get parent bioseq-set handle.

bool IsRemoved(void) const

Check if handle points to a removed bioseq.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsProtein(void) const

void SetInst_Repr(TInst_Repr v) const

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

TInst_Length GetInst_Length(void) const

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

bool IsSetInst_Repr(void) const

bool IsSetClass(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d) const

CScope & GetScope(void) const

Get scope this handle belongs to.

TInst_Repr GetInst_Repr(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

void SetInst_Ext(TInst_Ext &v) const

CBioseq_EditHandle AttachBioseq(CBioseq &seq, int index=-1) const

Attach an existing bioseq.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

bool HasParentEntry(void) const

Check if current seq-entry has a parent.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

bool IsSetData(void) const

CConstRef< CBioseq_set > GetBioseq_setCore(void) const

Return core data for the bioseq-set.

void Replace(const CSeq_graph &new_obj) const

Replace the Seq-graph with new Seq-graph object.

bool CanGetInst_Ext(void) const

int GetSeq_entry_Index(const CSeq_entry_Handle &handle) const

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

const string & GetTitle(void) const

bool IsSetTitle(void) const

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_loc & GetProduct(void) const

CSeqMap::ESegmentType GetType(void) const

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

vector< CSeqdesc::E_Choice > TDescChoices

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

CSeq_graph_Handle GetSeq_graph_Handle(void) const

Get original graph handle.

@ eNonRecursive

Deprecated.

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

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

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

const_iterator begin(void) const

@ eSeqData

real sequence data

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CRef< C > Ref(C *object)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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 bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

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.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus & GetLocus(void) const

Get the Locus member data.

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.

const TData & GetData(void) const

Get the Data member 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.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsSetData(void) const

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

TSub & SetSub(void)

Select the variant.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

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

void ResetSegs(void)

Reset Segs data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

void SetDim(TDim value)

Assign a value to Dim data member.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

vector< CRef< CSeq_id > > TIds

vector< CRef< CSeq_id > > TIds

bool IsDendiag(void) const

Check if variant Dendiag is selected.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

const TDendiag & GetDendiag(void) const

Get the variant data.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TIds & SetIds(void)

Assign a value to Ids data member.

list< CRef< CDense_diag > > TDendiag

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

bool IsDenseg(void) const

Check if variant Denseg is selected.

bool IsSetComment(void) const

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

bool IsSetData(void) const

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

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.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

void SetData(TData &value)

Assign a value to Data data member.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

const TRna & GetRna(void) const

Get the variant data.

bool IsSetProduct(void) const

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

@ eFrame_not_set

not set, code uses one

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

TFrom GetFrom(void) const

Get the From member data.

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

E_Choice

Choice variants.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

bool CanGetFrom(void) const

Check if it is safe to call GetFrom method.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_General

for other databases

@ e_not_set

No variant selected.

TByte & SetByte(void)

Select the variant.

void SetNumval(TNumval value)

Assign a value to Numval data member.

TValues & SetValues(void)

Assign a value to Values data member.

const TByte & GetByte(void) const

Get the variant data.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

bool CanGetLoc(void) const

Check if it is safe to call GetLoc method.

const TValues & GetValues(void) const

Get the Values member data.

bool IsByte(void) const

Check if variant Byte is selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

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

TSet & SetSet(void)

Select the variant.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetSeq_set(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void SetClass(TClass value)

Assign a value to Class data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_equiv

a set of equivalent maps or seqs

@ eClass_parts

parts for 2 or 3

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_conset

constructed sequence + parts

@ eClass_wgs_set

whole genome shotgun project

@ eClass_mut_set

set of mutations

@ eClass_pir

converted pir

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gibb

geninfo backbone

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_pdb_entry

a complete PDB entry

@ eClass_genbank

converted genbank

@ eClass_swissprot

converted SWISSPROT

@ eClass_segset

segmented sequence + parts

@ eClass_pub_set

all the seqs from a single publication

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

TRepr GetRepr(void) const

Get the Repr member data.

const TSeg & GetSeg(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void ResetDescr(void)

Reset Descr data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

void SetPub(TPub &value)

Assign a value to Pub data member.

const TInst & GetInst(void) const

Get the Inst member data.

TPub & SetPub(void)

Select the variant.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

void SetExt(TExt &value)

Assign a value to Ext data member.

bool IsSetRepr(void) const

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

TType GetType(void) const

Get the Type member data.

const TPub & GetPub(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

const TId & GetId(void) const

Get the Id member data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

list< CRef< CSeq_align > > TAlign

const Tdata & Get(void) const

Get the member data.

