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

CMacroFunction_TrimStopFromCompleteCDS::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!edit_feat || !scope)

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< best_id;

CMacroFunction_TrimStopFromCompleteCDS::x_ValidArguments()

(m_Args.empty());

void CMacroFunction_SynchronizeCDSPartials::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!edit_feat || !scope)

m_DataIter->SetModified();

m_DataIter->RunCommand(synch_cmd, m_CmdComposite);

(change || synch_cmd) {

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_SynchronizeCDSPartials::x_ValidArguments()

(m_Args.empty());

CMacroFunction_AdjustConsensusSpliceSites::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!edit_feat || !scope)

orig_feat.

(*edit_feat);

changed = worker.AdjustCDS(*edit_feat);

m_DataIter->SetModified();

m_DataIter->RunCommand(update_cmd, m_CmdComposite);

<<

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_AdjustConsensusSpliceSites::x_ValidArguments()

(m_Args.empty());

CMacroFunction_RemoveInvalidECNumbers::TheFunction()

(!

.IsSetEc() ||

.GetEc().empty())

vector< CProt_ref::EECNumberStatus > TVecStatus;

TVecStatus st_before;

replaced = 0;

TVecStatus::const_iterator it_bef = st_before.begin();

CProt_ref::TEc::const_iterator ec =

.GetEc().begin();

(; ec !=

.GetEc().end() && it_bef != st_before.end(); ++ec, ++it_bef) {

removed = (

)(st_before.size() -

.GetEc().size());

(replaced || removed) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

<<

<< replaced <<

;

<<

<< removed <<

;

CMacroFunction_RemoveInvalidECNumbers::x_ValidArguments()

(m_Args.empty());

void CMacroFunction_UpdateReplacedECNumbers::TheFunction()

del_improper_format = m_Args[0]->GetBool();

del_unrecognized = m_Args[1]->GetBool();

del_mult_replacement = m_Args[2]->GetBool();

scope = m_DataIter->GetScopedObject().scope;

(!prot_feat || !prot_feat->

().

() || !scope) {

(!

.IsSetEc() ||

.GetEc().empty())

locus_tag(

);

CProt_ref::TEc::iterator ec =

.SetEc().begin();

(ec !=

.SetEc().end()) {

removed =

;

<< locus_tag <<

<< *ec <<

<< repl_ec <<

;

(del_mult_replacement) {

<< locus_tag <<

<< *ec <<

;

ec =

.SetEc().erase(ec);

<< locus_tag <<

<< *ec <<

;

ec =

.SetEc().erase(ec);

(del_improper_format) {

<< locus_tag <<

<< *ec <<

;

ec =

.SetEc().erase(ec);

(

.GetEc().empty()) {

m_DataIter->SetModified();

CMacroFunction_UpdateReplacedECNumbers::x_ValidArguments()

arg_size = m_Args.size();

(

= 0;

< arg_size; ++

) {

CMacroFunction_UpdatemRNAProduct::TheFunction()

(!m_Args.empty()) {

scope = m_DataIter->GetScopedObject().scope;

(!prot_feat || !scope ||

product =

.GetName().front();

<< m_DataIter->GetBestDescr() <<

;

new_mrna->Assign(*mrna);

modified =

;

<<

;

(!

.IsSetExt() || (

.IsSetExt() && !

(

.GetExt().GetName(), product))){

.SetExt().SetName(product);

<<

<< product <<

;

->AddCommand(*chgFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

CMacroFunction_UpdatemRNAProduct::x_ValidArguments()

void CMacroFunction_RemoveFeature::TheFunction()

(!m_DataIter->IsFeature()) {

m_DataIter->SetToDelete(

);

delete_gene =

;

(m_Args.size() == 1 && m_Args[0]->GetBool()) {

scope = m_DataIter->GetScopedObject().scope;

->AddCommand(*del_cmd);

m_DataIter->RunCommand(

, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

;

<<

;

CMacroFunction_RemoveFeature::x_ValidArguments()

m_Args.empty() || (m_Args.size() == 1 && m_Args[0]->IsBool());

void CMacroFunction_CopyNameToCDSNote::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!prot_feat || !scope ||

product =

.GetName().front();

<< m_DataIter->GetBestDescr() <<

;

new_cds->Assign(*cds);

modified =

;

orig_comment = (new_cds->IsSetComment()) ? new_cds->GetComment() :

;

new_cds->SetComment(orig_comment);

<<

;

->AddCommand(*chgFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

CMacroFunction_CopyNameToCDSNote::x_ValidArguments()

(m_Args.empty());

scope = m_DataIter->GetScopedObject().scope;

remove_proteins =

;

