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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/src__quals_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/src_quals.cpp Source File

& message,

& fileName,

seqId = bioseq.

().front()->AsFastaString();

+

& fileName,

seqId = bioseq.

().front()->AsFastaString();

ostringstream message;

<<

<<

<<

;

(

.

()) {

(

.back() ==

) {

& fileName,

ostringstream message;

<<

<< fileName

<<

<<

(pEC, message.str(), seqId, currentLine);

& fileName,

+

;

list<string> id_strings;

(

& pId : bioseq.

()) {

id_strings.push_back(

);

id_strings.push_back(content);

(pId->IsGeneral()) {

id_strings.push_back(

);

pTextSeqId = pId->GetTextseq_Id();

(pTextSeqId && pTextSeqId->IsSetVersion()) {

pointPos =

.rfind(

);

(pointPos != string::npos) {

id_strings.push_back(versionlessId);

id_strings.push_back(content);

(

&

: id_strings) {

& line = linePtr ? *linePtr : it->second.line;

(!line.

()) {

lineNum = it->second.lineNum;

(

&

: id_strings) {

(!entry.second.line.empty()) {

unusedLines.emplace(entry.second.lineNum, entry.second.line);

(

& entry : unusedLines) {

vector<CTempString> tokens;

pair<size_t,size_t>

make_pair<size_t,size_t>(1,1);

make_pair<size_t,size_t>(3,3);

make_pair<size_t,size_t>(2,2);

make_pair<size_t,size_t>(1,3);

minStubLength=2;

maxStubLength=3;

size_type fastaLength = fastaString.

();

size_type currentPos=0;

size_type idStartPos=0;

currentField=0;

currentMinField=0;

currentMaxField=0;

(currentPos < fastaLength) {

(idStartPos == currentPos) {

nextBarPos = fastaString.

(

, currentPos);

(nextBarPos ==

) {

stubLength = nextBarPos - currentPos;

(stubLength<minStubLength || stubLength>maxStubLength) {

currentMinField = numFields.first;

currentMaxField = numFields.second;

currentPos=nextBarPos+1;

(currentMinField <= currentMaxField);

(currentField < currentMaxField) {

nextBarPos = fastaString.

(

, currentPos);

(nextBarPos ==

) {

(currentField < currentMinField-1) {

idStrings.emplace(fastaString.

(idStartPos));

(currentField >= currentMinField) {

length = nextBarPos-currentPos;

(length>=minStubLength && length<=maxStubLength) {

currentMinField = numFields.first;

currentMaxField = numFields.second;

idStartPos=currentPos;

currentPos=nextBarPos+1;

currentPos=nextBarPos+1;

(currentField == currentMaxField);

idStrings.emplace(fastaString.

(idStartPos, (currentPos-idStartPos)-1));

idStartPos=currentPos;

(currentField < currentMinField) {

(fastaString[fastaLength-1] ==

) {

(currentField < currentMaxField) {

(currentPos == fastaLength);

idStrings.emplace(fastaString.

(idStartPos, (currentPos-idStartPos)-1));

(idString.

()) {

(

(begin(idString), end(idString),

)<2) {

rval.first->second.lineNum,

+ idString +

,

(

: parsedIDs) {

pair<TLineMap::iterator,bool> rval;

rval.first->second.linePtr = linePtr;

linePtr = &rval.first->second.line;

rval.first->second.lineNum,

* ptr = (

*)

->Map(0, fileSize);

* end = ptr + fileSize;

(*ptr ==

|| *ptr ==

) {

* start = ptr;

* endline = (

*)memchr(ptr,

, end - ptr);

(endline ==

) endline = end;

(start < endline && *endline ==

)

);

(

&

: mods) {

& seqId,

& message,

(

&

: mods) {

new_value =

.GetValue();

.SetValue(new_value);

readModsFromTitle,

& commandLineMods,

& commandLineRemainder,

readModsFromTitle,

m_CommandLineMods(commandLineMods),

m_CommandLineRemainder(commandLineRemainder),

m_pNamedSrcFileMap(pNamedSrcFileMap),

m_pDefaultSrcFileMap(pDefaultSrcFileMap),

m_pMessageListener(pMessageListener),

m_ReadModsFromTitle(readModsFromTitle),

m_IsVerbose(isVerbose),

m_MergePolicy(mergePolicy)

seqId = bioseq.

().front()->AsFastaString();

pDescriptors = &(bioseq.