TDelta & SetDelta(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

TIupacna & SetIupacna(void)

Select the variant.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

bool IsDelta(void) const

Check if variant Delta is selected.

void ResetLinkage(void)

Reset Linkage data member.

bool IsSetType(void) const

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

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

E_Choice

Choice variants.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

EMol

molecule class in living organism

bool IsPub(void) const

Check if variant Pub is selected.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDelta & GetDelta(void) const

Get the variant data.

TSeg & SetSeg(void)

Select the variant.

void ResetLinkage_evidence(void)

Reset Linkage_evidence data member.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

TUser & SetUser(void)

Select the variant.

void SetRepr(TRepr value)

Assign a value to Repr data member.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

Tdata & Set(void)

Assign a value to data member.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

const Tdata & Get(void) const

Get the member data.

void SetLinkage(TLinkage value)

Assign a value to Linkage data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void ResetExt(void)

Reset Ext data member.

const TPub & GetPub(void) const

Get the Pub member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

list< CRef< CSeq_loc > > Tdata

const TNcbi8na & GetNcbi8na(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

void Reset(void)

Reset data member.

TMolinfo & SetMolinfo(void)

Select the variant.

void ResetSeq_data(void)

Reset Seq_data data member.

E_Choice Which(void) const

Which variant is currently selected.

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Embl

EMBL specific information.

@ e_Het

cofactor, etc associated but not bound

@ e_Org

if all from one organism

@ e_Num

a numbering system

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Prf

PRF specific information.

@ e_Mol_type

type of molecule

@ e_Sp

SWISSPROT specific info.

@ e_Dbxref

xref to other databases

@ e_Comment

a more extensive comment

@ e_Method

sequencing method

@ e_Modelev

model evidence for XM records

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Maploc

map location of this sequence

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_not_set

No variant selected.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

const TCit & GetCit(void) const

Get the Cit member data.

list< CRef< CSeq_entry > > TEntrys

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

void FeatureAdjustForInsert(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

void FeatureAdjustForTrim(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bAdjusted)

vector< CRef< objects::CSeq_align > > TAlignVec

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

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

Int4 delta(size_t dimension_, const Int4 *score_)

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

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

static void s_AdjustInternalCutLocations(TCuts &cuts, TSeqPos seq_length, EInternalTrimType internal_cut_conversion)

Adjust any internal cuts to terminal cuts.

void TrimSeqAlign(CBioseq_Handle bsh, CRef< CSeq_align > align, const TCuts &sorted_cuts)

Trim Seq-align annotation.

void SetLinkageType(CSeq_ext &ext, CSeq_gap::TType linkage_type)

SetLinkageType A function to set the linkage_type for gaps in a delta sequence.

void DivvyUpAlignments(const TVecOfSeqEntryHandles &vecOfSeqEntryHandles)

Call this if the alignments directly under these seq-entries are all jumbled up between each other.

static CSeq_id * s_MakeUniqueLocalId(void)

vector< CSeq_annot_Handle > TVecOfSeqAnnotsToErase

void AddBioseqToBioseq(const CBioseq_Handle &to, const CBioseq_Handle &add)

Attach one Bioseq to another.

bool HasRepairedIDs(const CUser_object &user, const CBioseq::TId &ids)

bool IsDeltaSeqGap(CConstRef< CDelta_seq > delta)

string MakeOriginalLabelForId(const CSeq_id &id)

void TrimSeqData(CBioseq_Handle bsh, CRef< CSeq_inst > inst, const TCuts &sorted_cuts)

Trim sequence data.

void s_AddLiteral(CSeq_inst &inst, const string &element)

CRef< CSeqdesc > FindUnverified(const CBioseq &seq)

static void s_AddBioseqToBioseq(const CBioseq_EditHandle &to, const CBioseq_EditHandle &add)

void ConvertRawToDeltaByNs(CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap, int gap_type, int linkage, int linkage_evidence)

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to d...

static void s_AddBioseqToSegset(CBioseq_set_EditHandle &segset, CBioseq_EditHandle &part)

static bool s_DivvyUpAlignments_ProcessAnnot_Dendiag(const CSeq_align_Handle &align, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapEntryToAlignVec &mapEntryToAlignVec)

static void s_AddBioseqToNucProtSet(CBioseq_set_EditHandle &nuc_prot, CBioseq_EditHandle &seq)

CMapWithOriginalOrderingIteration< CSeq_entry_Handle, TAlignVec > TMapEntryToAlignVec

void TrimSeqGraph(CBioseq_Handle bsh, CRef< CSeq_graph > graph, const TCuts &sorted_cuts)

Trim Seq-graph annotation.

