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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/subprep_util.cpp Source File

(!

|| !id_col) {

(row < id_col->GetData().GetSize() && !found) {

objects::CSeq_id::E_SIC compare =

->Compare(*row_id);

(compare == objects::CSeq_id::e_YES) {

}

(compare == objects::CSeq_id::e_DIFF) {

->Assign(*row_id);

(row < id_col->GetData().GetSize() && !found) {

objects::CBioseq_Handle bsh = seh.GetBioseqHandle (*row_id);

(objects::CBioseq::TId, id_it,

->GetId()) {

objects::CSeq_id::E_SIC compare =

->Compare(**id_it);

(compare == objects::CSeq_id::e_YES) {

->Assign(*row_id);

}

(compare == objects::CSeq_id::e_DIFF) {

->Assign(*row_id);

(!input_table || !input_table->IsSetColumns() || input_table->GetColumns().size() < 1) {

all_default =

;

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

(!(*cit)->IsSetHeader() || !(*cit)->GetHeader().IsSetTitle()

|| !

(expected_title, (*cit)->GetHeader().GetTitle())) {

all_default =

;

all_match =

;

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

first_val =

;

((*cit)->GetData().IsString()) {

first_val = (*cit)->GetData().GetString()[0];

}

((*cit)->GetData().IsId()) {

(all_default || !(*cit)->IsSetHeader() || !(*cit)->GetHeader().IsSetTitle() ||

((*cit)->GetHeader().GetTitle())) {

(*cit)->SetHeader().SetTitle(first_val);

}

(!

((*cit)->GetHeader().GetTitle(), first_val)) {

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

}

((*cit)->GetData().IsString()) {

title = (*cit)->GetHeader().GetTitle();

vector<CRef<objects::CSeq_id> > new_ids;

(

j = 0; j < (*cit)->GetData().GetString().

(); j++) {

= (*cit)->GetData().GetString()[j];

new_ids.push_back(

);

}

(exception &) {

->SetLocal().SetStr(

);

new_ids.push_back(

);

(

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

(*cit)->SetData().SetId().push_back(new_ids[j]);

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

}

((*cit)->GetData().IsInt()) {

vector<string> values;

(

j = 0; j < (*cit)->GetData().GetInt().

(); j++) {

(

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

(*cit)->SetData().SetString().push_back(values[j]);

}

((*cit)->GetData().IsReal()) {

vector<string> values;

(

j = 0; j < (*cit)->GetData().GetInt().

(); j++) {

(

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

(*cit)->SetData().SetString().push_back(values[j]);

;

vector<CRef<objects::CSeq_id> > already_seen;

(row < src_col->GetData().GetSize()) {

(!

(src_col->GetData().GetId()[

], dst_col, seh)) {

id_label =

;

((*sit)->Compare(*(src_col->GetData().GetId()[

])) == objects::CSeq_id::e_YES) {

+

;

already_seen.push_back(src_col->GetData().GetId()[

]);

(objects::CSeq_table::TColumns, cit,

.GetColumns()) {

((*cit)->IsSetData() && (*cit)->GetData().IsId()) {

(!id_col || !

|| !id_col->IsSetData() || !id_col->GetData().IsId()) {

(row < id_col->GetData().GetSize()) {

(id->Compare(*(id_col->GetData().GetId()[

])) == objects::CSeq_id::e_YES) {

(

= 0;

< src_id->GetData().GetSize() && i < src_col->GetData().GetSize();

++) {

(dst_col->GetData().GetString().size() >

&& !

(dst_col->GetData().GetString()[

], src_col->GetData().GetString()[

])) {

conflicting_columns = 0;

(objects::CSeq_table::TColumns, cit, src.GetColumns()) {

((*cit)->IsSetData() && !(*cit)->GetData().IsId()) {

conflicting_columns++;

conflicting_columns;

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

num_vals =

((*cit)->GetData().GetSize());

(

>= num_vals) {

((*cit)->GetData().IsString()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetString()[j] = (*cit)->GetData().GetString()[j + 1];

(*cit)->SetData().SetString().pop_back();

}

((*cit)->GetData().IsId()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetId()[j]->Assign(*((*cit)->GetData().GetId()[j + 1]));

