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NCBI C++ ToolKit: src/gui/objutils/macro_fn_aecr.cpp Source File

void CMacroFunction_SwapRelatedFeaturesQual_Depr::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!src_feat || !scope)

src_objs = m_Args[0]->GetObjects();

x_GetObjectsFromRef(src_objs, 0);

(src_objs.empty()) {

(feat_list.empty()) {

new_feat->Assign(*orig_feat);

objInfo(new_feat.GetPointer(), new_feat.GetPointer()->GetTypeInfo());

& dest_field = m_Args[2]->GetString();

(!

(&dest_objs, objInfo, dest_field) || dest_objs.empty()) {

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(src_it != src_objs.end() && dest_it != dest_objs.end()) {

m_QualsChangedCount += 2;

(m_QualsChangedCount) {

m_DataIter->SetModified();

m_DataIter->RunCommand(

, m_CmdComposite);

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_SwapRelatedFeaturesQual_Depr::x_ValidArguments()

(m_Args.size() != 3) {

(!(m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef()))

(

index = 1; index < m_Args.size(); ++index) {

& field_name = m_Args[0]->GetString();

res_oi = m_Args[0]->GetObjects();

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

m_QualsChangedCount = s_RemoveFields(m_DataIter, res_oi);

(m_QualsChangedCount) {

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

(

.empty())

;

first_ok = (

[0]->IsString() ||

[0]->AreObjects() ||

[0]->IsRef());

(

.size() == 1 && first_ok);

quals_changed = 0;

is_gene_suppressed_before =

;

is_gene_suppressed_after =

;

is_gene_suppressed_before = gene_xref && gene_xref->

();

dataiter->SetToDelete(

);

dataiter->SetToDelete(

);

.BasicCleanup(*seq_feat);

(!is_gene_suppressed_before && is_gene_suppressed_after)

bsrc->

().ResetDb();

dataiter->SetModified();

quals_changed;

bsrc.

().SetOrgname().ResetMod();

void CMacroFunction_RemoveModifier::TheFunction()

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_RemoveModifier::x_ValidArguments()

res_oi = m_Args[0]->GetObjects();

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

x_RmvOutsideFields(res_oi, *options);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

update_mrna = (m_Args.size() == 10) ? m_Args[9]->GetBool() :

;

scope = m_DataIter->GetScopedObject().scope;

m_DataIter->RunCommand(

, m_CmdComposite);

<<

+ prot_product +

;

x_LogFunction(

);

left_del =

[start_index + 1]->GetString();

remove_before_match =

;

(

[start_index]->GetBool()) {

remove_before_match =

[start_index + 2]->GetBool();

right_del =

[start_index + 4]->GetString();

remove_after_match =

;

(

[start_index + 3]->GetBool()) {

remove_after_match =

[start_index + 5]->GetBool();

case_insensitive =

[start_index + 6]->GetBool();

whole_word =

[start_index + 7]->GetBool();

after_match, right_del, remove_after_match,

case_insensitive, whole_word));

(

& it : resolved_objs) {

(

& iter : objs) {

(

= index;

<

.size(); ++

) {

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(remove_field && newValue.empty()) {

(!newValue.empty() && !

(&res_oi, oi, m_Args[0]->GetString())) {

res_oi = m_Args[0]->GetObjects();

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

(!newValue.empty()) {

vector<string> new_values;

x_SetFields(res_oi, newValue, existing_text, new_values);

m_Result->SetBool(

);

(m_QualsChangedCount) {

m_DataIter->SetModified();

m_Result->SetBool(

);

(

= 0;

< new_values.size(); ++

) {

<< m_DataIter->GetBestDescr() <<

<< new_values[

] <<

;

x_LogFunction(

);

(remove_field) {

(m_QualsChangedCount) {

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_nr =

.size();

(arg_nr < 3 && arg_nr > 5) {

first_ok =

[index]->IsString() ||

[index]->AreObjects() ||

[index]->IsRef();

(!first_ok)

;

second_ok =

[index]->IsString() ||

[index]->IsInt() ||

[index]->IsDouble();

(!second_ok)

;

(!

[++index]->IsString())

;

(arg_nr > 3 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 4 && !

[++index]->IsBool())

;

(

& it : objs) {

new_values.push_back(newValue);

new_values.push_back(newValue);

new_values.push_back(newValue);

(objs.size() > 1) {

new_values.push_back(newValue);

new_values.push_back(orig_value);

new_values.push_back(newValue);

void CMacroFunction_SetRnaProduct::TheFunction()

* seq_feat =

*

(

.GetPointer());

scope = m_DataIter->GetScopedObject().scope;

(!seq_feat || !seq_feat->

().

() || !scope)

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

m_QualsChangedCount++;

(!remainder.empty()) {

(remove_field) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr();

(newValue.empty() && remove_field) {

<<

;

<<

<< orig_value <<

;

CMacroFunction_SetRnaProduct::x_ValidArguments()

arg_nr = m_Args.size();

(arg_nr < 2 && arg_nr > 4) {

first_ok = m_Args[index]->IsString() || m_Args[index]->IsInt() || m_Args[index]->IsDouble();

(!first_ok)

;

(!m_Args[++index]->IsString())

;

(arg_nr > 2 && (!m_Args[++index]->IsString() && !m_Args[index]->IsBool()))

;

(arg_nr > 3 && !m_Args[++index]->IsBool())

;

void CMacroFunction_GetRnaProduct::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

m_Result->SetNotSet();

(m_Nested == eNotNested) {

m_Result->SetString(

);

new_node->SetString(

);

m_Result->SetRef(new_node);

CMacroFunction_GetRnaProduct::x_ValidArguments()

(m_Args.empty());

void CMacroFunction_RemoveRnaProduct::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!edit_feat || !edit_feat->

().

() || !scope)

m_DataIter->SetModified();

m_QualsChangedCount++;

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_RemoveRnaProduct::x_ValidArguments()

(m_Args.empty());

&

= m_Args[++index]->GetString();

case_sensitive = m_Args[++index]->GetBool();

is_regex = (++index < m_Args.size()) ? m_Args[index]->GetBool() :

;

m_Result->SetBool(

);

res_oi = m_Args[0]->GetObjects();

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

x_EditFields(res_oi, find_txt, repl_txt, s_GetLocFromName(

), case_sensitive, is_regex);

(m_QualsChangedCount) {

m_DataIter->SetModified();

m_Result->SetBool(

);

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

<< find_txt;

repl_txt.assign(

);

<<

<< repl_txt;

x_LogFunction(

);

& replace,

loc,

case_sensitive,

is_regex)

(pos !=

) {

=

.substr(0, pos) + replace +

.substr(pos + find.length());

(case_sensitive) {

(loc ==

) {

pos =

.length() - find.length();

=

.substr(0, pos) + replace +

.substr(pos + find.length());

& find_txt,

& repl_txt,

case_sensitive,

(

& it : resolved_objs) {

(

& iter : objs) {

(

(

, find_txt, repl_txt, loc, case_sensitive, is_regex)) {

(

(orig_val, find_txt, repl_txt, loc, case_sensitive, is_regex)) {

(

(

, find_txt, repl_txt, loc, case_sensitive, is_regex)) {

first_ok =

[0]->IsString() ||

[0]->AreObjects() ||

[0]->IsRef();

(

index = 1; index < 3; index++) {

(!

[index]->IsString() && !

[index]->IsInt()) {

(

.size() == 6) {

(!

.back()->IsBool())

(

[3]->IsString() &&

[4]->IsBool());

vector<string>

= {

,

,

};

vector<string> kMobileETypeTypes = {

,

,

,

IstRNAProductField(

& feat,

& field_name);

* seq_feat =

*

(

.GetPointer());

GetBioSourceDestObjects(oi, field_name,

);

SetFeatDestinationField(

(feat), field_name,

);

(field_name.empty())

orig_size = dest_objs.size();

((*subsrc)->IsSetSubtype() && (*subsrc)->GetSubtype() ==

) {

subsrc_oi((*subsrc).GetPointer(), (*subsrc)->GetTypeInfo());

(dest_objs.empty()) {

sub_src->SetSubtype(

);

subsrc_oi(sub_src.GetPointer(), sub_src->GetTypeInfo());

((*orgmod)->IsSetSubtype() && (*orgmod)->GetSubtype() ==

) {

orgmod_oi((*orgmod).GetPointer(), (*orgmod)->GetTypeInfo());

(dest_objs.empty()) {

orgmod->SetSubtype(

);

orgname->SetMod().push_back(orgmod);

bsrc->

().SetOrgname(*orgname);

bsrc->

().SetOrgname().SetMod().push_back(orgmod);

orgmod_oi(orgmod.GetPointer(), orgmod->GetTypeInfo());

dest_objs.size() - orig_size > 0;

(feat.