(bseq && bseq->

()) {

(!m_DataIter->HasBeenCompleted()) {

m_ProductToCds.clear();

m_DataIter->SetCompleted();

m_DataIter->RunCommand(delete_features_cmd, m_CmdComposite);

<<

<<

<<

;

x_LogFunction(

);

(

.empty());

void CMacroFunction_RemoveDuplFeatures::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

check_partials = m_Args[1]->GetBool();

case_sensitive = m_Args[2]->GetBool();

remove_proteins = m_Args[3]->GetBool();

(

feat_it1(bsh, sel); feat_it1; ++feat_it1) {

(

feat_it2(*scope, feat_it1->GetLocation(), sel); feat_it2; ++feat_it2) {

(feat_it1->GetSeq_feat_Handle() < feat_it2->GetSeq_feat_Handle()) {

duplicates.

(feat_it2->GetSeq_feat_Handle());

(duplicates.

())

m_DataIter->RunCommand(

, m_CmdComposite);

report[

] = duplicates.

();

x_LogChangedQuals(fnc_log);

CMacroFunction_RemoveDuplFeatures::x_ValidArguments()

(m_Args.size() != 4 || !m_Args[0]->IsString()) {

(

= 1;

< m_Args.size(); ++

) {

(!m_Args[

]->IsBool())

scope = m_DataIter->GetScopedObject().scope;

(!prot_feat || !prot_feat->

().

() || !scope)

(m_DataIter->IsHugeDataMode()) {

vector<string> seh_taxnames;

x_FixProteinNames(prot_feat->

().SetProt(), seh_taxnames);

(m_NewNames.empty()) {

& taxnames = m_DataIter->GetTaxnames();

x_FixProteinNames(prot_feat->

().SetProt(), taxnames);

(!m_NewNames.empty()) {

m_DataIter->SetModified();

(

= 0;

< m_NewNames.size(); ++

) {

<<

<< m_DataIter->GetBestDescr();

<<

<< m_OrigNames[

];

<<

<< m_NewNames[

];

x_LogFunction(

);

(

& it :

.SetName()) {

(

.empty());

(taxnames.empty())

new_prot(protein);

vector<string> pattern;

pattern.push_back(

);

pattern.push_back(

);

pattern.push_back(

);

pattern.push_back(

);

(vector<string>, name, taxnames) {

new_prot = protein.substr(0, pos) + protein.substr(pos + name->length());

(vector<string>, pat_it, pattern) {

->GetLocation().GetLabel(&new_loc);

<< descr <<

<<

->GetBestDescr() <<

<< new_loc;

(adjust_gene_cmd) {

->AddCommand(*adjust_gene_cmd);

<<

;

(

->GetData().IsCdregion()) {

(!

->HasBeenCompleted() && feat_iter) {

feat_iter->SetCreateGeneralIdFlag();

cds_change =

;

<<

;

<<

;

(!x_CheckInitFeature())

m_Modified = s_SetBothEndsPartial(*m_Seqfeat, *

, m_Args[0]->GetString(), m_Args[1]->GetBool());

m_RetranslateCDS = (m_Args.size() > 2) ? m_Args[2]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 4) ? m_Args[3]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy5 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

edit::CLocationEditPolicy::EPartialPolicy policy3 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSet;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eSet;

&& edit::CLocationEditPolicy::Is5AtEndOfSeq(feat.

(), bsh)

&& edit::CLocationEditPolicy::Is3AtEndOfSeq(feat.

(), bsh)) {

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSetAtEnd;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eSetAtEnd;

extend5(

), extend3(

);

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = s_RemoveBothPartials(*m_Seqfeat, *

, m_Args[0]->GetString());

m_RetranslateCDS = (m_Args.size() > 1) ? m_Args[1]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 3) ? m_Args[2]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy5 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

edit::CLocationEditPolicy::EPartialPolicy policy3 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eClear;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eClear;

&& !edit::CLocationEditPolicy::Is5AtEndOfSeq(feat.

(), bsh)

&& !edit::CLocationEditPolicy::Is3AtEndOfSeq(feat.