(*cit)->SetData().SetId().pop_back();

}

((*cit)->GetData().IsLoc()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetLoc()[j]->Assign(*((*cit)->GetData().GetLoc()[j + 1]));

(*cit)->SetData().SetLoc().pop_back();

}

((*cit)->GetData().IsInt()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetInt()[j] = (*cit)->GetData().GetInt()[j + 1];

(*cit)->SetData().SetInt().pop_back();

}

((*cit)->GetData().IsReal()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetReal()[j] = (*cit)->GetData().GetReal()[j + 1];

(*cit)->SetData().SetReal().pop_back();

}

((*cit)->GetData().IsBit()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetBit()[j] = (*cit)->GetData().GetBit()[j + 1];

(*cit)->SetData().SetBit().pop_back();

}

((*cit)->GetData().IsBytes()) {

(

j =

; j < num_vals - 1; j++) {

(*cit)->SetData().SetBytes()[j] = (*cit)->GetData().GetBytes()[j + 1];

(*cit)->SetData().SetBytes().pop_back();

(

= 0;

< src_id->GetData().GetSize() && i < src_col->GetData().GetSize();

++) {

(dst_col->SetData().SetString().size() < dst_id->GetData().GetSize()) {

dst_col->SetData().SetString().push_back (

);

dst_col->SetData().SetString()[

] = src_col->GetData().GetString()[

];

}

(exception &) {

(objects::CSeq_table::TColumns, cit, src.GetColumns()) {

((*cit)->IsSetData() && !(*cit)->GetData().IsId()) {

dst_col =

objects::CSeqTable_column();

dst_col->SetHeader().Assign((*cit)->GetHeader());

(!dst_col->GetHeader().IsSetTitle() && dst_col->GetHeader().IsSetField_name()) {

dst_col->SetHeader().SetTitle(dst_col->GetHeader().GetField_name());

dst->SetColumns().push_back(dst_col);

wxFileDialog table_save_file(parent,

(

), save_file_dir, save_file_name,

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

(table_save_file.ShowModal() == wxID_OK)

wxString path = table_save_file.GetPath();

wxString name = table_save_file.GetFilename();

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR, parent);

wxMessageBox(

(

)+name,

(

),

wxOK | wxICON_ERROR, parent);

(objects::CSeq_table::TColumns, cit, values_table->GetColumns()) {

exporter.

((*cit)->GetHeader().GetTitle());

(

= 0;

< values_table->GetNum_rows(); ++

) {

(objects::CSeq_table::TColumns, cit, values_table->GetColumns()) {

(

< (*cit)->GetData().GetSize()) {

((*cit)->GetData().IsId()) {

}

((*cit)->GetData().IsString()) {

exporter.

((*cit)->GetData().GetString()[

]);

exporter.

(blank);

save_file_dir = table_save_file.GetDirectory();

save_file_name = table_save_file.GetFilename();

num_rows = col->GetData().GetSize();

(col->GetData().IsString()) {

= col->GetData().GetString()[0];

(

= 1;

< num_rows;

++) {

new_val = col->GetData().GetString()[

];

new_val = default_val;

}

(col->GetData().IsInt()) {

= col->GetData().GetInt()[0];

(

= 1;

< num_rows;

++) {

(

!= col->GetData().GetInt()[

]) {

(!col || !col->IsSetData()) {

num_rows = col->GetData().GetSize();

(col->GetData().IsString()) {

(

= 0;

< num_rows;

++) {

new_val = col->GetData().GetString()[

];

(!col || !col->IsSetData()) {

num_rows = col->GetData().GetSize();

(col->GetData().IsString()) {

(

= 0;

< num_rows;

++) {

new_val = col->GetData().GetString()[

];

(!col || !col->IsSetData()) {

num_rows = col->GetData().GetSize();

(col->GetData().IsString()) {

(

= 0;

< num_rows;

++) {

new_val = col->GetData().GetString()[

];

(ival.GetFrom() > 3) {

ival.SetFrom(ival.GetFrom() - 3);

= bsh.GetBioseqLength();

(ival.GetTo() <

- 4) {

ival.SetTo(ival.GetTo() + 3);

objects::CBioseq_Handle bsh_match;

id_match =

;