() || field_name.empty())

orig_size =

.size();

field = field_name;

field =

;

field =

;

((*gbq_it)->IsSetQual() &&

((*gbq_it)->GetQual(), field)) {

gbqual_oi((*gbq_it).GetPointer(), (*gbq_it)->GetTypeInfo());

feat->

().push_back(new_gbqual);

gbqual_oi(new_gbqual.GetPointer(), new_gbqual->GetTypeInfo());

.size() - orig_size > 0;

(field_name.empty())

field = field_name;

field =

;

field =

;

((*gbq_it)->IsSetQual() &&

((*gbq_it)->GetQual(), field)) {

gbqual_oi((*gbq_it).GetPointer(), (*gbq_it)->GetTypeInfo());

(!

.empty());

IstRNAProductField(

& feat,

& field_name)

CreateNewGene(src_feat, scope);

CreateNewProtein(src_feat, scope);

new_gene->SetLocation(*gene_loc);

list<CMappedFeat> cds_feats;

(

& it : cds_feats) {

(it.IsSetProduct()) {

(!x_GetSourceFields(oi, index, src_objs))

(!x_GetDestFields(oi, ++index, dest_objs))

& action_type = m_Args[++index]->GetString();

= (++index < m_Args.size()) ? m_Args[index]->GetString() :

;

(src_feat && m_Args[1]->IsString() &&

(m_Args[1]->GetString(),

)) {

(

&& it : src_objs) {

src_val = x_GetSourceString(src);

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

m_QualsChangedCount++;

ChangeFields(src_objs, dest_objs);

(m_QualsChangedCount) {

(!dest_objs.empty()) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_size =

.size();

(arg_size != 3 && arg_size != 4) {

(

= 0;

< 2; ++

) {

(

= 2;

< arg_size; ++

) {

(!src_feat || !scope)

& dest_field =

[2]->GetString();

(dest_field.empty())

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*src_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

dest_feat->

().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

update_mrna =

[index]->GetBool();

& action_type =

[++index]->GetString();

(IstRNAProductField(*dest_feat, dest_field)) {

(

&& it : src_objs) {

dest_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(changed && fh) {

->AddCommand(*upd_cmd);

<<

<< message;

->AddCommand(*upd_cmd);

<<

+ prot_product +

;

(

index = 1; index <

.size(); ++index) {

(!rna_feat || !scope)

& src_feat =

[0]->GetString();

& dest_feat =

[2]->GetString();

(src_feat ==

&& src_feat == dest_feat)

((src_feat !=

&& src_feat !=

) || (dest_feat !=

&& dest_feat !=

))

& action_type =

[index]->GetString();

(src_feat ==

&& dest_feat ==

) {

dest_field =

[3]->GetString();

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*rna_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

(changed && fh) {

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(

&& it : src_objs) {

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(!

[0]->IsString() || !

[2]->IsString() || !

[4]->IsString())

(

index = 1; index < 4; index += 2) {

(!(

[index]->IsString() ||

[index]->AreObjects() ||

[index]->IsRef()))

(!src_feat || !scope)

& field_name =

[1]->GetString();

& action_type =

[++index]->GetString();

remove_field =

;

update_mrna =

;

arg_nr =

.size();

(++index < arg_nr) {

(

[index]->IsString()) {

(++index < arg_nr) {

remove_field =

[index]->GetBool();

(++index < arg_nr)

update_mrna =

[index]->GetBool();

(

[index]->IsBool()) {

remove_field =

[index]->GetBool();

(++index < arg_nr)

update_mrna =

[index]->GetBool();

(!newValue.empty()) {

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, field_name, objs)) {

dest_feat = CreateNewRelatedFeature(*src_feat, field_name, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, field_name, objs)) {

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

dest_feat->

().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

vector<string> new_values;

(objs, newValue, existing_text, new_values);

(

= 0;

< new_values.size(); ++

) {

<<

<< new_values[

] <<

;

(changed && fh) {

->AddCommand(*upd_cmd);

<<

+ prot_product +

;

->AddCommand(*upd_cmd);

<<

<< message;

(remove_field) {

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!GetFeatDestinationField(dest_feat, field_name, objs)) {

(

& it : objs) {

.BasicCleanup(*dest_feat);

->AddCommand(*upd_cmd);

<<

<< message;

arg_nr =

.size();

(arg_nr < 4 && arg_nr > 7) {

(; index < 4; ++index) {

(!

[index]->IsString())

(index < arg_nr && (!

[index]->IsString() && !

[index]->IsBool()))

;

(++index < arg_nr && !

[index]->IsBool())

;

(++index < arg_nr && !

[index]->IsBool())

;

(!src_feat || !scope)

case_sensitive =

[++index]->GetBool();

is_regex = (++index <

.size()) ?

[index]->GetBool() :

;

& field_name =

[1]->GetString();

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!GetFeatDestinationField(dest_feat, field_name, objs)) {

repl_txt.assign(

);

<<

<< repl_txt;

(

index = 2; index < 4; index++) {

(

.size() == 7) {

void CMacroFunction_RmvRelFeatQual::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!src_feat || !scope)

& field_name = m_Args[1]->GetString();

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!GetFeatDestinationField(dest_feat, field_name, objs)) {

(

& it : objs) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

.BasicCleanup(*dest_feat);

m_DataIter->RunCommand(

, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

CMacroFunction_RmvRelFeatQual::x_ValidArguments()

(m_Args.size() != 2)

(m_Args[0]->IsString() && m_Args[1]->IsString());

scope = m_DataIter->GetScopedObject().scope;

(!src_feat || !scope)

& field_name = m_Args[1]->GetString();

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!GetFeatDestinationField(dest_feat, field_name, objs)) {

x_RmvOutsideFields(objs, *options);

(m_QualsChangedCount) {

m_DataIter->RunCommand(

, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

update_mrna = (m_Args.size() == 11) ? m_Args[10]->GetBool() :

;

scope = m_DataIter->GetScopedObject().scope;

m_DataIter->RunCommand(

, m_CmdComposite);

<<

+ prot_product +

;

x_LogFunction(

);

(!src_objs.empty() && !dest_objs.empty());

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(src_it != src_objs.end()) {

new_oi(dest_it->field.AddNewElement());

(

& it : src_prim_objs) {

(dest_it == dest_objs.end()) {

(index >=

.size())

(!

.empty());

& dest_field =

[index]->GetString();

valid = GetDestinationObjects(

, oi, dest_field,

);

(valid &&

.empty())

!

.empty();

(src.

() ==

) {

->GetLabel(&src_val);

(!x_GetSourceFields(oi, index, src_objs))

(!x_GetDestFields(oi, ++index, dest_objs))

& capitalization = m_Args[++index]->GetString();

& action_type = m_Args[++index]->GetString();

= (++index < m_Args.size()) ? m_Args[index]->GetString() :

;

(src_feat && m_Args[1]->IsString() &&

(m_Args[1]->GetString(),

)) {

(

&& it : src_objs) {

src_val = x_GetSourceString(src);

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

m_QualsChangedCount++;

ChangeFields(src_objs, dest_objs);

(m_QualsChangedCount) {

(!dest_objs.empty()) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

as =

.size();

(!(as == 5 || as == 6)) {

(

= 0;

< 2; ++

) {

src_index = 0, dest_index = 1;

|| m_Args.size() == 4) {

src_set = x_DoFieldsExist(oi, src_objs, src_index);

dest_set = x_DoFieldsExist(oi, dest_objs, dest_index);

(!src_set && !dest_set)

is_gene_suppressed_before =

;

is_gene_suppressed_after =

;

is_gene_suppressed_before = gene_xref && gene_xref->

();

x_SetFields(oi, src_objs, src_index);

x_SetFields(oi, dest_objs, dest_index);

(src_set && dest_set) {

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(src_it != src_objs.end() && dest_it != dest_objs.end()) {

new_oi(dest_it->field.AddNewElement());

x_SwapFields(src_prim_objs.front().field, dest_prim_objs.front().field);

(!src_set) {

x_CopyFields(dest_objs, src_objs);

(!dest_set) {

x_CopyFields(src_objs, dest_objs);

.BasicCleanup(*seq_feat);

is_gene_suppressed_after = gene_xref->

();

(!is_gene_suppressed_before && is_gene_suppressed_after)

bsrc->

().ResetDb();

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

.size() < 2) {

(

& it :

) {

(index >=

.size())

(!

.empty());

(index >=

.size())

(!