(), bsh)) {

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eClearNotAtEnd;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eClearNotAtEnd;

extend5 =

, extend3 =

;

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = s_Set5EndPartial(*m_Seqfeat, *

, m_Args[0]->GetString(), m_Args[1]->GetBool());

m_RetranslateCDS = (m_Args.size() > 2) ? m_Args[2]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 4) ? m_Args[3]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy5 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSet;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSetAtEnd;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eSetForFrame;

extend3 =

;

policy(

edit::CLocationEditPolicy(policy5, edit::CLocationEditPolicy::ePartialPolicy_eNoChange, extend5, extend3));

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = s_Set3EndPartial(*m_Seqfeat, *

, m_Args[0]->GetString(), m_Args[1]->GetBool());

m_RetranslateCDS = (m_Args.size() > 2) ? m_Args[2]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 4) ? m_Args[3]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy3 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eSet;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eSetAtEnd;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd;

extend5 =

;

policy(

edit::CLocationEditPolicy(edit::CLocationEditPolicy::ePartialPolicy_eNoChange, policy3, extend5, extend3));

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = s_Clear5EndPartial(*m_Seqfeat, *

, m_Args[0]->GetString());

m_RetranslateCDS = (m_Args.size() > 1) ? m_Args[1]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 3) ? m_Args[2]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy5 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eClear;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eClearNotAtEnd;

policy5 = edit::CLocationEditPolicy::ePartialPolicy_eClearForGoodEnd;

extend5 =

, extend3 =

;

policy(

edit::CLocationEditPolicy(policy5, edit::CLocationEditPolicy::ePartialPolicy_eNoChange, extend5, extend3));

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = s_Clear3EndPartial(*m_Seqfeat, *

, m_Args[0]->GetString());

m_RetranslateCDS = (m_Args.size() > 1) ? m_Args[1]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 3) ? m_Args[2]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

edit::CLocationEditPolicy::EPartialPolicy policy3 = edit::CLocationEditPolicy::ePartialPolicy_eNoChange;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eClear;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eClearNotAtEnd;

policy3 = edit::CLocationEditPolicy::ePartialPolicy_eClearForGoodEnd;

extend5 =

, extend3 =

;

policy(

edit::CLocationEditPolicy(edit::CLocationEditPolicy::ePartialPolicy_eNoChange, policy3, extend5, extend3));

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_RetranslateCDS = (m_Args.size() > 2) ? m_Args[2]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 4) ? m_Args[3]->GetBool() :

;

m_Modified = s_ConvertLocationStrand(*m_Seqfeat, *

, m_Args[0]->GetString(), m_Args[1]->GetString());

m_DataIter->SetModified();

m_Seqfeat->GetLocation().GetLabel(&new_loc);

<<

<< m_DataIter->GetBestDescr() <<

<< new_loc;

x_RetranslateCDS(

);

(m_AdjustGene && !m_Seqfeat->GetData().IsGene()) {

new_gene->

(*overlap_gene);

change_gene = s_ConvertLocationStrand(*new_gene, *

, m_Args[0]->GetString(), m_Args[1]->GetString());

->AddCommand(*chgFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

;

x_LogFunction(

);

modified =

;

from = str_from;

(start_any || strand_from == current_strand) {

(strand_to != current_strand) {

(

= 2;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_RetranslateCDS = (m_Args.size() > 1) ? m_Args[1]->GetBool() :

;

m_AdjustGene = (m_Args.size() == 3) ? m_Args[2]->GetBool() :

;

m_Modified = s_ConvertLocationType(*m_Seqfeat, *

, m_Args[0]->GetString());

m_DataIter->SetModified();

m_Seqfeat->GetLocation().GetLabel(&new_loc);

<<

<< m_DataIter->GetBestDescr() <<

<< new_loc;

x_RetranslateCDS(

);

(m_AdjustGene && !m_Seqfeat->GetData().IsGene()) {

new_gene->

(*overlap_gene);

change_gene = s_ConvertLocationType(*new_gene, *

, m_Args[0]->GetString());

->AddCommand(*chgFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

;

x_LogFunction(

);

edit::CLocationEditPolicy::EMergePolicy merge_type = edit::CLocationEditPolicy::eMergePolicy_NoChange;

merge_type = edit::CLocationEditPolicy::eMergePolicy_Join;

merge_type = edit::CLocationEditPolicy::eMergePolicy_Order;

merge_type = edit::CLocationEditPolicy::eMergePolicy_SingleInterval;

policy->SetMergePolicy(merge_type);

policy->ApplyPolicyToFeature(feat, scope);

(

= 1;

<

.size(); ++

) {

(!x_CheckInitFeature())

m_Modified = edit::CLocationEditPolicy::Extend5(*m_Seqfeat, *

);

m_RetranslateCDS = (m_Args.empty()) ?

: m_Args[0]->GetBool();

m_AdjustGene = (m_Args.size() == 2) ? m_Args[1]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

(

& it :

) {

(!x_CheckInitFeature())

m_Modified = edit::CLocationEditPolicy::Extend3(*m_Seqfeat, *

);

m_RetranslateCDS = (m_Args.empty()) ?