(objects::CBioseq::TId, id_it, protein->GetSeq().GetId()) {

bsh_match = seh.GetScope().GetBioseqHandle(**id_it);

(objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_na); b_iter ; ++b_iter ) {

(nuc_count == 0) {

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR,

);

}

(nuc_count > 1) {

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR,

);

seq_id->Assign(*(bsh_match.GetSeqId()));

protein_entry->Assign(*protein);

protein_entry->SetSeq().ResetId();

protein_entry->SetSeq().SetId().push_back(product_id);

objects::CSeq_entry_Handle protein_h = seh.GetScope().AddTopLevelSeqEntry(*protein_entry);

found_start_codon =

;

found_stop_codon =

;

(alignment && alignment->IsSetSegs() && alignment->GetSegs().IsSpliced()) {

seq_id->Assign(*match_loc->GetId());

(objects::CSpliced_seg::TExons, exon_it, alignment->GetSegs().GetSpliced().GetExons()) {

(*exon_it)->GetGenomic_start(),

(*exon_it)->GetGenomic_end()));

((*exon_it)->IsSetGenomic_strand()) {

exon->SetStrand((*exon_it)->GetGenomic_strand());

cds_loc->SetMix().Set().push_back(exon);

(objects::CSpliced_seg::TModifiers, mod_it,

alignment->GetSegs().GetSpliced().GetModifiers()) {

((*mod_it)->IsStart_codon_found()) {

found_start_codon = (*mod_it)->GetStart_codon_found();

((*mod_it)->IsStop_codon_found()) {

found_stop_codon = (*mod_it)->GetStop_codon_found();

(!cds_loc->IsMix()) {

=

+

+

;

wxOK | wxICON_ERROR,

);

(cds_loc->GetMix().Get().size() == 1) {

cds_loc->Assign(*exon);

(!found_start_codon) {

(found_stop_codon) {

(cds_loc->IsMix()) {

seh.GetScope().RemoveTopLevelSeqEntry(protein_h);

->AddCommand(*add_seqentry);

new_cds->SetLocation(*cds_loc);

(partial5 || partial3) {

new_cds->SetPartial(

);

new_cds->SetData().SetCdregion();

product_id->Assign(*(protein_entry->GetSeq().GetId().front()));

new_cds->SetProduct().SetWhole(*product_id);

->AddCommand(*add_cds);

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR,

);

(entry->IsSet()) {

(objects::CBioseq_set::TSeq_set, it, entry->SetSet().SetSeq_set()) {

}

(entry->IsSeq()) {

(!entry->GetSeq().IsAa()) {

objects::CSourceModParser

(

objects::CSourceModParser::eHandleBadMod_Ignore );

= entry->GetSeq().GetClosestDescriptor(objects::CSeqdesc::e_Title);

& title(

&

(title_desc->GetTitle()));

.ApplyAllMods(entry->SetSeq());

(entry->IsSeq()) {

(entry->GetSeq().IsAa()) {

new_entry->Assign(*entry);

->AddCommand(*subcmd);

}

(entry->IsSet()) {

(entry->GetSet().GetClass() == objects::CBioseq_set::eClass_nuc_prot) {

new_entry->Assign(*entry);

->AddCommand(*subcmd);

(seh.IsSet() && seh.GetSet().IsEmptySeq_set() && entry->GetSet().IsSetClass()) {

new_set->Assign(*(seh.GetSet().GetCompleteBioseq_set()));

new_set->SetClass(entry->GetSet().GetClass());

->AddCommand(*set_cmd);

(seh.IsSet() && seh.GetSet().IsEmptySeq_set() && entry->GetSet().IsSetDescr()) {

(objects::CBioseq_set::TDescr::Tdata, dit, entry->GetSet().GetDescr().Get()) {

->AddCommand(*cmdAddDesc);

(objects::CBioseq_set::TSeq_set, it, entry->GetSet().GetSeq_set()) {

new_entry->Assign(**it);

(entry->GetSet().IsSetDescr()) {

(objects::CBioseq_set::TDescr::Tdata, dit, entry->GetSet().GetDescr().Get()) {

new_entry->SetDescr().Set().push_back(desc);

same_num =

;

objects::CBioseq_CI b_iter(entry, objects::CSeq_inst::eMol_na);