.empty());

(field_name.empty())

orgname->

().push_back(orgmod);

bsrc->

().SetOrgname(*orgname);

orgname =

(&(bsrc->

().SetOrgname()));

orgname->

().push_back(orgmod);

(field_name.empty())

feat->

().push_back(new_gbqual);

swapped =

;

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(src_it != src_objs.end() && dest_it != dest_objs.end()) {

new_oi(dest_it->field.AddNewElement());

(src_prim_objs.front().field, dest_prim_objs.front().field);

scope = m_DataIter->GetScopedObject().scope;

(!src_feat || !scope)

src_index = 0, dest_index = 1;

(m_Args.size() == 5) {

(m_Args[dest_index]->GetString().empty() || m_Args[dest_index + 1]->GetString().empty())

& dest_feattype = m_Args[dest_index]->GetString();

& dest_field = m_Args[dest_index + 1]->GetString();

m_Args[src_index]->GetString() :

;

m_ConstDestFeat.Reset(

);

m_EditDestFeat.Reset(

);

m_CreatedFeat.Reset(

);

src_set = x_DoFieldsExist(oi, src_objs, src_index);

(IstRNAProductField(*src_feat, src_field)) {

dest_set = x_DoDestFeatFieldsExist(*src_feat, dest_objs, dest_feattype, dest_field);

(!src_set && !dest_set)

x_SetFields(oi, src_objs, src_index);

x_SetOrCreateDestFeatFields(*src_feat, dest_objs, dest_index + 1);

(src_set && dest_set) {

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(src_it != src_objs.end() && dest_it != dest_objs.end()) {

new_oi(dest_it->field.AddNewElement());

x_SwapFields(src_prim_objs.front().field, dest_prim_objs.front().field);

(m_EditDestFeat && IstRNAProductField(*m_EditDestFeat, dest_field)) {

(src_it != src_objs.end()) {

dest_str = m_EditDestFeat->GetData().GetRna().GetRnaProductName();

m_EditDestFeat->SetData().SetRna().SetRnaProductName(

, remainder);

m_QualsChangedCount++;

(IstRNAProductField(*src_feat, src_field)) {

(dest_it != dest_objs.end()) {

new_oi(dest_it->field.AddNewElement());

seq_feat->

().SetRna().SetRnaProductName(

, remainder);

m_QualsChangedCount++;

(!src_set) {

x_CopyFields(dest_objs, src_objs);

(IstRNAProductField(*seq_feat, src_field)) {

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(dest_it != dest_objs.end()) {

seq_feat->

().SetRna().SetRnaProductName(dest_val, remainder);

m_QualsChangedCount++;

(m_EditDestFeat && IstRNAProductField(*m_EditDestFeat, dest_field)) {

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

(src_it != src_objs.end()) {

rna_str = m_EditDestFeat->GetData().GetRna().GetRnaProductName();

m_QualsChangedCount++;

(m_EditDestFeat && IstRNAProductField(*m_EditDestFeat, dest_field)) {

m_EditDestFeat->SetData().SetRna().SetRnaProductName(

, remainder);

(it->parent.GetName() ==

&& m_EditDestFeat) {

& qual_name = m_Args[m_Args.size() - 2]->GetString();

m_EditDestFeat->RemoveQualifier(qual_name);

(!dest_set) {

x_CopyFields(src_objs, dest_objs);

(m_EditDestFeat && IstRNAProductField(*m_EditDestFeat, dest_field)) {

CMQueryNodeValue::TObs::iterator src_it = src_objs.begin();

(src_it != src_objs.end()) {

m_EditDestFeat->SetData().SetRna().SetRnaProductName(src_val, remainder);

m_QualsChangedCount++;

(IstRNAProductField(*seq_feat, src_field)) {

CMQueryNodeValue::TObs::iterator dest_it = dest_objs.begin();

(dest_it != dest_objs.end()) {

m_QualsChangedCount++;

(IstRNAProductField(*seq_feat, src_field)) {

update_mrna = (m_Args.back()->GetDataType() ==

) ? m_Args.back()->GetBool() :

;

.BasicCleanup(*seq_feat);

(m_EditDestFeat) {

.BasicCleanup(*m_EditDestFeat);

(m_CreatedFeat) {

.BasicCleanup(*m_CreatedFeat);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

(m_ConstDestFeat && m_EditDestFeat) {

->AddCommand(*upd_cmd);

<<

<< message;

(m_CreatedFeat) {

->AddCommand(*upd_cmd);

<<

<< message;

m_DataIter->RunCommand(

, m_CmdComposite);

m_DataIter->RunCommand(upd_cmd, m_CmdComposite);

<<

+ prot_product +

;

x_LogFunction(

);

(!feat_list.empty() && feat_list.size() == 1) {

(!

->GetData().GetRna().GetRnaProductName().empty());

(!

.empty());

(index >=

.size())

& dest_field =

[index]->GetString();

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

->SetData().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

first_ok = (

[0]->IsString() ||

[0]->AreObjects() ||

[0]->IsRef());

(

index = 1; index <

.size() - 1; ++index) {

(!

[index]->IsString()) {

(

.back()->IsBool());

(!src_feat || !scope)

& dest_field =

[2]->GetString();

(dest_field.empty())

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*src_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

dest_feat->

().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

& capitalization =

[index]->GetString();

update_mrna =

[++index]->GetBool();

& action_type =

[++index]->GetString();

(IstRNAProductField(*dest_feat, dest_field)) {

(

&& it : src_objs) {

dest_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(changed && fh) {

->AddCommand(*upd_cmd);

<<

<< message;

->AddCommand(*upd_cmd);

<<

+ prot_product +

;

(

index = 1; index <

.size(); ++index) {

(!rna_feat || !scope)

& src_feat =

[0]->GetString();

& dest_feat =

[2]->GetString();

(src_feat ==

&& src_feat == dest_feat)

((src_feat !=

&& src_feat !=

) || (dest_feat !=

&& dest_feat !=

))

& capitalization =

[index]->GetString();

& action_type =

[++index]->GetString();

(src_feat ==

&& dest_feat ==

) {

dest_field =

[3]->GetString();

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*rna_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

(changed && fh) {

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(

&& it : src_objs) {

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

nr_args =

.size();

(nr_args < 7 || nr_args > 8)

(!

[0]->IsString() || !

[2]->IsString())

(

index = 1; index < 4; index += 2) {

(!(

[index]->IsString() ||

[index]->AreObjects() ||

[index]->IsRef()))

(

index = 4; index < nr_args; ++index) {

(index != 5 && !

[index]->IsString())

(

[5]->IsBool());

& capitalization =

[++index]->GetString();

& action_type =

[++index]->GetString();

(

&& it : src_objs) {

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(!dest_objs.empty()) {

as =

.size();

(as < 1 || as > 5) {

(

= 0;

< 2; ++

) {

(

index = 2; index < as; ++index) {

(!

[index]->IsString()) {

(!src_feat || !scope)

& dest_field =

[2]->GetString();

(dest_field.empty())

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*src_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

dest_feat->

().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

& capitalization =

[index]->GetString();

update_mrna =

[++index]->GetBool();

& action_type =

[++index]->GetString();

(IstRNAProductField(*dest_feat, dest_field)) {

(

&& it : src_objs) {

dest_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(changed && fh) {

->AddCommand(*upd_cmd);

<<

<< message;

->AddCommand(*upd_cmd);

<<

+ prot_product +

;

(

index = 1; index <

.size(); ++index) {

(!rna_feat || !scope)

& src_feat =

[0]->GetString();

& dest_feat =

[2]->GetString();

(src_feat ==

&& src_feat == dest_feat)

((src_feat !=

&& src_feat !=

) || (dest_feat !=

&& dest_feat !=

))

& capitalization =

[index]->GetString();

& action_type =

[++index]->GetString();

(src_feat ==

&& dest_feat ==

) {

dest_field =

[3]->GetString();

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*rna_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

(changed && fh) {

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(src_feat ==

&& dest_feat ==

) {

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(

&& it : src_objs) {

edit_feat->

().SetRna().SetRnaProductName(src_val, remainder);

(!

[0]->IsString() || !

[2]->IsString())

(

index = 1; index < 4; index += 2) {

(!(

[index]->IsString() ||

[index]->AreObjects() ||

[index]->IsRef()))

(

index = 4; index <

.size(); ++index) {

(!

[index]->IsString())

text_portion = parsed_obj.

();

(text_portion.empty()) {

& dest_field =

[index]->GetString();

GetDestinationObjects(obj, oi, dest_field, dest_objs);

dest_objs =

[index]->GetObjects();

& capitalization =

[++index]->GetString();

& action_type =

[++index]->GetString();

edit_feat->

().SetRna().SetRnaProductName(text_portion, remainder);

(dest_objs.empty())

new_oi(dest_objs.front().field.AddNewElement());

as =

.size();

(as != 4 && as != 5) {

(

index = 2; index < as; ++index) {

(!src_feat || !scope)

text_portion = parsed_obj.

();

(text_portion.empty()) {

& dest_field =

[2]->GetString();

(dest_field.empty())

changed =

,

=

;

(!feat_list.empty() && feat_list.size() == 1) {

dest_feat->

(*feat_list.front());

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

dest_feat = CreateNewRelatedFeature(*src_feat, dest_field, *scope);

(!dest_feat)

;

(!SetFeatDestinationField(dest_feat, dest_field, dest_objs)) {

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

dest_feat->

().SetProt().Assign((*it)->GetData().GetProt());

edit_feat->

().erase(it);

(edit_feat->

().empty()) {

& capitalization =

[index]->GetString();

update_mrna =

[++index]->GetBool();

& action_type =

[++index]->GetString();

(IstRNAProductField(*dest_feat, dest_field)) {

dest_feat->

().SetRna().SetRnaProductName(text_portion, remainder);

(changed && fh) {

<<

<< message;

(

index = 1; index <

.size(); ++index) {

scope = m_DataIter->GetScopedObject().scope;

(!scope || !

