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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/mod__reader_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/mod_reader.cpp Source File

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,

(excluded_mods.begin(), excluded_mods.end(),

[](

& mod_name) { return GetCanonicalName(mod_name); });

(ignored_mods.begin(), ignored_mods.end(),

[](

& mod_name) { return GetCanonicalName(mod_name); });

rejected_mods.clear();

unordered_set<string> current_set;

conflicting_mods;

(

&

: mods) {

!allow_multiple_values)) {

rejected_mods.push_back(

);

message =

+

.GetName() +

;

rejected_mods.push_back(

);

message =

+

.GetName() +

;

rejected_mods.push_back(

);

first_occurrence = current_set.insert(canonical_name).second;

(!first_occurrence) {

it = accepted_mods.

(canonical_name);

(it != accepted_mods.

() &&

=

+

.GetName() +

+

.GetValue() +

;

(!allow_multiple_values) {

=

+

.GetName() +

;

(it != accepted_mods.

()) {

conflicting_mods[canonical_name] = it->second;

accepted_mods.

(it);

conflicting_mods[canonical_name].push_back(

);

accepted_mods[canonical_name].push_back(

);

fPostMessage(reportMod,

, sev, subcode);

accepted_mods[canonical_name].push_back(

);

(

& conflicts : conflicting_mods) {

rejected_mods.splice(rejected_mods.end(), conflicts.second);

(

& mod_entry : mods) {

& canonical_name = mod_entry.first;

dest[canonical_name] = mod_entry.second;

dest.

(make_move_iterator(mods.begin()),

make_move_iterator(mods.end()));

(

& mod_entry : mods) {

& canonical_name = mod_entry.first;

& dest_mod_list = dest[canonical_name];

dest_mod_list.splice(

std::move(mod_entry.second));

dest_mod_list = std::move(mod_entry.second);

(

& mod_entry : mods) {

& canonical_name = mod_entry.first;

& dest_mod_list = dest[canonical_name];

(dest_mod_list.empty()) {

dest_mod_list = std::move(mod_entry.second);

dest_mod_list.splice(

std::move(mod_entry.second));

mod_entry.first;

(mod_entry.second.size() == 1);

mod_entry.second.front().GetValue();

normalized_name;

normalized = unnormalized;

new_end = unique(normalized.begin(),

[](

,

) {

return ((a==

|| a==

|| a==

) &&

(b==

|| b==

|| b==

)); });

normalized.erase(new_end, normalized.end());

(

& c : normalized) {

(c ==

|| c ==

) {

(mod_handler, bioseq, skipped_mods,

, fPostMessage);

skipped_mods.clear();

list<string> applied_mods;

(

& mod_entry : mod_handler.

()) {

applied =

;

(descr_mod_apply.

(mod_entry)) {

(mod_name ==

){

(mod_name ==

) {

feat_mod_apply.

(mod_entry)) {

skipped_mods.insert(skipped_mods.end(),

mod_entry.second.begin(),

mod_entry.second.end());

(

& modData : mod_entry.second) {

=

+ modData.GetName() +

;

=

+ canonicalName +

;

skipped_mods.insert(skipped_mods.end(),

mod_entry.second.begin(),

mod_entry.second.end());

(!applied_mods.empty()) {

=

;

(

& applied_mod : applied_mods) {

+=

+ applied_mod;

& mod_name = mod_data.

();

& mod_value = mod_data.

();

=

+ mod_name +

+ mod_value +

;

skipped_mods.push_back(mod_data);

(mod_name ==

) {

(mod_entry, seq_inst, skipped_mods, fPostMessage);

(mod_name ==

) {

(mod_entry, seq_inst, skipped_mods, fPostMessage);

(mod_name ==

) {

(mod_entry, seq_inst, skipped_mods, fPostMessage);

seq_inst.

(it->second);

list<string> id_list;

(

&

: mod_entry.second) {

& vals =

.GetValue();

list<CTempString> value_sublist;

(

&

: value_sublist) {

id_list.insert(id_list.end(), idrange.

(), idrange.

());

id_list.push_back(

);

(id_list.empty()) {

list<CRef<CSeq_id>> secondary_ids;

(id_list.begin(), id_list.end(), back_inserter(secondary_ids),

[](

& id_string) {

(

(id_string)); });

seq_inst.

().SetReplaces().SetIds() = std::move(secondary_ids);

& seqId,

m_pMessageListener(pMessageListener)

start_pos = 0;

(start_pos < title.

()) {

lb_pos, end_pos, eq_pos;

(eq_pos < end_pos) {

((lb_pos > start_pos) ) {

(!left_remainder.empty()) {

(!remainder.empty()) {

remainder.append(

);

remainder.append(left_remainder);

mods.emplace_back(name,

);

start_pos = end_pos+1;

(!right_remainder.empty()) {

(!remainder.empty()) {

remainder.append(

);

remainder.append(right_remainder);

start_pos = 0;

(start_pos < title.

()) {

lb_pos, end_pos, eq_pos;

(eq_pos < end_pos) {

start_pos = end_pos+1;

* s = line.

() + start;

num_unmatched_left_brackets = 0;

(

< line.