( ; b_iter ; ++b_iter ) {

objects::CFeat_CI fit (*b_iter);

counts.push_back(this_count);

(this_count == 0) {

(common_num == -1) {

common_num = this_count;

}

(common_num != this_count) {

summary =

;

(

&& same_num) {

vector<int>::iterator cit = counts.begin();

(cit != counts.end()) {

vector<int>::iterator cit2 = cit;

(cit2 != counts.end()) {

(*cit == *cit2) {

cit2 = counts.erase(cit2);

(this_num == 1) {

summary +=

;

summary +=

;

summary =

;

vector<string> tf_strings;

tf_strings.push_back(

);

tf_strings.push_back(

);

(choices.size() != 2) {

(

->GetColumns().front()->IsSetData()) {

=

(

->GetColumns().front()->GetData().GetId().size());

->Assign(*

.GetLocation().GetId());

->SetColumns()[0]->SetData().SetId().push_back(

);

(

.IsSetId() &&

.GetId().IsLocal() &&

.GetId().GetLocal().IsId()) {

(

.IsSetComment()) {

(

.IsSetExcept() &&

.IsSetExcept_text()) {

(

.IsSetQual()) {

(objects::CSeq_feat::TQual, it,

.GetQual()) {

((*it)->IsSetQual() && (*it)->IsSetVal()) {

qual = (*it)->GetQual();

= (*it)->GetVal();

(!(*it)->RelaxedMatch(f1, f2)) {

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

->SetColumns().push_back(id_col);

objects::CFeat_CI fi(entry, objects::SAnnotSelector(feat.GetData().GetSubtype()));

objects::CSeq_entry_Handle entry,

objects::CSeqFeatData::ESubtype subtype,

(featid_col && featid_col->IsSetData() && featid_col->GetData().GetSize() >

) {

feature_id = featid_col->GetData().GetString()[

];

feat->Assign(*(orig_feat.GetOriginalSeq_feat()));

feat->SetId().SetLocal().SetId(

);

}

(exception &) {

feat->SetLocation().SetInt().SetId().Assign(*(id_col->GetData().GetId()[

]));

start = start_col->GetData().GetInt()[

];

stop = stop_col->GetData().GetInt()[

];

feat->SetLocation().SetInt().SetFrom(stop - 1);

feat->SetLocation().SetInt().SetTo(start - 1);

feat->SetLocation().SetInt().SetFrom(start - 1);

feat->SetLocation().SetInt().SetTo(stop - 1);

&& col->GetData().GetSize() >

) {

(col->GetData().IsString()) {

}

(col->GetData().IsInt()) {

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR,

);

objects::CSeqFeatData::E_Choice feature_type = objects::CSeqFeatData::GetTypeFromSubtype(subtype);

(feature_type) {

objects::CSeqFeatData::e_Imp:

objects::CFeatList& feats(*objects::CSeqFeatData::GetFeatList());

= feats.GetStoragekey(subtype);

feat->SetData().SetImp().SetKey(

);

objects::CSeqFeatData::e_Cdregion:

feat->SetData().SetCdregion();

change_existing =

;

(feat->IsSetId() && feat->GetId().IsLocal() && feat->GetId().GetLocal().IsId()) {

feat->GetId().GetLocal().GetId());

change_existing =

;

(!change_existing) {

objects::CBioseq_Handle bh = entry.GetScope().GetBioseqHandle(*(id_col->GetData().GetId()[

]));

objects::CSeq_entry_Handle seh = bh.GetSeq_entry_Handle();

vecColEditFactories.push_back(

(

c = 0; c <

->GetColumns().