)

text_portion;

& field = m_Args[0]->GetString();

res_oi = m_Args[index]->GetObjects();

(!res_oi.empty()) {

(!res_oi.empty()) {

text_portion = text_holder.

();

(text_portion.empty())

x_SetFieldType(m_Args[++index]->GetString());

fieldname = (m_Type == eFieldValue) ? m_Args[++index]->GetString() :

;

(m_Type == eFieldError) {

(

, eWrongArguments,

);

capitalization, action_type;

(++index < m_Args.size()) {

capitalization = m_Args[index]->GetString();

(++index < m_Args.size()) {

action_type = m_Args[index]->GetString();

(capitalization.empty() || action_type.empty()) {

= (++index < m_Args.size()) ? m_Args[index]->GetString() :

;

( ; strcomm_it; ++strcomm_it) {

=

;

=

;

new_desc->

(*strcomm_it);

(m_Type == eFieldValue) {

user_object.

(fieldname, text_portion);

m_QualsChangedCount++;

(m_Type == eFieldValue) {

(user_object.

(fieldname)) {

user_field.

().SetStr(orig_val);

m_QualsChangedCount++;

user_object.

(fieldname, text_portion);

m_QualsChangedCount++;

(m_Type == eDbName) {

(m_Type == eFieldName) {

user_field.

().SetStr(orig_val);

m_QualsChangedCount++;

(m_QualsChangedCount) {

->AddCommand(*ecmd);

user_object.

(fieldname, text_portion);

m_QualsChangedCount++;

m_QualsChangedCount++;

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->RunCommand(

, m_CmdComposite);

=

;

+=

+ fieldname +

;

+=

;

+=

;

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

(

index = 1; index <

.size(); ++index) {

& field =

[0]->GetString();

res_oi =

[0]->GetObjects();

(res_oi.empty())

;

parsed_text = options->GetSelectedText(full_text);

(options->ShouldRemoveFromParsed()) {

(

* desc =

*

(it->second.GetNCPointer())) {

(desc->IsTitle()) {

orig_val = desc->GetTitle();

options->RemoveSelectedText(orig_val);

(!orig_val.empty()) {

desc->SetTitle() = orig_val;

->AddCommand(*chg_cmd);

(!res_oi.empty()) {

options->RemoveSelectedText(orig_val);

(orig_val.empty()) {

as =

.size();

(as < 7 || as > 10) {

(!

[1]->IsString() || !

[2]->IsBool() || !

[3]->IsString()) {

(

= 4;

< as; ++

) {

(bsh && bsh.

()) {

(!bsh)

;

(title_ci && !title_ci->

().empty()) {

new_desc->

(*title_ci);

(!user.

().empty()) {

& left_del =

[start_index]->GetString();

options->SetStartDigits();

options->SetStartLetters();

options->SetStartText(left_del);

options->SetIncludeStart(

[++start_index]->GetBool());

& right_del =

[++start_index]->GetString();

options->SetStopDigits();

options->SetStopLetters();

options->SetStopText(right_del);

options->SetIncludeStop(

[++start_index]->GetBool());

options->SetCaseInsensitive(!

[++start_index]->GetBool());

options->SetWholeWord(

[++start_index]->GetBool());

nr_args =

.size();

(++start_index < nr_args) {

options->SetShouldRemove(

[start_index]->GetBool());

(++start_index < nr_args) {

options->SetShouldRmvBeforePattern(

[start_index]->GetBool());

(++start_index < nr_args) {

options->SetShouldRmvAfterPattern(

[start_index]->GetBool());

(!rna_feat || !scope)

& src_feat =

[0]->GetString();

(src_feat !=

)

(!feat_list.empty() && feat_list.size() == 1) {

gene_feat->

(*feat_list.front());

(

[index]->IsString()) {

(

[index]->AreObjects()) {

res_oi =

[index]->GetObjects();

(

[index]->IsRef()) {

parsed_text = options->GetSelectedText(full_text);

(!parsed_text.empty() && options->ShouldRemoveFromParsed()) {

options->RemoveSelectedText(orig_val);

(orig_val.empty()) {

as =

.size();

(as < 8 || as > 11) {

(!

[2]->IsString() || !

[3]->IsBool() || !

[4]->IsString()) {

(

= 5;

< as; ++

) {

void CMacroFunction_LocalID::TheFunction()

(!user.

().empty()) {

(m_Result->IsNotSet()) {

(m_Result->IsNotSet()) {

CMacroFunction_LocalID::x_ValidArguments()

(m_Args.empty());

res_oi = m_Args[0]->GetObjects();

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

.size() != 2 || !first_ok)

(!

[1]->IsSimpleType()) {

scope = m_DataIter->GetScopedObject().scope;

(!scope || !bseq || bseq->

())

& dblink = m_Args[index]->GetString();

& existing_text_option = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

vector<pair<CSeqdesc_CI, CRef<CSeqdesc>>> changed_descs;

(desc_it->GetUser().GetType().IsStr() && desc_it->GetUser().GetType().GetStr() ==

) {

new_desc->

(*desc_it);

found_user_field =

;

found_user_field =

;

m_QualsChangedCount++;

m_QualsChangedCount++;

(

& it : field.

().SetStrs()) {

orig_value = it;

m_QualsChangedCount++;

m_QualsChangedCount++;

changed_descs.push_back(make_pair(desc_it, new_desc));

(changed_descs.empty()) {

m_QualsChangedCount++;

(!changed_descs.empty()) {

(

& it : changed_descs) {

->AddCommand(*chg_cmd);

(m_QualsChangedCount) {

report[

+ dblink] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

(remove_field) {

(desc_it->GetUser().GetType().IsStr() && desc_it->GetUser().GetType().GetStr() ==

) {

new_desc->

(*desc_it);

m_QualsChangedCount++;

->AddCommand(*(

(desc_it.GetSeq_entry_Handle(), *desc_it)));

->AddCommand(*chg_cmd);

(m_QualsChangedCount) {

report[

+ dblink +

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

(m_QualsChangedCount) {

m_DataIter->RunCommand(

, m_CmdComposite);

(!user_object_desc || dblink.empty())

new_field->

().SetStr(dblink);

del = (newValue.find(

) !=

) ?

:

;

(del.empty() && newValue.find(

) !=

) {

new_field->

().SetStrs().push_back(newValue);

vector<string> values;

(

&& it : values)

(!tmp_values.empty()) {

tmp_values += del +

;

(!tmp_values.empty()) {

tmp_values += del +

;

tmp_values += newValue;

del = (newValue.find(

) !=

) ?

:

;

(del.empty() && newValue.find(

) !=

) {

user_field.

().SetStrs().push_back(newValue);

arg_nr =

.size();

(arg_nr < 3 || arg_nr > 5) {

(!

[index]->IsString())

;

(!

[index]->IsString() && !

[index]->IsInt())

(!

[++index]->IsString())

;

(arg_nr > 3 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 4 && !

[++index]->IsBool())

;

CMacroFunction_AddUnverified::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!scope || !bseq || bseq->

())

vector<pair<CSeqdesc_CI, CRef<CSeqdesc>>> changed_descs;

(desc_it->GetUser().IsUnverified()) {

& present_user = desc_it->GetUser();

new_desc->Assign(*desc_it);

changed_descs.push_back(make_pair(desc_it, new_desc));

(changed_descs.empty()) {

m_QualsChangedCount++;

m_DataIter->RunCommand(

, m_CmdComposite);

(

& it : changed_descs) {

->AddCommand(*chg_cmd);

m_QualsChangedCount++;

m_DataIter->RunCommand(

, m_CmdComposite);

(m_QualsChangedCount) {

<< m_QualsChangedCount <<

;

CMacroFunction_AddUnverified::x_ValidArguments()

(m_Args.size() == 1 && m_Args[0]->IsString());

void CMacroFunction_ParseToDBLink::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!scope || !bseq || bseq->

())

text_portion;

(m_Args[index]->IsString()) {

& field = m_Args[index]->

();

(m_Args[index]->AreObjects()) {

res_oi = m_Args[index]->GetObjects();

(!res_oi.empty()) {

(m_Args[index]->IsRef()) {

(!res_oi.empty()) {

text_portion = text_holder.