: m_Args[0]->GetBool();

m_AdjustGene = (m_Args.size() == 2) ? m_Args[1]->GetBool() :

;

x_RetranslateCDSAdjustGene(

);

(

& it :

) {

scope = m_DataIter->GetScopedObject().scope;

frame = s_GetFrameFromName(m_Args[0]->GetString());

modified = s_SetCDSFrame(*cds, frame, *scope);

m_DataIter->SetModified();

(!m_DataIter->HasBeenCompleted() && feat_iter) {

feat_iter->SetCreateGeneralIdFlag();

m_DataIter->SetCompleted();

m_DataIter->RunCommand(upd_cmd, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

<< m_Args[0]->GetString() <<

;

x_LogFunction(

);

(frame_type) {

modified =

;

(orig_frame != new_frame) {

cds.

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

(!product || !product.

()) {

orig_prot_seq;

tmp_cds->

().SetCdregion().SetFrame(fr);

new_prot_seq;

new_prot_seq.erase(new_prot_seq.end() - 1);

scope = m_DataIter->GetScopedObject().scope;

(!from_feat || !const_feat || !scope) {

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

x_LogFunction(

);

x_SetConvertOptions(converter);

keep_orig(

);

m_DataIter->RunCommand(convert_cmd, m_CmdComposite);

<<

<< m_DataIter->GetBestDescr() <<

<< to_feat;

x_LogFunction(

);

& opt_label = (*it)->GetLabel();

(*it)->SetBool()->SetVal(

[index]->GetBool());

(*it)->SetBool()->SetVal(

[index]->GetBool());

(*it)->SetBool()->SetVal(

[index]->GetBool());

& opt_label = (*it)->GetLabel();

(*it)->SetString()->SetVal(

[1]->GetString());

& opt_label = (*it)->GetLabel();

(*it)->SetString()->SetVal(

[1]->GetString());

& opt_label = (*it)->GetLabel();

(*it)->SetString()->SetVal(

[1]->GetString());

& opt_label = (*it)->GetLabel();

(*it)->SetBool()->SetVal(

[1]->GetBool());

(

index =

.size() - 1; index <

.size() - 3; --index) {

void CMacroFunction_AddGeneXref::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

m_DataIter->SetModified();

<<

<< m_DataIter->GetBestDescr();

CMacroFunction_AddGeneXref::x_ValidArguments()

(m_Args.empty());

scope = m_DataIter->GetScopedObject().scope;

(!edit_feat || !edit_feat->

() || !scope) {

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

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

removed(

);

CSeq_feat::TXref::iterator xref_it = edit_feat->

().begin();

(xref_it != edit_feat->

().end()) {

((*xref_it)->IsSetData() && (*xref_it)->GetData().IsGene() &&

s_GeneXrefMatchesSuppression((*xref_it)->GetData().GetGene(), suppr_type) &&

s_GeneXrefMatchesNecessary((*xref_it)->GetData().GetGene(), *edit_feat, *scope, necessary_type)) {

xref_it = edit_feat->

().erase(xref_it);

m_DataIter->SetModified();

<<

<< m_DataIter->GetBestDescr();

x_LogFunction(

);

(

.size() != 2) {

(necessary_type) {

(suppr_type) {

(strand1 == strand2) {

(start1 > start2);

(start1 < start2);

strand1 < strand2;

product1 < product2;

void CMacroFunction_JoinShorttRNAs::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!bseq || !scope)

vector<CConstRef<CSeq_feat> > tRNAFeats;

& feature = *feat_it->GetOriginalSeq_feat();

tRNAFeats.push_back(feat_it->GetOriginalSeq_feat());

it = tRNAFeats.begin();

modified =

;

(it != tRNAFeats.end()) {

vector<string> comments;

rnaLoc->Add((*next)->GetLocation());

((*next)->IsSetComment()) {

comments.push_back((*next)->GetComment());

->AddCommand(*delGene);

geneLoc->Add((*next)->GetLocation());

->AddCommand(*delNext);

newtRNA->Assign(**it);

rnaLoc->Add((*it)->GetLocation());

newtRNA->SetLocation(*rnaLoc);

(!comments.empty()) {

origComment = (*it)->IsSetComment() ? (*it)->GetComment() :

;

(origComment.empty()) {

origComment = comments[0];

( ; index < comments.size(); ++index) {

(!origComment.empty()) {

newtRNA->SetComment(origComment);