void GetSortedCuts(CBioseq_Handle bsh, const TCuts &cuts, TCuts &sorted_cuts, EInternalTrimType internal_cut_conversion)

1) Adjust any internal cuts to terminal cuts according to option.

bool Does3primerAbutGap(const CSeq_feat &feat, CBioseq_Handle seq_hl)

void SetTargetedLocusName(CBioseq_Handle seq, const string &tls)

void SortSeqDescr(CSeq_descr &descr)

vector< CConstRef< CSeq_align > > TAlignVec

bool IsUnverifiedMisassembled(const CBioseq &seq)

void AddSeqdescToSeqDescr(const CSeqdesc &desc, CSeq_descr &seq_descr)

static void s_AddBioseqToPartsSet(CBioseq_set_EditHandle &parts, CBioseq_EditHandle &seq)

void AddSeqEntryToSeqEntry(const CSeq_entry_Handle &target, const CSeq_entry_Handle &insert)

Attach one Seq-entry to another.

void AddSeqdescToBioseq(const CSeqdesc &desc, CBioseq &seq)

void AddLocalIdUserObjects(CSeq_entry &entry)

Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID...

CRef< CSeq_entry > SeqEntryFromSeqSubmit(const CSeq_submit &submit)

Create a Seq-entry from a Seq-submit.

void s_AddGap(CSeq_inst &inst, size_t n_len, bool is_unknown, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)

void ResetLinkageEvidence(CSeq_ext &ext)

ResetLinkageEvidence A function to clear linkage evidence for gaps in a delta sequence.

map< CSeq_entry_Handle, CSeq_entry_Handle > TMapDescendentToInputEntry

bool s_FindSegment(const CDense_seg &denseg, CDense_seg::TDim row, TSeqPos pos, CDense_seg::TNumseg &seg, TSeqPos &seg_start)

CConstRef< CDelta_seq > GetDeltaSeqForPosition(const unsigned pos, const CBioseq_Handle seq_hl, CScope *scope, unsigned &left_endpoint)

void s_BasicValidation(CBioseq_Handle bsh, const TCuts &cuts)

bool IsSeqDescInList(const CSeqdesc &desc, const CSeq_descr &set)

static bool s_DivvyUpAlignments_ProcessAnnot_Denseg(const CSeq_align_Handle &align, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapEntryToAlignVec &mapEntryToAlignVec)

void RemoveUserObjectType(CSeq_entry &entry, CUser_object::EObjectType type)

Removes User-object descriptors of a certain type from the seq-entry.

void TrimSequenceAndAnnotation(CBioseq_Handle bsh, const TCuts &cuts, EInternalTrimType internal_cut_conversion)

Implementation detail: first trim all associated annotation, then trim sequence data.

bool IsUnverifiedOrganism(const CBioseq &seq)

static void s_DivvyUpAlignments_ProcessAnnot(const CSeq_annot_Handle &annot_h, const TMapDescendentToInputEntry &mapDescendentToInputEntry, TMapSeqAnnotToDest &mapSeqAnnotToDest, TVecOfSeqAnnotsToErase &vecOfSeqAnnotToErase)

static void s_UpdateSeqGraphLoc(CRef< CSeq_graph > graph, const TCuts &sorted_cuts)

CRef< CBioseq > SetNewProteinSequence(CScope &new_scope, CRef< CSeq_feat > cds, CRef< CSeq_inst > new_inst)

Secondary function needed after trimming Seq-feat.

void SetLinkageTypeScaffold(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

SetLinkageTypeScaffold A special case of SetLinkageType.

static void s_SeqLocDelete(CRef< CSeq_loc > loc, TSeqPos from, TSeqPos to, bool &bCompleteCut, bool &bTrimmed)

void SetLinkageTypeLinkedRepeat(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

CSeq_id::E_Choice TypeFromLabel(const string &label)

void DeleteProteinAndRenormalizeNucProtSet(const CSeq_feat_Handle &feat_h)

Secondary function needed after trimming Seq-feat.

bool Does5primerAbutGap(const CSeq_feat &feat, CBioseq_Handle seq_hl)

static void s_MakeGroupsForUniqueValues(const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)

void SegregateSetsByBioseqList(const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)

Split a Seq-entry, where the second part holds the given bioseqs.

string GetTargetedLocusNameConsensus(const string &tls1, const string &tls2)

CMapWithOriginalOrderingIteration< CRef< CSeq_annot >, CSeq_entry_Handle > TMapSeqAnnotToDest

void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)

void TrimSeqFeat(CRef< CSeq_feat > feat, const TCuts &sorted_cuts, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &partial_start, bool &partial_stop)