();

(text_portion.empty())

(m_Args[++index]->IsString()) {

dblink = m_Args[index]->GetString();

capitalization = m_Args[++index]->GetString();

action_type = m_Args[++index]->GetString();

= (++index < m_Args.size()) ? m_Args[index]->GetString() :

;

vector<pair<CSeqdesc_CI, CRef<CSeqdesc>>> changed_descs;

(desc_it->GetUser().GetType().IsStr() && desc_it->GetUser().GetType().GetStr() ==

) {

new_desc->Assign(*desc_it);

found_user_field =

;

found_user_field =

;

m_QualsChangedCount++;

m_QualsChangedCount++;

(

& it : field.

().SetStrs()) {

orig_value = it;

m_QualsChangedCount++;

m_QualsChangedCount++;

changed_descs.push_back(make_pair(desc_it, new_desc));

(changed_descs.empty()) {

new_desc->SetUser().SetType().SetStr(

);

m_QualsChangedCount++;

(!changed_descs.empty()) {

(

& it : changed_descs) {

->AddCommand(*chg_cmd);

(m_QualsChangedCount) {

m_DataIter->RunCommand(

, m_CmdComposite);

report[

+ dblink] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_ParseToDBLink::x_ValidArguments()

(m_Args.size() > 5 || m_Args.size() < 4) {

(!(m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef()))

(

index = 1; index < m_Args.size(); ++index) {

& subtype_name = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

vector<string> new_values;

* const_feat =

*

(

.GetPointer());

(const_bsrc && m_IsBiosrc) {

x_AddBioSrcModifier(subtype_name, newValue);

(const_feat && !m_IsBiosrc) {

m_QualsChangedCount += s_AddGBQualifier(*seqfeat, subtype_name, newValue);

new_values.push_back(newValue);

(

&& it : res_oi) {

SetQualStringValue(value_oi, sat_value);

new_values.push_back(sat_value);

orig_sat_type = sat_type;

good_type = (found_it !=

.end()) ?

:

;

(!sat_name.empty()) {

sat_name = sat_type +

+ sat_name;

sat_name = sat_type;

SetQualStringValue(value_oi, sat_value);

new_values.push_back(sat_value);

SetQualStringValue(value_oi, met_value);

new_values.push_back(met_value);

orig_met_type = met_type;

found_it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(), met_type);

good_type = (found_it != kMobileETypeTypes.end()) ?

:

;

SetQualStringValue(value_oi, met_value);

new_values.push_back(met_value);

m_QualsChangedCount++;

new_values.push_back(new_val.

());

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr();

(

= 0;

< new_values.size(); ++

) {

<<

<< new_values[

] <<

;

x_LogFunction(

);

(remove_field) {

(!res_oi.empty()) {

(

&& it : res_oi) {

(!newValue.empty()) {

SetQualStringValue(value_oi, newValue);

m_QualsChangedCount++;

(

&& it : res_oi) {

(!newValue.empty()) {

SetQualStringValue(value_oi, newValue);

m_QualsChangedCount++;

(

&& it : res_oi) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

.BasicCleanup(*seq_feat);

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_size =

.size();

(arg_size < 5 || arg_size > 7)

(!

[1]->IsString() || !

[2]->IsString())

;

type_ok =

[3]->IsString() ||

[3]->IsInt() ||

[3]->IsDouble();

(!type_ok)

;

(!

[4]->IsString())

;

(arg_size > 5 && (!

[5]->IsString() && !

[5]->IsBool()))

;

(arg_size > 6 && !

[6]->IsBool())

;

qualifier = qual_name;

apply_value = newValue;

qualifier =

;

qualifier =

;

(!apply_value.empty()) {

added =

;

orgname->

().push_back(orgmod);

bsrc.

().SetOrgname(*orgname);

bsrc.

().SetOrgname().SetMod().push_back(orgmod);

added =

;

scope = m_DataIter->GetScopedObject().scope;

m_Result->SetNotSet();

(!feat || !scope || !feat->

())

& qual_value = feat->

(

);

(!qual_value.empty()) {

(m_FieldType) {

eSatelliteType:

= s_GetSatelliteType(qual_value);

eSatelliteName:

= s_GetSatelliteName(qual_value);

(m_Nested == eNotNested) {

m_Result->SetString(

);

m_Result->SetRef(new_node);

.substr(0, pos);

new_type =

;

(!name.empty()) {

new_name =

+ name;

(

.empty()) {

good_type = (found_it !=

.end()) ?

:

;

new_name =

+

+ new_name;

new_type + new_name;

(

.empty());

scope = m_DataIter->GetScopedObject().scope;

m_Result->SetNotSet();

(!feat || !scope || !feat->

())

(!qual_value.empty()) {

(m_FieldType) {

eMobileElemTType:

= s_GetMobileElemTType(qual_value);

eMobileElemTName:

= s_GetMobileElemTName(qual_value);

(m_Nested == eNotNested) {

m_Result->SetString(

);

m_Result->SetRef(new_node);

it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(),

);

it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(),

);

name =

.substr(pos + 1,

);

it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(),

);

(it != kMobileETypeTypes.end()) ? name :

;

it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(),

);

(!

.empty()) {

found_it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(),

);

good_type = (found_it != kMobileETypeTypes.end()) ?

:

;

(!name.empty()) {

(

.empty());

void CMacroFunction_EditSubfield::TheFunction()

& subfield = m_Args[1]->GetString();

(subfield.empty())

&

= m_Args[++index]->GetString();

case_sensitive = m_Args[++index]->GetBool();

is_regex = (++index < m_Args.size()) ? m_Args[index]->GetBool() :

;

(m_Args[0]->AreObjects()) {

(m_Args[0]->IsRef()) {

x_GetObjectsFromRef(objs, 0);

(

&& it : objs) {

SetQualStringValue(value_oi, newValue);

orig_sat_type = sat_type;

good_type = (found_it !=

.end()) ?

:

;

(!sat_name.empty())

sat_name = sat_type +

+ sat_name;

SetQualStringValue(value_oi, newValue);

SetQualStringValue(value_oi, newValue);

orig_met_type = met_type;

found_it = find(kMobileETypeTypes.begin(), kMobileETypeTypes.end(), met_type);

good_type = (found_it != kMobileETypeTypes.end()) ?

:

;

SetQualStringValue(value_oi, newValue);

inst, coll, id;

SetQualStringValue(value_oi, newValue);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

<< find_txt;

repl_txt.assign(

);

<<

<< repl_txt;

CMacroFunction_EditSubfield::x_ValidArguments()

(m_Args.size() != 7)

first_ok = m_Args[0]->AreObjects() || m_Args[0]->IsRef();

(!first_ok || !m_Args[1]->IsString()) {

(

index = 2; index < 4; index++) {

(!m_Args[index]->IsString() && !m_Args[index]->IsInt()) {

(m_Args[4]->IsString() && m_Args[5]->IsBool() && m_Args[6]->IsBool());

void CMacroFunction_RemoveSubfield::TheFunction()

& subfield = m_Args[1]->GetString();

(subfield.empty())

(m_Args[0]->AreObjects()) {

objs = m_Args[0]->GetObjects();

(m_Args[0]->IsRef()) {

x_GetObjectsFromRef(objs, 0);

(

&& it : objs) {

inst, coll, id;

(!newValue.empty()) {

SetQualStringValue(value_oi, newValue);

m_QualsChangedCount++;

(m_QualsChangedCount) {

scope = m_DataIter->GetScopedObject().scope;

.BasicCleanup(*seq_feat);

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

CMacroFunction_RemoveSubfield::x_ValidArguments()

m_Args.size() == 2 && (m_Args[0]->AreObjects() || m_Args[0]->IsRef()) && m_Args[1]->IsString();

(ch ==

|| ch ==

|| ch ==

|| ch ==

|| ch ==

) {

,

,

,

,

,

,

,

,

,

,

};

(pos != string::npos) {

vector<string> replacements;

(codon.length() == 3 &&

(codon.c_str()[0])) {

this_codon = codon.substr(0, 1);

replacements.push_back(this_codon);

(

= 1;

< 3;

++) {

num_now = replacements.size();

(

j = 1; j < ch.length(); j++) {

(

k = 0; k < num_now; k++) {

cpy = replacements[k];

replacements.push_back(cpy);

(

k = 0; k < num_now; k++) {

(

j = 0; j < ch.length(); j++) {

replacements[j * num_now + k].append(ch.substr(j, 1));

replacements.push_back(codon);

replacements;

void CMacroFunction_SetCodonsRecognized::TheFunction()

(m_Args[0]->IsRef()) {

(m_Args[0]->IsString()) {

= m_Args[0]->GetString();

(

.empty()) {

edit_feat->

().SetRna().SetExt().SetTRNA().ResetCodon();

(

.empty())

(

j = 0; j <

.size(); j++)

edit_feat->

().SetRna().SetExt().SetTRNA().SetCodon().push_back(val);

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_SetCodonsRecognized::x_ValidArguments()

(m_Args.size() == 1 && (m_Args[0]->IsRef() || m_Args[0]->IsString()));

void CMacroFunction_SetStructCommField::TheFunction()

* bioseq =

*

(

.GetPointer());

(!(bioseq && bioseq->

()) &&

& field_name = m_Args[index]->GetString();

& field_value = m_Args[++index]->GetString();

& existing_text_option = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!field_value.empty()) {

user_object->

(field_name, field_value);

m_QualsChangedCount++;

(user_object->

(field_name)) {

user_field.