()->GetData().GetSize(); c++) {

}

(problems.empty()) {

problems.assign(add.begin(), add.end());

(pos < problems.size() && pos < add.size()) {

problems[pos] +=

;

problems[pos] += add[pos];

(pos < add.size()) {

problems.push_back(add[pos]);

vector<string>& problems)

vector<string> add_values;

(

j = 0; j < val_col->GetData().GetSize(); j++) {

add_values.push_back(val_col->GetData().GetString()[j]);

vector<string> add_problems = rule_col->

(add_values);

num_table_columns = values_table->GetColumns().size();

(num_table_columns > 1) {

(!last_col->IsSetHeader()

|| !last_col->GetHeader().IsSetTitle()

values_table->SetColumns().pop_back();

(

((*col_it)->GetLabel(), col->GetHeader().GetTitle())) {

(

((*col_it)->GetLabel(), col->GetHeader().GetTitle())) {

vector<string> problems;

(

->GetColumns()[

]->IsSetData()

&& (

->GetColumns()[

]->GetData().IsString())) {

problems_col->SetHeader().SetTitle(

);

problems_col->SetData().SetString();

->SetColumns().push_back(problems_col);

(vector<string>, it, problems) {

problems_col->SetData().SetString().push_back(*it);

(feat.IsSetId() && feat.GetId().IsLocal() && feat.GetId().GetLocal().IsId()) {

objects::CFeat_CI fi(entry, objects::SAnnotSelector(feat.GetData().GetSubtype()));

objects::CSeq_feat& this_feat= *(fi->GetSeq_feat());

vector<wxString> exts;

exts.push_back(

(

));

exts.push_back(

(

));

vector<wxString>::const_iterator it;

(it = exts.begin(); it != exts.end(); it++) {

(it != exts.begin())

filter +=

(

);

filter +=

(

) + *it;

filter +=

(

) + *it;

found =

;

objects::CSeq_entry_EditHandle eh = entry.GetEditHandle();

(objects::CSeqdesc_CI desc_ci( entry, objects::CSeqdesc::e_User);

objects::CUser_object& u = desc_ci->GetUser();

new_user->Assign (u);

new_desc->SetUser(*new_user);

objects::CUser_field& new_field = new_user->SetField(field_name);

new_field.SetData().SetStr(

);

eh.RemoveSeqdesc(*desc_ci);

eh.AddSeqdesc(*new_desc);

new_desc->SetUser(*new_user);

objects::CUser_field& new_field = new_user->SetField(field_name);

new_field.SetData().SetStr(

);

entry.GetEditHandle().SetDescr().Set().push_back(new_desc);

(objects::CUser_object::TData, fit, user.GetData()) {

((*fit)->IsSetLabel()

&& (*fit)->GetLabel().IsStr()

&& (*fit)->IsSetData()

&& (*fit)->GetData().IsStr()) {

= (*fit)->GetData().GetStr();

alt_email =

;

(pos != string::npos) {

alt_email =

;

objects::CSeqdesc_CI it (entry, objects::CSeqdesc::e_User);

objects::CUser_field& new_field = u.SetField(

);

new_field.SetData().SetStr(alt_email);

found =

;

objects::CSeq_entry_EditHandle eh = entry.GetEditHandle();

(objects::CSeqdesc_CI desc_ci( entry, objects::CSeqdesc::e_User);

objects::CUser_object& u = desc_ci->GetUser();

new_user->Assign (u);

new_desc->SetUser(*new_user);

eh.RemoveSeqdesc(*desc_ci);

eh.AddSeqdesc(*new_desc);

new_desc->SetUser(*new_user);

entry.GetEditHandle().SetDescr().Set().push_back(new_desc);

(pos == string::npos) {

= email.substr(pos);

(pos == string::npos) {

(

objects::CSeq_entry& entry,

(entry.IsSeq()) {

(entry.GetSeq().IsAa()) {

(entry.GetSeq().IsSetDescr()) {

(objects::CBioseq::TDescr::Tdata, desc_it, entry.GetSeq().GetDescr().Get()) {

((*desc_it)->IsTitle()) {

title = (*desc_it)->GetTitle();

(objects::CBioseq::TId, id_it, entry.GetSeq().GetId()) {

->Assign(**id_it);

id_col->SetData().SetId().push_back(

);

pos_col->SetData().SetInt().push_back(pos);

np_col->SetData().SetString().push_back(np);

title_col->SetData().SetString().push_back(title);