<<

<< loc_ci.GetSize() <<

<< newtRNA->GetData().GetRna().GetRnaProductName();

newGene->Assign(*gene);

newGene->SetLocation(*geneLoc);

newGene->GetLocation().GetLabel(&

);

<<

<<

<<

<<

;

m_DataIter->RunCommand(

, m_CmdComposite);

CMacroFunction_JoinShorttRNAs::x_ValidArguments()

(m_Args.empty());

scope = m_DataIter->GetScopedObject().scope;

it = find_if(

.begin(),

.end(), [](

&

) { return (NStr::Find(str,

) != NPOS); });

(it ==

.end()) {

replaced = 0;

(

index = 0; index < prot_seq.size(); ++index) {

(prot_seq[index] ==

) {

(codon ==

) {

code_break->

(*nuc_loc);

code_break->

().SetNcbieaa(

);

cds_feat->

().SetCdregion().SetCode_break().push_back(code_break);

<<

<< index + 1;

<<

<< prot_label <<

;

(!m_DataIter->HasBeenCompleted() && feat_iter) {

feat_iter->SetCreateGeneralIdFlag();

m_DataIter->SetCompleted();

transl_change =

;

m_DataIter->RunCommand(retransl_cmd, m_CmdComposite);

m_DataIter->SetModified();

<<

<< replaced <<

;

x_LogFunction(

);

(

.empty());

prot_loc->

(*prot_pnt);

void CMacroFunction_RetranslateCDS::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

obey_stop_codon = m_Args[0]->GetBool();

(!m_DataIter->HasBeenCompleted() && feat_iter) {

feat_iter->SetCreateGeneralIdFlag();

m_DataIter->SetCompleted();

transl_change =

;

m_DataIter->RunCommand(retransl_cmd, m_CmdComposite);

(cds_change || transl_change) {

m_DataIter->SetModified();

<<

<< m_DataIter->GetBestDescr();

CMacroFunction_RetranslateCDS::x_ValidArguments()

(!bseq || !scope)

(index <

.size()) {

(

[index]->GetInt() < 1) {

(!x_SetCurrentBioseq())

x_HandleNegativeCoordinates(0);

x_HandleNegativeCoordinates(1);

strand = x_GetStrand(m_Args.back()->GetString());

(to > m_Bsh.GetBioseqLength() - 1) {

to = m_Bsh.GetBioseqLength() - 1;

(m_Args[2]->GetBool()) {

(m_Args[3]->GetBool()) {

(

.size() != 5)

(!x_SetCurrentBioseq())

strand = x_GetStrand(m_Args.back()->GetString());

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

(m_Args[1]->GetBool()) {

(

.size() != 3)

(!x_SetCurrentBioseq())

x_HandleNegativeCoordinates(0);

strand = x_GetStrand(m_Args.back()->GetString());

(point > m_Bsh.GetBioseqLength() - 1) {

point = m_Bsh.GetBioseqLength() - 1;

->SetPnt().SetPoint(point);

->SetPnt().SetId().Assign(*m_Bsh.GetCompleteBioseq()->GetFirstId());

->SetPnt().SetStrand(strand);

(m_Args[1]->GetBool()) {

(m_Args[2]->GetBool()) {

(

.size() != 4)

add_redundant =

[index]->GetBool();

(add_redundant) {

(location_obj.empty()) {

(

(location_obj.front().field.GetName(),

)) {

arg_size =

.size();

(index < arg_size) {

field =

[index]->GetString();

(field ==

) {

qualifier =

[++index]->GetString();

->SetQual().push_back(new_gbqual);

(index < arg_size) {

scope = m_DataIter->GetScopedObject().scope;

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

())

m_NewFeat->SetData().SetCdregion();

m_NewFeat->SetData().SetCdregion().SetCode(*

);

find_best_frame =

;

fr_index = 2;

find_best_frame =

;

(m_Args[fr_index]->GetInt()) {

(!x_SetLocation(3) || !x_ShouldAddRedundant(4))

x_SetAdditionalFields(6);

add_mRNA = m_Args[5]->GetBool();

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

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

new_mrna->

().SetRna().SetExt().SetName(protein_name);

(m_Location->IsPnt()) {

(find_best_frame) {

ambiguous =

;

m_NewFeat->SetData().SetCdregion().SetFrame(codon_start);

(!protein_name.empty()) {

->SetData().SetProt().SetName().push_back(protein_name);

(!protein_descr.empty()) {

->SetData().SetProt().SetDesc(protein_descr);

.BasicCleanup(*m_NewFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< best_id;

x_LogFunction(

);

good =

[0]->IsString()

&&

[1]->IsString()

(

.size() > 6) {

(

index = 6; index <

.size(); ++index) {

(!