().SetStr(orig_val);

m_QualsChangedCount++;

user_object->

(field_name, field_value);

m_QualsChangedCount++;

(m_QualsChangedCount) {

(!edit_bseq)

;

(!seqdesc)

;

user_field.

().SetStr(orig_val);

m_QualsChangedCount++;

user_field.

().SetStr(field_value);

m_QualsChangedCount++;

m_QualsChangedCount++;

(m_QualsChangedCount) {

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< field_name <<

<< field_value <<

;

(remove_field) {

m_QualsChangedCount++;

(!edit_bseq)

;

(!seqdesc)

;

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

CMacroFunction_SetStructCommField::x_ValidArguments()

(m_Args.size() < 3 || m_Args.size() > 6)

(m_Args[0]->IsRef()) {

(!m_Args[0]->IsString()) {

(

= 1;

< m_Args.size(); ++

) {

(!m_Args[

]->IsString() && !m_Args[

]->IsBool()) {

* bioseq =

*

(

.GetPointer());

(!(bioseq && bioseq->

()) &&

& db_name = m_Args[index]->GetString();

=

;

=

;

& existing_text_option = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!db_name.empty()) {

m_DataIter->SetModified();

found_user =

;

new_seqdesc->

(*desc_it);

m_QualsChangedCount += s_UpdateStructCommentDb(*new_seqdesc,

, db_name, existing_text);

m_QualsChangedCount += s_UpdateStructCommentDb(*new_seqdesc,

, db_name, existing_text);

(m_QualsChangedCount) {

->AddCommand(*ecmd);

m_DataIter->RunCommand(

, m_CmdComposite);

m_DataIter->SetModified();

m_QualsChangedCount += s_UpdateStructCommentDb(*user_object,

, db_name, existing_text);

m_QualsChangedCount += s_UpdateStructCommentDb(*user_object,

, db_name, existing_text);

m_DataIter->SetModified();

(m_QualsChangedCount) {

<< m_DataIter->GetBestDescr() <<

<< db_name <<

;

x_LogFunction(

);

(remove_field) {

m_QualsChangedCount++;

m_DataIter->SetModified();

m_QualsChangedCount++;

m_DataIter->SetModified();

new_seqdesc->

(*desc_it);

m_QualsChangedCount++;

m_QualsChangedCount++;

(m_QualsChangedCount) {

->AddCommand(*ecmd);

m_DataIter->RunCommand(

, m_CmdComposite);

(m_QualsChangedCount) {

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

seqdesc->

(*user_obj);

(!edit_bseq)

;

& descriptors = edit_bseq->

().Set();

descriptors.push_back(seqdesc);

(!

[0]->IsString() || !

[1]->IsString()) {

(

.size() > 2 && (!

[index]->IsString() && !

[index]->IsBool()))

(

.size() > 3 && !

[++index]->IsBool())

(!seqdesc.

()) {

user_field.

().SetStr(orig_val);

user_field.

().SetStr(root);

(!user_object.

())

;

& user_fields = user_object.

();

(CUser_object::TData::iterator it = user_fields.begin(); it != user_fields.end(); ++it) {

(*it, *(user_fields.end() - 1));

CMacroFunction_ValueFromTable::TheFunction()

&

= m_Args[0]->GetString();

col = (

)m_Args[1]->GetInt();

m_Result->SetNotSet();

= m_DataIter->GetValueFromTable(col - 1);

m_Result->SetString(

);

CMacroFunction_ValueFromTable::x_ValidArguments()

(m_Args.size() != 2)

(m_Args[0]->IsString() && m_Args[1]->IsInt());

CMacroFunction_GeneQual::TheFunction()

field_name = m_Args[0]->GetString();

field_name =

+ field_name;

found_qual =

;

(

&& it : tmp_result.

()) {

m_Result->SetObjects().push_back(it);

(!found_qual && feat->

()) {

(

&& it : feat->

()) {

(it->IsSetData() && it->GetData().IsGene()) {

gene_xref = &(it->SetData().SetGene());

m_Result->GetObjects().empty()) {

m_Result->SetNotSet();

CMacroFunction_GeneQual::x_ValidArguments()

voucher_type;

voucher_part = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(m_Args[0]->IsString()) {

voucher_type = m_Args[0]->

();

(m_Args[0]->AreObjects()) {

objs = m_Args[0]->GetObjects();

(m_Args[0]->IsRef()) {

x_GetObjectsFromRef(objs, 0);

(voucher_type.empty() && objs.empty()) {

(!voucher_type.empty()) {

(!newValue.empty()) {

has_voucher =

;

orgmod = *mod_it;

(orgmod->IsSetSubtype() && orgmod->GetSubtype() == subtype) {

x_ApplyPart(*orgmod, part, newValue, existing_text);

has_voucher =

;

new_mod = x_AddNewQual(subtype, part, newValue);

bsrc->

().SetOrgname().SetMod().push_back(new_mod);

m_QualsChangedCount++;

new_mod = x_AddNewQual(subtype, part, newValue);

bsrc->

().SetOrgname().SetMod().push_back(new_mod);

m_QualsChangedCount++;

(remove_field) {

orgmod = *mod_it;

(orgmod->IsSetSubtype() && orgmod->GetSubtype() == subtype) {

x_RemovePart(*orgmod, part);

m_QualsChangedCount++;

(orgmod->GetSubname().empty())

bsrc->

().SetOrgname().ResetMod();

(

&& it : objs) {

(!

)

;

(!newValue.empty()) {

x_ApplyPart(*

, part, newValue, existing_text);

new_mod = x_AddNewQual(

->GetSubtype(), part, newValue);

bsrc->

().SetOrgname().SetMod().push_back(new_mod);

m_QualsChangedCount++;

(remove_field) {

x_RemovePart(*

, part);

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

(!newValue.empty()) {

report[

+ voucher_part] = m_QualsChangedCount;

(remove_field) {

report[

+ voucher_part] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

arg_nr =

.size();

(arg_nr < 4 || arg_nr > 6)

first_ok =

[0]->IsString() ||

[0]->AreObjects() ||

[0]->IsRef();

(!first_ok)

;

(!

[1]->IsString())

;

third_ok =

[2]->IsString() ||

[2]->IsInt() ||

[2]->IsDouble();

(!third_ok)

;

(!

[3]->IsString())

;

(arg_nr > 4 && (!

[4]->IsString() && !

[4]->IsBool()))

;

(arg_nr > 5 && !

[5]->IsBool())

;

orig_inst, orig_coll, orig_id;

update = [&newValue, existing_text,

](

&

,

& orig_value)

inst{ orig_inst }, coll{ orig_coll },

{ orig_id };

inst, coll, id;

inst, coll, id;

void CMacroFunction_SetAutodefOption::TheFunction()

field_name = m_Args[index]->GetString();

& field_value = m_Args[++index]->GetString();

& existing_text_option = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

user_object->

(field_name, field_value);

m_QualsChangedCount++;

(user_object->

(field_name)) {

user_field.

().SetStr(orig_val);

m_QualsChangedCount++;

user_object->

(field_name, field_value);

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< field_name <<

<< field_value <<

;

CMacroFunction_SetAutodefOption::x_ValidArguments()

(m_Args.size() < 3 || m_Args.size() > 4)

(

= 0;

< m_Args.size(); ++

) {

(!m_Args[

]->IsString()) {

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

bool IsSetOrgMod(void) const

bool IsSetOrgname(void) const

static bool CleanupUserObject(CUser_object &object)

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

static int CodonToIndex(char base1, char base2, char base3)

bool IsSuppressed(void) const

Subclass of the IQueryParseUserObject which is held as the user-defined object in each CQueryParseNod...

class CMacroExecException

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

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

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static string MakeStructuredVoucher(const string &inst, const string &coll, const string &id)

static bool ParseStructuredVoucher(const string &str, string &inst, string &coll, string &id)

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

string GetRnaProductName(void) const

void SetRnaProductName(const string &product, string &remainder)

ESubtype GetSubtype(void) const

@ eSubtype_mat_peptide_aa

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void AddQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

CUser_field & SetValue(int value)

set a data field to a given value Int8 and TGi values can be stored into 'str' field if the value doe...

void SetObjectType(EObjectType obj_type)

void AddUnverifiedOrganism()

void AddUnverifiedContaminant()

bool RemoveNamedField(const string &field_name, NStr::ECase ecase=NStr::eCase)

@ eObjectType_StructuredComment

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

bool IsAutodefOptions() const

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

void AddUnverifiedMisassembled()

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

EObjectType GetObjectType() const

void AddUnverifiedFeature()

static auto & FixCapitalizationInString

static const string kSatelliteTypes[]

static void cleanup(void)

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

static const char table_name[]

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

static const char location[]

Utility macros and typedefs for exploring NCBI objects from general.asn.