}

(entry.IsSet() && entry.GetSet().IsSetSeq_set()) {

(objects::CBioseq_set::TSeq_set, seq_it, entry.GetSet().GetSeq_set()) {

id_col->SetData().SetId();

pos_col->SetHeader().SetTitle(

);

pos_col->SetData().SetInt();

np_col->SetHeader().SetTitle(

);

np_col->SetData().SetString();

title_col->SetHeader().SetTitle(

);

title_col->SetData().SetString();

->SetColumns().push_back(id_col);

->SetColumns().push_back(pos_col);

->SetColumns().push_back(np_col);

->SetColumns().push_back(title_col);

=

->GetNum_rows();

pos = pos_col->GetData().GetInt()[

- 1] + 1;

->SetColumns().push_back(id_col);

->SetColumns().push_back(pos_col);

->SetColumns().push_back(np_col);

->SetColumns().push_back(title_col);

(id_col->GetData().IsString()) {

= id_col->GetData().GetString()[pos];

problems->SetHeader().SetTitle(

);

problems->SetData().SetString();

vector<string> id_strings;

any_problems =

;

any_nuc =

;

id_col = orig_id_col;

(

= 0;

< new_ids->GetNum_rows();

++) {

id_strings.push_back(

);

problems->SetData().SetString().push_back(

);

any_problems =

;

}

(

.length() > max_len) {

problems->SetData().SetString().push_back(

);

any_problems =

;

problems->SetData().SetString().push_back(

);

(

= 0;

< id_col->GetData().GetSize();

++) {

id_strings.push_back(

);

(dup_ids.size() > 0) {

(

= 0;

< new_ids->GetNum_rows();

++) {

found =

;

(vector<string>, s_it, dup_ids) {

= problems->GetData().GetString()[

];

problems->SetData().SetString()[

] =

;

any_problems =

;

(!any_problems) {

num_duplicates = 0;

num_too_long = 0;

(objects::CSeqTable_column::TData::TString, s_it, problems->GetData().GetString()) {

(num_duplicates > 0) {

(num_too_long > 0) {

(num_too_long > 0) {

any_changes =

;

new_str->SetHeader().SetTitle(

);

new_str->SetData().SetString();

num_seq = pos_col->GetData().GetInt().back();

(old_pos_col && old_pos_col->GetData().GetInt().size() > 0) {

num_seq += old_pos_col->GetData().GetInt().back();

reserve_char = ceil(

((

)num_seq)) + 1;

vector<string> id_strings;

(

= 0;

< new_ids->GetNum_rows();

++) {

(

.length() > max_len) {

=

.substr(0, max_len - reserve_char);

new_str->SetData().SetString().push_back(

);

any_changes =

;

new_str->SetData().SetString().push_back(

);

id_strings.push_back(

);

(

= 0;

< id_col->GetData().GetSize();

++) {

id_strings.push_back(

);

(dup_ids.size() > 0) {

vector<int> high_offset;

(vector<string>, s_it, dup_ids) {

high_offset.push_back(0);

(vector<string>, i_it, id_strings) {

(vector<string>, s_it, dup_ids) {

(

> high_offset[dup_pos]) {

high_offset[dup_pos] =

;

}

(exception &) {

(

= 0;

< new_ids->GetNum_rows();

++) {

(vector<string>, s_it, dup_ids) {

high_offset[dup_pos]++;

any_changes =

;

seq_id_it; ++seq_id_it)

( seq_id_it->Equals(*seq_id) ) {

seq_id_it->Assign(*new_seq_id);

objects::CSeq_entry *pEntry = bioseq.GetParentEntry();

( ; pEntry; pEntry = pEntry->GetParentEntry() ) {

( ! pEntry->IsSet() ) {

objects::CBioseq_set & bioseq_set = pEntry->SetSet();

( ! bioseq_set.IsSetAnnot() ) {

(objects::CBioseq_set::TAnnot, annot_it, bioseq_set.SetAnnot() ) {

(entry.IsSeq()) {

objects::CSeqTable_column::TData::TId::iterator orig_it = id_col->SetData().SetId().begin();

objects::CSeqTable_column::TData::TString::iterator new_it = new_id_col->SetData().SetString().begin();

(orig_it != id_col->SetData().SetId().end() && new_it != new_id_col->SetData().SetString().end()) {