Trim Seq-feat annotation.

static void s_AddProtToNuc(const CBioseq_EditHandle &nuc, const CBioseq_EditHandle &prot)

void RetranslateCdregion(CBioseq_Handle nuc_bsh, bool isPartialStart, bool isPartialStop, CRef< CSeq_inst > trimmed_nuc_inst, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)

Secondary function needed after trimming Seq-feat.

static void s_SeqIntervalDelete(CRef< CSeq_interval > interval, TSeqPos cut_from, TSeqPos cut_to, bool &bCompleteCut, bool &bTrimmed)

const string & GetTargetedLocusName(const CGene_ref &gene)

bool IsUnverifiedContaminant(const CBioseq &seq)

bool IsUnverifiedFeature(const CBioseq &seq)

void s_CutDensegSegment(CRef< CSeq_align > align, CDense_seg::TDim row, TSeqPos pos)

void BioseqSetDescriptorPropagateDown(const CBioseq_set_Handle &bioseq_set_h, const vector< CSeqdesc::E_Choice > &choices_to_delete)

Moves descriptors down to children of the given bioseq-set.

TLocAdjustmentVector NormalizeUnknownLengthGaps(CSeq_inst &inst, TSeqPos unknown_length)

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific lengt...

void AdjustCdregionFrame(TSeqPos original_nuc_len, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)

Secondary function needed after trimming Seq-feat.

static void s_AddPartToSegmentedBioseq(const CBioseq_EditHandle &seg, const CBioseq_EditHandle &part)

static TRange s_GetRetainedRange(const TCuts &sorted_merged_cuts, TSeqPos seqLength)

void AddLinkageEvidence(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence.

static void s_PromoteSingletonSetsInSet(const CBioseq_set_Handle &bioseq_set_h)

CRef< CUser_field > MakeOriginalIdField(const CSeq_id &id)

void AddBioseqToBioseqSet(const CBioseq_set_Handle &set, const CBioseq_Handle &seq)

Add a Bioseq to a Bioseq-set.

static bool s_IsSingletonSet(const CBioseq_set_Handle &bioseq_set)

string GenerateTargetedLocusName(CBioseq_Handle seq)

void AddSeqdescToBioseqSet(const CSeqdesc &desc, CBioseq_set &set)

bool AddSeqdescToSeqEntryRecursively(CSeq_entry &entry, CSeqdesc &desc)

void UpdateSeqLength(CAutoInitRef< CDelta_ext > &pDeltaExt, CBioseq_Handle &complete_bsh, CSeqMap_CI &seqmap_ci, CSeq_inst_Base::TLength &new_length)

Update sequence length.

static void s_MergeCuts(TCuts &sorted_cuts)

Assumes sorted_cuts are sorted in Ascending order!

bool IsMatchingIdMissing(const CUser_field &field, const CBioseq::TId &ids)

string LabelFromType(CSeq_id::E_Choice choice)

void BioseqSetDescriptorPropagateUp(CBioseq_set_Handle set)

Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the...

void HandleCollidingIds(CSeq_entry &entry)

static void s_GetTrimCoordinates(CBioseq_Handle bsh, const TCuts &sorted_cuts, TSeqPos &trim_start, TSeqPos &trim_stop)

vector< TLocAdjustment > TLocAdjustmentVector

vector< CSeq_entry_Handle > TVecOfSeqEntryHandles

EInternalTrimType

Any internal cut listed in TCuts will be converted to a terminal cut using one of these options.

pair< TSeqPos, int > TLocAdjustment

#define ERASE_SEQDESC_ON_BIOSEQ(Itr, Var)

ERASE_SEQDESC_ON_BIOSEQ.

#define EDIT_EACH_SEQDESC_ON_BIOSEQ(Itr, Var)

#define EDIT_EACH_SEQDESC_ON_SEQSET(Itr, Var)

#define ERASE_SEQDESC_ON_SEQSET(Itr, Var)

ERASE_SEQDESC_ON_SEQSET.

#define FIELD_EQUALS(Var, Fld, Value)

FIELD_EQUALS base macro.

#define RAW_FIELD_IS_EMPTY(Var, Fld)

RAW_FIELD_IS_EMPTY base macro.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

constexpr auto to_array(T const (&a)[N])

#define row(bind, expected)

set< CConstRef< T >, SSerialObjectLessThan< T > > Type

map< CConstRef< T >, string > TMapObjToTextAsn

TMapObjToTextAsn m_ObjAsnCache

bool operator()(const CConstRef< T > &lhs, const CConstRef< T > &rhs) const

const string & x_GetAsnText(const CConstRef< T > &obj) const

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