[index]->IsString()) {

scope = m_DataIter->GetScopedObject().scope;

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

())

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

m_NewFeat->SetData().SetRna().Assign(*rna_ref);

(!x_SetLocation(2) || !x_ShouldAddRedundant(3))

x_SetAdditionalFields(4);

.BasicCleanup(*m_NewFeat);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< m_Args[0]->GetString() <<

<< best_id;

x_LogFunction(

);

(

.size() > 4) {

(

index = 4; index <

.size(); ++index) {

scope = m_DataIter->GetScopedObject().scope;

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

())

(!x_SetLocation(0))

x_SetAdditionalFields(1);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< best_id;

x_LogFunction(

);

(

.size() > 1) {

(

index = 1; index <

.size(); ++index) {

scope = m_DataIter->GetScopedObject().scope;

(!bseq || !scope)

oi(m_NewFeat, m_NewFeat->GetTypeInfo());

& new_str = m_Args[1]->

();

(!SetQualStringValue(new_oi, new_str)) {

(!x_SetLocation(2) || !x_ShouldAddRedundant(3))

x_SetAdditionalFields(4);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< best_id;

x_LogFunction(

);

(

.size() > 4) {

(

index = 4; index <

.size(); ++index) {

CMacroFunction_RestoreRNAEditing::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

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

good_cds =

;

prot_vec.GetSeqData(0, prot_vec.size(), prot_seq);

(!prot_seq.empty() && prot_seq.front() !=

) {

(prot_name == *name_it) {

m_DataIter->SetModified();

new_inst->Assign(prot_bsh.

());

new_inst->ResetSeq_data();

new_inst->ResetExt();

new_inst->SetRepr(objects::CSeq_inst::eRepr_raw);

new_inst->SetSeq_data().SetNcbieaa().Set(prot_seq);

new_inst->SetLength(

(prot_seq.length()));

upd_cmd->AddCommand(*chgInst);

m_DataIter->RunCommand(upd_cmd, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_RestoreRNAEditing::x_ValidArguments()

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

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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.

bool TruncateCDSAtStop(CSeq_feat &cds, CScope &scope)

TruncateCDSAtStop A function to truncate a CDS location after the first stop codon in the protein tra...

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

static bool s_IsBioseqGood_Strict(const objects::CBioseq_Handle &bsh)

const CSeq_id * GetFirstId() const

static bool IsGeneXrefUnnecessary(const CSeq_feat &sf, CScope &scope, const CGene_ref &gene_xref)

Calculates whether a Gene-xref is unnecessary (because it refers to the same gene as would be calcula...

static bool FixRNAEditingCodingRegion(CSeq_feat &cds)

From GB-7563 An action has been requested that will do the following: 1.

void AddCommand(IEditCommand &command)

static CRef< CConvertFeatureBase > Create(objects::CSeqFeatData::ESubtype subtype_from, objects::CSeqFeatData::ESubtype subtype_to)

static const string s_PlaceOnProt

static const string s_RemoveTranscriptID

static const string s_SiteType

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

static const string s_BondType

virtual string GetDescription()

static const string s_NcrnaClass

static const string s_RemovemRNA

vector< CRef< CConversionOption > > TOptions

static const string s_RemoveGene

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

bool IsSuppressed(void) const

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

CMacroBioData_FeatIterBase - iterates over any type of features.

class CMacroExecException

class CMacroExecException

static bool IsValidECNumberFormat(const string &ecno)

Verify correct form of EC number.

static const string & GetECNumberReplacement(const string &old_ecno)

Return a replaced EC number's replacement.

EECNumberStatus

Enzyme Commission number status.

@ eEC_replaced

Obsolete synonym for some other EC number.

@ eEC_ambiguous

Valid wildcard for a broader family.

@ eEC_specific

Specifically identifies a valid classification.

static EECNumberStatus GetECNumberStatus(const string &ecno)

Determine an EC number's validity and specificity.

@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

static E_Choice GetTypeFromSubtype(ESubtype subtype)

namespace ncbi::objects::

void SetGeneXref(CGene_ref &value)

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

static bool GetBestId(CSeq_id_Handle, CScope &, string &)

iterator_bool insert(const value_type &val)

CRef< objects::CSeq_entry > CreateTranslatedProteinSequence(CRef< objects::CSeq_feat > cds, objects::CBioseq_Handle nuc_h, bool create_general_only, int *offset=nullptr)

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

static const string kConversionNotSupported

static auto & FindOrgNames

static void cleanup(void)

static const struct name_t names[]

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

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

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

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.