((*id_it)->Compare(**orig_it) == objects::CSeq_id::e_YES) {

new_id->SetLocal().SetStr(*new_it);

(*id_it)->Assign(*new_id);

orig_it = id_col->SetData().SetId().erase(orig_it);

new_it = new_id_col->SetData().SetString().erase(new_it);

}

(entry.IsSet()) {

(objects::CBioseq_set::TSeq_set, it, entry.SetSet().SetSeq_set()) {

already_got_one =

;

objects::CFeat_CI

(bh, objects::SAnnotSelector(objects::CSeqFeatData::e_Imp));

(

->GetData().GetImp().IsSetKey()

|| (

->IsSetComment() &&

(

->GetComment(), comment)))) {

already_got_one =

;

already_got_one;

already_got_one =

;

objects::CFeat_CI

(bh, objects::SAnnotSelector(subtype));

already_got_one =

;

already_got_one;

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.

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

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.

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.

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.

User-defined methods of the data storage class.

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

void Field(const string &value)

static CRef< CFeatureSeqTableColumnBase > Create(const string &sTitle, objects::CSeqFeatData::ESubtype subtype=objects::CSeqFeatData::eSubtype_any)

virtual vector< string > IsValid(const vector< string > &values)

static wxString GetDialogFilter(EFileType fileType)

Output filtering parameters.

@ ePassThrough

all zeroes - no filtering

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

@ eWizardType_uncultured_samples

@ eWizardType_microsatellite

@ eWizardType_rrna_its_igs

Template class for iteration on objects of class C.

void SetMolinfoForProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_feat > AddProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

std::ofstream out("events_result.xml")

main entry point for tests

vector< CRef< CFeatureSeqTableColumnBase > > TFeatureSeqTableColumnList

static const int kNumSatelliteTypes

const string kPartialStart

static const string kSatelliteTypes[]

const string kPartialStop

const string kStopColLabel

const string kStartColLabel

const char * kSequenceIdColLabel

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

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

static 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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ eNocase

Case insensitive compare.

static const char label[]

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

static const int kSkipColumns

bool MatchColumnName(string name1, string name2)

CRef< CSeqTable_column > FindSeqTableColumnByName(CRef< objects::CSeq_table > values_table, string column_name)

CRef< CSeqTable_column > AddIntColumnToTable(CRef< CSeq_table > table, string label)

CRef< CSeqTable_column > AddStringColumnToTable(CRef< CSeq_table > table, string label)

void AddValueToTable(CRef< CSeq_table > table, string subtype_name, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)

bool RelaxedMatch(CRef< objects::CSeq_id > id1, CRef< objects::CSeq_id > id2)

#define row(bind, expected)

@ eExistingText_replace_old

int CombineTables(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

bool AreAnyColumnValuesMissing(CRef< objects::CSeqTable_column > col)

int CountColumnRowConflicts(CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

int AddFeatureToSeqTable(const objects::CSeq_feat &f, CRef< objects::CSeq_table > table)

static CRef< objects::CSeqTable_column > s_MakeTitleCol()

static CRef< objects::CSeqTable_column > s_MakePosCol()

bool AddSeqEntryToSeqEntry(const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only)

bool SaveTableFile(wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table)

CSourceRequirements::EWizardType GetWizardTypeFromName(string wizard_name)

int CountTableColumnConflicts(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

CRef< objects::CUser_object > MakeWizardObject()

CRef< objects::CUser_object > MakeBankItSubmissionObject()

bool IsValidEmail(string email)

CRef< objects::CSeq_table > GetIdsFromSeqEntry(const objects::CSeq_entry &entry)

const string kSMARTComment

bool IsWizardObject(const objects::CUser_object &user)

static TWizardName s_WizardNames[]

bool IsBankItSubmissionObject(const objects::CUser_object &user)

CRef< CCmdComposite > AddFeatureSeqTableToSeqEntry(CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