().Set());

CSeq_descr::Tdata::iterator title_it;

find_if(pDescriptors->begin(), pDescriptors->end(),

(title_it != pDescriptors->end()) {

pTitleDesc = *title_it;

& title = (*title_it)->

();

titleRemainder;

remainder = titleRemainder + remainder;

(!remainder.empty()) {

pDescriptors->push_back(pTitleDesc);

pTitleDesc->

() = remainder;

current_title =

pTitleDesc->

() = current_title.empty() ?

current_title +

+ remainder;

(title_it != pDescriptors->end() &&

(*title_it)->GetTitle().empty()) {

pDescriptors->erase(title_it);

(pDescriptors->empty()) {

& commandLineStr,

readModsFromTitle,

commandLineRemainder;

TMods commandLineMods;

fReportCommandLineError =

TModList rejectedMods;

fReportCommandLineError);

commandLineMods = mod_handler.

();

commandLineRemainder,

(isVerbose && pDefaultSrcFileMap) {

const string m_CommandLineRemainder

CApplyMods(const TMods &commandLineMods, const string &m_CommandLineRemainder, CMemorySrcFileMap *pNamedSrcFileMap, CMemorySrcFileMap *pDefaultSrcFileMap, ILineErrorListener *pMessageListener, bool readModsFromTitle, bool isVerbose, TMergePolicy mergePolicy=CModHandler::ePreserve)

TMergePolicy m_MergePolicy

void x_GetModsFromFileMap(CMemorySrcFileMap &fileMap, const CBioseq &bioseq, CModHandler::FReportError fReportError, CModHandler &mod_handler, string &remainder)

CModHandler::TModList TModList

CMemorySrcFileMap * m_pDefaultSrcFileMap

void operator()(CBioseq &bioseq)

CMemorySrcFileMap * m_pNamedSrcFileMap

ILineErrorListener * m_pMessageListener

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.

ILineErrorListener * m_pEC

void MapFile(const string &fileName, bool allowAcc)

unordered_map< string, size_t > m_ProcessedIdsToLineNum

unique_ptr< CMemoryFileMap > m_pFileMap

void x_ProcessLine(const CTempString &line, TModList &mods)

void x_RegisterLine(size_t lineNum, const CTempString &line, bool allowAcc)

CModHandler::TModList TModList

bool GetMods(const CBioseq &bioseq, TModList &mods, bool isVerbose)

vector< CTempString > m_ColumnNames

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

void SetExcludedMods(const vector< string > &excluded_mods)

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

static const string & GetCanonicalName(const TModEntry &mod_entry)

map< string, list< CModData > > TMods

const TMods & GetMods(void) const

list< CModData > TModList

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

void SetMods(const TMods &mods)

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

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

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

const_iterator end() const

const_iterator find(const key_type &key) const

EDiagSev

Severity level for the posted diagnostics.

@ 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.

static E_Choice WhichInverseSeqId(const CTempString &SeqIdCode)

Converts a string to a choice, no need to require a member.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

CRef< C > Ref(C *object)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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)

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

void clear(void)

Clears the string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

CTempString substr(size_type pos) const

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

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

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 TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a 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.

@ eTrunc_End

Truncate trailing whitespace only.

E_Choice

Choice variants.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

list< CRef< CSeqdesc > > Tdata

void ResetDescr(void)

Reset Descr data member.

TTitle & SetTitle(void)

Select the variant.

const TTitle & GetTitle(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

constexpr bool empty(list< Ts... >) noexcept

void VisitAllBioseqs(objects::CSeq_entry &entry, _M &&m)

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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

static void s_PostProcessID(string &id)

static void sReportMissingMods(ILineErrorListener *pEC, const string &fileName, const CBioseq &bioseq)

static void sReportDuplicateIds(ILineErrorListener *pEC, const string &fileName, size_t currentLine, size_t previousLine, const CTempString &seqId)

static void s_PreprocessNoteMods(CModHandler::TModList &mods)

static void sReportMultipleMatches(ILineErrorListener *pEC, const string &fileName, size_t lineNum, const CBioseq &bioseq)

static bool s_ParseFastaIdString(const CTempString &fastaString, set< CTempString, PNocase_Generic< CTempString >> &idStrings)

static void sReportError(ILineErrorListener *pEC, EDiagSev severity, int subcode, const string &seqId, const string &message, ILineError::EProblem problemType=ILineError::eProblem_GeneralParsingError)

void g_ApplyMods(CMemorySrcFileMap *pNamedSrcFileMap, CMemorySrcFileMap *pDefaultSrcFileMap, const string &commandLineStr, bool readModsFromTitle, bool isVerbose, CModHandler::EHandleExisting mergePolicy, ILineErrorListener *pEC, CSeq_entry &entry)

static void sReportUnusedMods(ILineErrorListener *pEC, const string &fileName, size_t lineNum, const CTempString &seqId)

static pair< size_t, size_t > s_IdTypeToNumFields(CSeq_id::E_Choice choice)

static void s_AppendMods(const CModHandler::TModList &mods, string &title)

static void sPostError(ILineErrorListener *pEC, const string &message, const CTempString &seqId, size_t lineNum=0)

Define Case-insensitive string comparison methods.

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