#define NCBI_RETHROW2(prev_exception, exception_class, err_code, message, extra)

Re-throw exception with extra parameter.

@ eUnknown

Unknown exception.

void x_FixProteinNames(objects::CProt_ref &prot, const vector< string > &taxnames)

static bool s_Set5EndPartial(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend5=false)

CRef< objects::CScope > m_Scope

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_SetConvertOptions(CRef< CConvertFeatureBase > converter)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_Clear5EndPartial(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)

static ECdsFrame s_GetFrameFromName(const string &name)

static bool s_ShouldBeMerged(const CSeq_feat &feat1, const CSeq_feat &feat2)

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

CRef< CMacroCmdComposite > m_CmdComposite

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_ConvertLocationType(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

CConstRef< objects::CSeq_feat > m_Origfeat

list< SResolvedField > TObs

void x_RetranslateCDS(CNcbiOstrstream &log)

static string s_FixProteinNameFormat(const string &protein, const vector< string > &taxnames)

void Dereference()

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

static bool s_GeneXrefMatchesSuppression(const objects::CGene_ref &gene, objects::EGene_xref_suppression_type suppr_type)

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

Resolve name to the list of objects.

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.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool x_SetCurrentBioseq()

class CMacroFunction_MakeLocation Generates different type of seq-loc objects

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

CRef< objects::CSeq_feat > m_Seqfeat

const string & GetString() const

EType GetDataType() const

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

objects::CRNA_ref::EType GetRNAType(const string &rna_type)

bool x_ShouldAddRedundant(size_t index)

class CMacroFunction_ApplyFeature Generates different types of apply feature commands

objects::CBioseq_Handle m_Bsh

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static objects::ENa_strand s_GetStrandFromString(const string &str)

void x_RetranslateCDSAdjustGene(const string &descr)

bool x_SetLocation(size_t index)

vector< string > m_NewNames

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_GeneXrefMatchesNecessary(const objects::CGene_ref &gene, const objects::CSeq_feat &feat, objects::CScope &scope, objects::EGene_xref_necessary_type necessary_type)

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...

static bool s_SetBothEndsPartial(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend=false)

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

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool GetLocusTagFromProtRef(const objects::CSeq_feat &prot_feat, objects::CScope &scope, string &locus_tag)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_SortShorttRNAs(const CConstRef< CSeq_feat > &feat1, const CConstRef< CSeq_feat > &feat2)

class CMacroFunction_JoinShorttRNAs JoinShorttRNAs() - joins short (< 50bp) tRNAs and extends the cor...

objects::ENa_strand x_GetStrand(const string &str)

CRef< objects::CSeq_loc > m_Location

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_Clear3EndPartial(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)

DEFINE_MACRO_FUNCNAME(CMacroFunction_TrimStopFromCompleteCDS, "TrimStopsFromCompleteCDS")

class CMacroFunction_TrimStopFromCompleteCDS TrimStopsFromCompleteCDS()

CRef< objects::CSeq_feat > m_NewFeat

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_RemoveBothPartials(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)

void x_LogFunction(CNcbiOstrstream &logstr)

CRef< objects::CSeq_loc > x_GetProteinLoc(const objects::CSeq_id &prot_id, TSeqPos pos) const

bool x_CheckInitFeature()

static bool s_Set3EndPartial(objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend3=false)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_SetAdditionalFields(size_t index)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

vector< string > m_OrigNames

static bool s_ConvertLocationStrand(objects::CSeq_feat &feat, objects::CScope &scope, const string &str_from, const string &str_to)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static objects::CCdregion::TFrame s_FindMatchingFrame(const objects::CSeq_feat &cds, objects::CScope &scope)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

CIRef< IMacroBioDataIter > m_DataIter

static bool s_SetCDSFrame(objects::CSeq_feat &cds, ECdsFrame frame_type, objects::CScope &scope)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_HandleNegativeCoordinates(size_t index)

objects::CBioseq_Handle m_Bsh

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

objects::CBioseq_Handle GetBioseqForSeqFeat(const objects::CSeq_feat &f, objects::CScope &scope)

C & SerialAssign(C &dest, const C &src, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

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

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

static const TObjectType * SafeCast(TTypeInfo type)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

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

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

CObjectInfo AddNewElement(void) const

Add and return new element object.

ETypeFamily GetTypeFamily(void) const

Get data type family.

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end o...

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

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

void ChangeSeqLocId(CSeq_loc *loc, bool best, CScope *scope)

Change each of the CSeq_ids embedded in a CSeq_loc to the best or worst CSeq_id accoring to the value...