CRef< CCmdComposite > RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry(objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)

static void AddProblemsToColumn(CRef< objects::CSeqTable_column > val_col, CRef< CFeatureSeqTableColumnBase > rule_col, vector< string > &problems)

void ParseTitlesToNewSeqEntries(CRef< objects::CSeq_entry > entry)

void AddProblemsColumnToFeatureSeqTable(CRef< objects::CSeq_table > table, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

bool IsSynonymForFalse(const string &val)

static CRef< objects::CSeqTable_column > s_MakeIdTableIdCol()

bool AreAnyColumnValuesPresent(CRef< objects::CSeqTable_column > col, string default_val)

static CRef< objects::CSeqTable_column > s_MakeNpCol()

void AddFeatureSeqTableRowToSeqEntry(CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, unsigned int row, TFeatureSeqTableColumnList &vecColEditFactories, CRef< CCmdComposite > cmd)

void SetWizardFieldInSeqEntryNoUndo(objects::CSeq_entry_Handle entry, string field_name, string value)

string GetDescAlternateEmailAddress(const objects::CSeqdesc &desc)

wxString GetAsnSqnExtensions()

static void TransformSeqAnnot(objects::CSeq_annot &annot, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)

int FindRowForSeqId(CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id)

static void AddIdsFromSeqEntryToTable(const objects::CSeq_entry &entry, CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeqTable_column > pos_col, CRef< objects::CSeqTable_column > np_col, CRef< objects::CSeqTable_column > title_col, int &pos, size_t &row)

CRef< CFeatureSeqTableColumnBase > GetColumnRuleForFeatureSeqTable(CRef< objects::CSeqTable_column > col, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

const string kBankItAltEmailPrefix

CRef< objects::CSeqTable_column > FindSeqIDColumn(const objects::CSeq_table &table)

bool IsSynonymForTrue(const string &val)

static void s_ReportMixError()

string SummarizeIdProblems(CRef< objects::CSeqTable_column > problems)

void DeleteTableRow(CRef< objects::CSeq_table > table, int row)

static void TransformSeqAnnots(objects::CBioseq &bioseq, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)

string GetAlternateEmailAddress(objects::CSeq_entry_Handle entry)

static int k_NumWizardNames

static bool OneRowOk(CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col, objects::CSeq_entry_Handle seh)

bool AlreadyHasFeature(objects::CBioseq_Handle bh, string key, string comment)

void RemoveProblemsColumn(CRef< objects::CSeq_table > values_table)

void SetAlternateEmailAddress(objects::CSeq_entry_Handle entry, string alt_email)

bool DoesColumnHaveValue(CRef< objects::CSeqTable_column > col, string val)

static void s_ExtendIntervalToEnd(objects::CSeq_interval &ival, objects::CBioseq_Handle bsh)

string GetFieldFromWizardObject(const objects::CUser_object &user, string field_name)

bool AreAllColumnValuesTheSame(CRef< objects::CSeqTable_column > col, string default_val)

void ApplyReplacementIds(objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)

const string kIdDuplicate

vector< string > GetTrueFalseList()

string CheckFeatureAnnotation(objects::CSeq_entry_Handle entry, bool &is_ok)

bool AddProteinToSeqEntry(const objects::CSeq_entry *protein, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool create_general_only)

void FixTableAfterImport(CRef< objects::CSeq_table > input_table)

const string kBankitSubmissionLabel

string FindBadRows(CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh)

static void CombineColumns(CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

CRef< objects::CSeq_table > GetFeaturesFromSeqEntry(objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)

bool IsTrueFalseList(const vector< string > &choices)

static bool s_OkToAddFeature(const objects::CSeq_feat &f1, const objects::CSeq_feat &f2, const TFeatureSeqTableColumnList &reqs)

void SetUserAlternateEmailAddress(objects::CUser_object &u, string alt_email)

CRef< objects::CSeqTable_column > GetSeqIdProblems(CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)

bool HasLocalIntFeatureId(const objects::CSeq_feat &feat)

static string GetIdValueFromColumn(CRef< objects::CSeqTable_column > id_col, int pos)

CRef< objects::CSeqTable_column > GetReplacementSeqIds(CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)

void MergeStringVectors(vector< string > &problems, vector< string > add)

TWizardNameList GetWizardNameList()

vector< TWizardName > TWizardNameList

vector< string > FindNonUniqueStrings(const vector< string > &values)

pair< CSourceRequirements::EWizardType, string > TWizardName

const string kWizardLabel

wxString ToWxString(const string &s)

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