m_fReportError(fReportError),
62m_SkippedMods(skipped_mods) {}
71 staticunordered_set<string> protein_quals = {
"protein-desc",
"protein",
"ec-number",
"activity"};
73protein_quals.find(
x_GetModName(mod_entry)) != protein_quals.end()) {
77 for(
const auto& mod_data : mod_entry.second) {
79 string msg=
"Cannot apply protein modifier to nucleotide sequence. The following modifier will be ignored: "+ mod_data.GetName();
82 for(
const auto& mod_data : mod_entry.second) {
90 for(
const auto& mod_data : mod_entry.second) {
91qual_names.
insert(mod_data.GetName());
94 boolfirst_name =
true;
95 for(
const auto& name : qual_names) {
100name_string +=
", ";
104 string msg=
"Cannot apply protein modifier to nucleotide sequence. The following modifiers will be ignored: " 105+ name_string +
".";
122 if(mod_name ==
"protein-desc") {
128 if(mod_name ==
"protein") {
130 for(
const auto&
mod: mod_entry.second) {
138 if(mod_name ==
"ec-number") {
140 for(
const auto&
mod: mod_entry.second) {
141ec_numbers.push_back(
mod.GetValue());
148 if(mod_name ==
"activity") {
150 for(
const auto&
mod: mod_entry.second) {
151activity.push_back(
mod.GetValue());
201pSeqLoc->SetWhole(*pSeqId);
211 if(pAnnot && pAnnot->IsFtable()) {
212 for(
autopSeqfeat : pAnnot->SetData().SetFtable()) {
214fVerifyFeature(*pSeqfeat)) {
230pSeqfeat->SetData(*fCreateFeatData());
231pSeqfeat->SetLocation(
const_cast<CSeq_loc&
>(feat_loc));
234pAnnot->SetData().SetFtable().push_back(pSeqfeat);
TSkippedMods & m_SkippedMods
FReportError m_fReportError
bool Apply(const TModEntry &mod_entry)
virtual ~CFeatModApply(void)
CRef< CSeq_feat > x_FindSeqfeat(FVerifyFeat fVerifyFeat)
CModAdder::TSkippedMods TSkippedMods
CRef< CSeq_feat > x_CreateSeqfeat(FCreateFeatData fCreateFeatData, const CSeq_loc &feat_loc)
function< CRef< CSeqFeatData >()> FCreateFeatData
CRef< CSeq_feat > m_pProtein
CModHandler::TMods::value_type TModEntry
static const string & x_GetModName(const TModEntry &mod_entry)
bool x_TryProtRefMod(const TModEntry &mod_entry)
function< bool(const CSeq_feat &)> FVerifyFeat
static const string & x_GetModValue(const TModEntry &mod_entry)
CRef< CSeq_loc > x_GetWholeSeqLoc(void)
CSeq_feat & x_SetProtein(void)
CModAdder::FReportError FReportError
static const string & GetCanonicalName(const TModEntry &mod_entry)
static const string & AssertReturnSingleValue(const TModEntry &mod_entry)
namespace ncbi::objects::
iterator_bool insert(const value_type &val)
Include a standard set of the NCBI C++ Toolkit most basic headers.
static const struct name_t names[]
@ eDiag_Warning
Warning message.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
static int BestRank(const CRef< CSeq_id > &id)
CRef< C > Ref(C *object)
Helper functions to get CRef<> and CConstRef<> objects.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
C::value_type FindBestChoice(const C &container, F score_func)
Find the best choice (lowest score) for values in a container.
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.
const TData & GetData(void) const
Get the Data member data.
void SetData(TData &value)
Assign a value to Data data member.
bool IsSetAnnot(void) const
Check if a value has been assigned to Annot data member.
TAnnot & SetAnnot(void)
Assign a value to Annot data member.
const TId & GetId(void) const
Get the Id member data.
const GenericPointer< typename T::ValueType > T2 value
Useful/utility classes and methods.
@ eModSubcode_ProteinModOnNucseq
static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)
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