#define EDIT_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

#define ERASE_USERFIELD_ON_USEROBJECT(Itr, Var)

ERASE_USERFIELD_ON_USEROBJECT.

const TResidue codons[4][4]

#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.

const CMemberId & GetId(void) const

const string & GetName(void) const

objects::ECapChange ConvertStringtoCapitalOption(const string &cap_name)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

virtual bool x_ChangeFields(CObjectInfo &src, CObjectInfo &dest)

virtual void TheFunction()

class CMacroFunction_EditStringQual Usage: EditStringQual(field_name|rt_obj, find_text,...

bool StringsAreEquivalent(const string &name1, const string &name2)

bool RemoveFirstName(objects::CName_std &std_name)

static bool s_EditText(string &str, const string &find, const string &repl, ESearchLoc loc, bool case_sensitive, bool is_regex=false)

bool SetQualStringValue(CObjectInfo &oi, const string &value)

Functions make the action and collect statistics.

void CleanupForTaxnameChange(CObjectInfo oi)

void SetString(const string &data)

Set/get underlying data type.

void x_RemovePart(objects::COrgMod &orgmod, NMacroUtil::EStructVoucherPart part)

static void s_MoveSuffixToTheEnd(objects::CUser_object &user_object)

virtual void TheFunction()

Function implementation.

static bool s_IsATGC(char ch)

CMacroFunction_SetCodonsRecognized SetCodonsRecognized(field_name) The field_name specifies one of th...

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_SetOrCreateDestFeatFields(const objects::CSeq_feat &src_feat, CMQueryNodeValue::TObs &result, size_t index)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

objects::CSeqFeatData::ESubtype GetFeatSubtype(const string &feat_type)

void x_SetFields(CMQueryNodeValue::TObs &objs, const string &newValue, objects::edit::EExistingText existing_text, vector< string > &new_values)

CRef< CMacroCmdComposite > m_CmdComposite

static void s_ResetModSubsrcQuals(CBioSource &bsrc)

static bool s_AddSrcSubSource(objects::CBioSource &bsrc, int subtype, const string &value)

const char * kMobileElementTType

static string s_GetMobileElemTType(const string &value)

static vector< string > ParseDegenerateCodons(string codon)

bool x_GetSourceFields(CObjectInfo oi, size_t index, CMQueryNodeValue::TObs &result)

virtual bool x_ChangeFields(CObjectInfo &src, CObjectInfo &dest)=0

virtual void TheFunction()

Function implementation.

static bool s_SetEnumValue(CObjectInfo &obj, const string &str)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

bool x_GetSpecialField(const string &field, CMQueryNodeValue::TObs &objs, objects::CScope &scope)

CMQueryNodeValue::EType GetPrimitiveFromRef(CMQueryNodeValue &node)

void x_SetNewPrimitiveValue(CObjectInfo &oi, const string &newValue, objects::edit::EExistingText existing_text, vector< string > &new_values)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

static void s_AddNewDBlinkValue(CUser_field &user_field, const string &newValue)

AddDBLink(dblink_type, newValue, existing_text, delimiter, remove_blank) The last parameter is option...

static string s_GetMobileElemTName(const string &value)

virtual void TheFunction()

class CMacroFunction_ConvertStringQual ConvertStringQual(src_field, dst_field, capitalization,...

bool ResolveAndSetSimpleTypeValue(CObjectInfo &oi, const string &field_name, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)

Resolve dot qualified ASN.1 node_name using the object information instance provided as a parameter (...

bool RemoveFieldByName(CMQueryNodeValue::SResolvedField &res_field)

Remove the object information instance corresponding to field, using information about its parent nod...

list< SResolvedField > TObs

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

static string s_GetEnumValue(CObjectInfo &obj)

bool GetSimpleTypeValue(CObjectInfo &oi, const string &field_name, CMQueryNodeValue &value)

Get single node data from the node specified by parameter of type CObjectInfo and additionally field ...

virtual void TheFunction()

class CMacroFunction_SetStringQual Expected Syntax: SetStringQual(field_name, newValue,...

bool x_CheckArguments(size_t index) const

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

void Dereference()

If it is a reference it is resolved to the first non reference type in the hierarchy.

const TObs & GetObjects() const

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool x_SetFields(CObjectInfo oi, CMQueryNodeValue::TObs &result, size_t index)

void GetPrimitiveObjInfosWithContainers(CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)

bool ResolveIdentToObjects(const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)

Resolve name to the list of objects.

static void s_SetFeatField(CRef< CSeq_feat > feat, CObjectInfo &oi, const string &field_name, CMQueryNodeValue::TObs &result)

const char * kStrCommFieldValue

bool SetSimpleTypeValue(CObjectInfo &oi, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)

Set single node data to the node specified by parameter of type CObjectInfo.

static const string s_GetExpansion(const string &ch)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

CConstRef< objects::CSeq_feat > m_ConstDestFeat

void RemoveGeneXref(objects::CSeq_feat &feat)

void ChangeFields(CMQueryNodeValue::TObs &src_objs, CMQueryNodeValue::TObs &dest_objs)

void SetDataType(EType dt)

bool x_MakeNewStructuredComment(const string &db_name, const string &kPrefix, const string &kSuffix)

string GetStringValue(CRef< CMQueryNodeValue > &value)

converts ints and doubles into string, by changing the type of the value

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

void x_AddBioSrcModifier(const string &subtype, const string &newValue)

void x_ParseFields(CMQueryNodeValue::TObs &dest_objs, const string &text_portion, objects::edit::EExistingText existing_text)

string x_GetSourceString(CObjectInfo &src)

static bool s_AddNewUserField(CRef< CSeqdesc > &user_object_desc, const string &dblink, const string &newValue)

const char * kSatelliteType

const char * kSatelliteName

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_RmvOutsideFields(CMQueryNodeValue::TObs &resolved_objs, const CRemoveTextOptions &options)

CObjectInfo GetPrimitiveObjInfo(const CObjectInfo &info)

bool x_GetDestFields(CObjectInfo oi, size_t index, CMQueryNodeValue::TObs &result)

const string & GetString() const

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

EType GetDataType() const

CRef< CRemoveTextOptions > x_GetRemoveTextOptions(size_t start_index) const

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

CRef< objects::CSeq_feat > m_EditDestFeat

const char * kStrCommFieldName

bool x_DoFieldsExist(CObjectInfo oi, CMQueryNodeValue::TObs &result, size_t index)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

void GetPrimitiveObjectInfos(CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)

virtual void TheFunction()

class CMacroFunction_ConvertStringQual ConvertStringQual(src_field, dst_field, capitalization,...

EStructVoucherPart GetSVPartFromString(const string voucher_part)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

static string s_MakeSatellite(const string &type, const string &name)

Int4 m_QualsChangedCount

Number of changed qualifiers during the function call.

bool GetFieldsByName(CMQueryNodeValue::TObs *results, const CObjectInfo &oi_i, const string &field_name)

Resolve existing dot qualified ASN.1 name (field_name) starting from the object information instance ...

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

bool x_DoDestFeatFieldsExist(const objects::CSeq_feat &src_feat, CMQueryNodeValue::TObs &result, const string &dest_feattype, const string &dest_field)

bool IsTaxname(CMQueryNodeValue::SResolvedField &res)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

class CMacroFunction_CopyStringQual Expected syntax: CopyStringQual( src_field, dest_field,...

CRef< objects::edit::CParseTextOptions > x_GetParseOptions(size_t start_index)

static string s_GetSatelliteName(const string &value)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

static const string kAmbiguities

static int s_AddGBQualifier(objects::CSeq_feat &feat, const string &qual_name, const string &newValue)

static void s_SetVectorValue(CUser_field &user_field, const string &newValue, const string &del)

virtual void TheFunction()

Function implementation.