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

Merge ranges in the seq-loc.

CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)

Get reverse complement of the seq-loc (?)

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

Get the encoding CDS feature of a given protein sequence.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

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

Finds gene for feature, but obeys SeqFeatXref directives.

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

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

@ eProductToLocation

Map from the feature's product to location.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

const CSeqFeatData & GetData(void) const

bool IsProtein(void) const

bool IsSetData(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

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

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

void SetCoding(TCoding coding)

void SetIupacCoding(void)

Set coding to either Iupacaa or Iupacna depending on molecule type.

TObjectType * GetPointer(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.

bool IsNull(void) const THROWS_NONE

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

#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.

bool IsOssEmpty(CNcbiOstrstream &oss)

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert Int8 to string.

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

Case-sensitive equality of a substring with another string.

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

Case-insensitive equality of a substring with another string.

static 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 & ToLower(string &str)

Convert string to lower case – string& version.

static const char label[]

EPartial_both_clear_constraint

Access to EPartial_both_clear_constraint's attributes (values, names) as defined in spec.

EPartial_3_clear_constraint

Access to EPartial_3_clear_constraint's attributes (values, names) as defined in spec.

EPartial_3_set_constraint

Access to EPartial_3_set_constraint's attributes (values, names) as defined in spec.

EPartial_both_set_constraint

Access to EPartial_both_set_constraint's attributes (values, names) as defined in spec.

EGene_xref_suppression_type

Access to EGene_xref_suppression_type's attributes (values, names) as defined in spec.

EGene_xref_necessary_type

Access to EGene_xref_necessary_type's attributes (values, names) as defined in spec.

EFeature_location_strand_from

Access to EFeature_location_strand_from's attributes (values, names) as defined in spec.

EPartial_5_clear_constraint

Access to EPartial_5_clear_constraint's attributes (values, names) as defined in spec.

EPartial_5_set_constraint

Access to EPartial_5_set_constraint's attributes (values, names) as defined in spec.

EFeature_location_strand_to

Access to EFeature_location_strand_to's attributes (values, names) as defined in spec.

@ ePartial_both_clear_constraint_all

@ ePartial_3_clear_constraint_good_end

@ ePartial_3_clear_constraint_not_at_end

@ ePartial_3_clear_constraint_all

@ ePartial_3_set_constraint_all

@ ePartial_3_set_constraint_bad_end

@ ePartial_3_set_constraint_at_end

@ ePartial_both_set_constraint_all

@ eGene_xref_suppression_type_non_suppressing

@ eGene_xref_suppression_type_any

@ eGene_xref_suppression_type_suppressing

@ eGene_xref_necessary_type_any

@ eGene_xref_necessary_type_unnecessary

@ eGene_xref_necessary_type_necessary

@ ePartial_5_clear_constraint_all

@ ePartial_5_clear_constraint_not_at_end

@ ePartial_5_clear_constraint_good_start

@ ePartial_5_set_constraint_bad_start

@ ePartial_5_set_constraint_frame_not_one

@ ePartial_5_set_constraint_at_end

@ ePartial_5_set_constraint_all

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

TType GetType(void) const

Get the Type member data.

EType

type of RNA feature

void SetType(TType value)

Assign a value to Type data member.

void SetAa(TAa &value)

Assign a value to Aa data member.

TXref & SetXref(void)

Assign a value to Xref data member.

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

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.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

void ResetXref(void)

Reset Xref data member.

const TRna & GetRna(void) const

Get the variant data.

bool IsSetProduct(void) const

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

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetFrame(void) const

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

bool IsSetLocation(void) const

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

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

@ e_not_set

No variant selected.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

unsigned int

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

Functions that resolve field names described in asn format.

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

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

#define FOR_EACH_NAME_ON_PROTREF(Itr, Var)

FOR_EACH_NAME_ON_PROTREF EDIT_EACH_NAME_ON_PROTREF.

@ eExistingText_append_semi

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...

CRef< CCmdChangeSeq_feat > AdjustGene(const objects::CSeq_feat &orig_feat, const objects::CSeq_feat &new_feat, objects::CScope &scope)

CRef< CCmdComposite > GetSynchronizeProteinPartialsCommand(objects::CScope &scope, const objects::CSeq_feat &cds)

CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)

void GetProductToCDSMap(objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

CRef< CCmdComposite > TrimStopsFromCompleteCDS(const objects::CSeq_feat &cds, objects::CScope &scope)

CRef< CCmdComposite > GetDeleteAllFeaturesCommand(objects::CSeq_entry_Handle seh, size_t &count, bool remove_proteins=true)

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

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