())

num_unmatched_left_brackets++;

(num_unmatched_left_brackets == 1)

(num_unmatched_left_brackets == 1)

(eq_pos<stop);

(num_unmatched_left_brackets == 0) {

num_unmatched_left_brackets--;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void transform(Container &c, UnaryFunction *op)

IObjtoolsListener * m_pMessageListener

CDefaultModErrorReporter(const string &seqId, int lineNum, IObjtoolsListener *pMessageListener)

void operator()(const CModData &mod, const string &msg, EDiagSev sev, EModSubcode subcode)

bool Apply(const TModEntry &mod_entry)

bool Apply(const TModEntry &mod_entry)

static CLineErrorEx * Create(EProblem eProblem, EDiagSev eSeverity, int code, int subcode, const std::string &strSeqId, unsigned int uLine, const std::string &strErrorMessage=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

static void Apply(const CModHandler &mod_handler, CBioseq &bioseq, TSkippedMods &skipped_mods, FPostMessage fPostMessage=nullptr)

static void x_SetMoleculeFromMolType(const TModEntry &mod_entry, CSeq_inst &seq_inst)

static void x_ReportInvalidValue(const CModData &mod_data, TSkippedMods &skipped_mods, FPostMessage fPostMessage)

static void x_SetStrand(const TModEntry &mod_entry, CSeq_inst &seq_inst, TSkippedMods &skipped_mods, FPostMessage fPostMessage)

static const string & x_GetModName(const TModEntry &mod_entry)

static void x_SetHist(const TModEntry &mod_entry, CSeq_inst &seq_inst)

static void x_SetMolecule(const TModEntry &mod_entry, CSeq_inst &seq_inst, TSkippedMods &skipped_mods, FPostMessage fPostMessage)

list< CModData > TSkippedMods

static bool x_TrySeqInstMod(const TModEntry &mod_entry, CSeq_inst &seq_inst, TSkippedMods &skipped_mods, FPostMessage fPostMessage)

CModHandler::FReportError FReportError

CModHandler::TModEntry TModEntry

static const string & x_GetModValue(const TModEntry &mod_entry)

static void x_SetTopology(const TModEntry &mod_entry, CSeq_inst &seq_inst, TSkippedMods &skipped_mods, FPostMessage fPostMessage)

const string & GetValue(void) const

const string & GetName(void) const

void SetExcludedMods(const vector< string > &excluded_mods)

function< void(const CModData &mod, const string &message, EDiagSev severity, EModSubcode subcode)> FReportError

static bool x_MultipleValuesAllowed(const string &canonical_name)

static const string & GetCanonicalName(const TModEntry &mod_entry)

void SetIgnoredMods(const list< string > &ignored_mods)

TNameSet m_IgnoredModifiers

const TMods & GetMods(void) const

list< CModData > TModList

void AddMods(const TModList &mods, EHandleExisting handle_existing, TModList &rejected_mods, FReportError fReportError=nullptr)

TNameSet m_ExcludedModifiers

static const TNameSet sm_MultipleValuesForbidden

static const TNameSet sm_DeprecatedModifiers

static const string & AssertReturnSingleValue(const TModEntry &mod_entry)

static string x_GetNormalizedString(const string &name)

unordered_set< string > TNameSet

void SetMods(const TMods &mods)

TMods::value_type TModEntry

void x_SaveMods(TMods &&mods, EHandleExisting handle_existing, TMods &dest)

static bool x_IsDeprecated(const string &canonical_name)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CModHandler::TModList TModList

static bool HasMods(const CTempString &title)

static bool x_FindBrackets(const CTempString &line, size_t &start, size_t &stop, size_t &eq_pos)

static void Apply(const CTempString &title, TModList &mods, string &remainder)

@ eProblem_GeneralParsingError

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

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

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ 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.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

const_iterator end(void) const

const_iterator begin(void) const

CRef< C > Ref(C *object)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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

Split a string using specified delimiters.

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

Truncate whitespace in a string (in-place)

const char * data(void) const

Return a pointer to the array represented.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

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

Case-insensitive equality of a substring with another string.

size_type size(void) const

Return the length of the represented array.

static string & ToLower(string &str)

Convert string to lower case – string& version.

static const size_type npos

@ fSplit_Tokenize

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

void SetHist(THist &value)

Assign a value to Hist data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetTopology(TTopology value)

Assign a value to Topology data member.

EMol

molecule class in living organism

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eTopology_tandem

some part of tandem repeat

@ eMol_na

just a nucleic acid

@ eStrand_other

default ds for DNA, ss for RNA, pept

@ eStrand_ds

double strand

@ eStrand_ss

single strand

static const unordered_map< string, CSeq_inst::ETopology > s_TopologyStringToEnum

static string s_GetNormalizedString(const string &unnormalized)

static const unordered_map< string, string > s_ModNameMap

static const unordered_map< string, CSeq_inst::EMol > s_MolStringToEnum

static const unordered_map< string, CSeq_inst::EStrand > s_StrandStringToEnum

const unordered_map< CMolInfo::TBiomol, CSeq_inst::EMol > g_BiomolEnumToMolEnum

const TStringToEnumMap< CMolInfo::TBiomol > g_BiomolStringToEnum

string g_GetNormalizedModVal(const string &unnormalized)

const GenericPointer< typename T::ValueType > T2 value

@ eModSubcode_Unrecognized

@ eModSubcode_ConflictingValues

@ eModSubcode_InvalidValue

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

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