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

CRef< objects::COrgMod > x_AddNewQual(objects::COrgMod::TSubtype subtype, NMacroUtil::EStructVoucherPart part, const string &newValue)

bool ResolveIdentToSimple(const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)

Resolve name to simple types value.

bool SetFieldsByName(CMQueryNodeValue::TObs *results, CObjectInfo &oi_i, const string &field_name)

Resolve not necessarily existing dot qualified ASN.1 name (field_name) starting from the object infor...

void x_CopyFields(CMQueryNodeValue::TObs &src_objs, CMQueryNodeValue::TObs &dest_objs)

virtual void TheFunction()

Function implementation.

static string s_GatherExistingValues(CUser_field &user_field, const string &newValue, const string &del)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

void x_GetObjectsFromRef(CMQueryNodeValue::TObs &objects, const size_t &index)

objects::edit::EExistingText ActionTypeToExistingTextOption(const string &action_type, const string &delimiter)

CRef< CMQueryNodeValue > m_Result

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

static Int4 s_RemoveFields(CIRef< IMacroBioDataIter > &dataiter, CMQueryNodeValue::TObs &objs)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

void x_SetFieldType(const string &strcomm_field)

bool IsSatelliteSubfield(const string &field)

static int s_UpdateStructCommentDb(objects::CSeqdesc &seqdesc, const string &field, const string &db_name, objects::edit::EExistingText existing_text)

objects::ECapChange m_CapChange

static ESearchLoc s_GetLocFromName(const string &name)

bool IsMobileElementTSubfield(const string &field)

const char * kMobileElementTQual

static string s_MakeMobileElementT(const string &type, const string &name)

virtual void TheFunction()

class CMacroFunction_CopyStringQual Expected syntax: CopyStringQual( src_field, dest_field,...

static const string kReplacements[]

bool x_SwapFields(CObjectInfo &src, CObjectInfo &dest)

static void s_AddUnverifiedType(CUser_object &user, NMacroUtil::EUnverifiedType type)

class CMacroFunction_AddUnverified AddUnverified("Features"); The user object will be added only to n...

string x_GetSourceString(CObjectInfo &src)

void x_LogFunction(CNcbiOstrstream &logstr)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

bool ApplyFirstName(objects::CName_std &std_name, const string &newValue, objects::edit::EExistingText existing_text)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool IsBiosourceModifier(const string &field)

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

virtual bool x_ChangeFields(CObjectInfo &src, CObjectInfo &dest)

static void s_SetBioSourceField(CRef< CBioSource > bsrc, CObjectInfo &oi, const string &field_name, CMQueryNodeValue::TObs &dest_objs)

bool EditText(string &str) const

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

CRef< objects::CSeq_feat > m_CreatedFeat

void x_SetField(CConstRef< CObject > &obj, const string &fieldname, CMQueryNodeValue::TObs &result)

void SwapGbQualWithValues(CMQueryNodeValue::TObs &objs)

void SetObjects(const TObs &obs)

static const char * sm_FunctionName

EditRelatedFeatureQual(feat_type, field_name, find_text, repl_text, location, case_sensitive,...

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

string x_GetSourceString(CObjectInfo &src)

const char * kMobileElementTName

DEFINE_MACRO_FUNCNAME(CMacroFunction_CopyFeatQual, "CopyFeatureQual")

CopyFeatureQual(src_field, dest_feature_type, dest_feature_field, update_mrna, existing_text_opt,...

virtual bool x_ChangeFields(CObjectInfo &src, CObjectInfo &dest)

void x_ApplyPart(objects::COrgMod &orgmod, NMacroUtil::EStructVoucherPart part, const string &newValue, objects::edit::EExistingText existing_text)

static bool s_AddSrcOrgMod(objects::CBioSource &bsrc, int subtype, const string &value)

EUnverifiedType GetUnverifiedType(const string &value)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

CIRef< IMacroBioDataIter > m_DataIter

static bool s_SwapFields(CObjectInfo &src, CObjectInfo &dest)

vector< CConstRef< objects::CSeq_feat > > TVecFeatList

virtual bool x_ValidArguments(void) const

Tests the number and the type of function arguments.

vector< pair< objects::CSeqdesc_CI, CRef< objects::CSeqdesc > > > m_ChangedDescriptors

virtual void TheFunction()

Function implementation.

objects::edit::EExistingText m_ExistingText

void RemoveEmptyDescriptors(objects::CBioseq &bseq)

const char * kStrCommDbname

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_EditFields(CMQueryNodeValue::TObs &resolved_objs, const string &find_txt, const string &repl_txt, ESearchLoc loc, bool case_sensitive, bool is_regex)

static string s_GetSatelliteType(const string &value)

size_t TMemberIndex

Type used for indexing class members and choice variants.

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

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

static const TObjectType * SafeCast(TTypeInfo type)

@ ePrimitiveValueString

string|char*|const char*

@ ePrimitiveValueInteger

(signed|unsigned) (char|short|int|long)

@ ePrimitiveValueChar

char

@ ePrimitiveValueBool

bool

@ ePrimitiveValueEnum

enum

@ ePrimitiveValueReal

float|double

CElementIterator BeginElements(void) const

Create container elements iterator.

CObjectInfo AddNewPointedElement(void) const

add new pointer element, create new pointed object and return it

CObjectInfo GetPointedObject(void) const

Get data and type information of object to which this type refers.

bool GetPrimitiveValueBool(void) const

Get boolean data.

const CMemberInfo * GetMemberInfo(void) const

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

CObjectInfo GetMember(void) const

Get class member data.

void SetPrimitiveValueString(const string &value)

void SetPrimitiveValueBool(bool value)

Set boolean data.

int GetPrimitiveValueInt(void) const

Get data as int.

void SetPrimitiveValueInt8(Int8 value)

void SetPrimitiveValueInt4(Int4 value)

CObjectInfo AddNewElement(void) const

Add and return new element object.

CMemberIterator GetClassMemberIterator(TMemberIndex index) const

Create class member iterator that initially points to specified member.

ETypeFamily GetTypeFamily(void) const

Get data type family.

void GetPrimitiveValueString(string &value) const

Get string data.

double GetPrimitiveValueDouble(void) const

Get data as double.

CMemberIterator FindClassMember(const string &memberName) const

Find class member by its name.

Int4 GetPrimitiveValueInt4(void) const

Get data as Int4.

void SetPrimitiveValueDouble(double value)

const string & GetName(void) const

Get type name.

void SetPrimitiveValueInt(int value)

EPrimitiveValueType GetPrimitiveValueType(void) const

Get type of primitive value.

Int8 GetPrimitiveValueInt8(void) const

Get data as Int8.

bool IsSet(void) const

Is member assigned a value.

CObjectTypeInfo GetElementType(void) const

Get type information of an element of container.

void GetCdssForGene(const CMappedFeat &gene_feat, list< CMappedFeat > &cds_feats, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

TObjectType & GetObject(void) const

Get object.

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

size_t Replace(CTempStringEx search, CTempString replace, CRegexp::TCompile compile_flags=CRegexp::fCompile_default, CRegexp::TMatch match_flags=CRegexp::fMatch_default, size_t max_replace=0)

Replace occurrences of a substring within a string by pattern.

unsigned int TCompile

Type definitions used for code clarity.

string GetResult(void)

Get result string.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#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 bool StringToBool(const CTempString str)

Convert string to bool.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

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 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 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 const string BoolToString(bool value)

Convert bool to string.

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

Truncate whitespace in a string (in-place)

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

Convert int to string.

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 EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static SIZE_TYPE FindCase(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 sensitive search.

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

Convert string to long.

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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

bool IsSetOrg(void) const

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

bool IsSetSubtype(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

void ResetSubtype(void)

Reset Subtype data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetData(void) const

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

bool IsStr(void) const

Check if variant Str is selected.

bool IsStrs(void) const

Check if variant Strs is selected.

const TStrs & GetStrs(void) const

Get the variant data.

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.

void SetNum(TNum value)

Assign a value to Num 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 SetType(TType &value)

Assign a value to Type data member.

void ResetNum(void)

Reset Num data member.

void SetData(TData &value)

Assign a value to Data data member.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

@ e_not_set

No variant selected.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

const TSubname & GetSubname(void) const

Get the Subname member data.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetSubname(void) const

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

TMod & SetMod(void)

Assign a value to Mod data member.

void SetSubname(const TSubname &value)

Assign a value to Subname data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

const TName & GetName(void) const

Get the Name member data.

TType GetType(void) const

Get the Type member data.

bool IsSetType(void) const

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

TXref & SetXref(void)

Assign a value to Xref data member.

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.

bool IsProt(void) const

Check if variant Prot is selected.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

void ResetXref(void)

Reset Xref data member.

const TRna & GetRna(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetProduct(void) const

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

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

bool IsGenbank(void) const

Check if variant Genbank is selected.

const TUser & GetUser(void) const

Get the variant data.

const TTitle & GetTitle(void) const

Get the variant data.

const TGenbank & GetGenbank(void) const

Get the variant data.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TUser & SetUser(void)

Select the variant.

bool IsUser(void) const

Check if variant User is selected.

@ e_User

user defined object

@ e_Title

a title for this sequence

unsigned int

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

Functions that resolve field names described in asn format.

const struct ncbi::grid::netcache::search::fields::CREATED created

const GenericPointer< typename T::ValueType > T2 value

static const char delimiter[]

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define ERASE_ORGMOD_ON_BIOSOURCE(Itr, Var)

ERASE_ORGMOD_ON_BIOSOURCE.

#define EDIT_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)

#define EDIT_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

#define EDIT_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

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

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

@ eExistingText_append_semi

@ eExistingText_leave_old

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

CRef< CCmdComposite > UpdatemRNAProduct(const objects::CSeq_feat &protein, objects::CScope &scope, string &message)

void SetProteinFeature(objects::CSeq_feat &prot, objects::CBioseq_Handle product, const objects::CSeq_feat &cds)

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