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NCBI C++ ToolKit: src/objtools/flatfile/xgbparint.cpp Source File

(

it =

; it != end_it; ++it) {

(it->choice) {

temp +=

;

(current != end(tokens))

(tokens.size() == 1) {

current_it = begin(tokens);

(

scanner_it =

(current_it);

scanner_it != end(tokens);

(scanner_it != end(tokens) &&

(

current_it = begin(tokens);

current_it != end(tokens);

scanner_it =

(current_it);

(scanner_it != end(tokens)) {

(scanner_it != end(tokens)) {

(scanner_it != end(tokens) &&

current_col)

temp_string = line.substr(0, current_col + 1) +

;

(

c,

current_pos,

& line)

pos = current_pos;

(pos < line.size()) {

(line[pos] == c) {

(accession.empty()) {

IsAlpha = [](

c) {

(c); };

it = find_if_not(begin(accession),

(it == end(accession)) {

prefix_length = distance(begin(accession), it);

(prefix_length != 2) {

it = find_if_not(it, end(accession), IsAlpha);

(it == end(accession)) {

prefix_length = distance(begin(accession), it);

(prefix_length == 3 || prefix_length == 7) {

prefix_length;

}

(accession.size() >= 3 &&

accession[2] ==

) {

(prefix_length == 1 ||

prefix_length == 2 ||

prefix_length == 4 ||

prefix_length == 6) {

prefix_length;

(

& accession,

& current_col,

& line,

accver)

length = line.size();

string_view tempString(line.c_str() + current_col, length - current_col);

accessionLength = prefixLength;

tempString = tempString.substr(prefixLength);

notDigitPos = tempString.find_first_not_of(

);

(notDigitPos != string_view::npos) {

accessionLength += notDigitPos;

(accver && tempString[notDigitPos] ==

) {

(tempString.size() > notDigitPos) {

tempString = tempString.substr(notDigitPos + 1);

notDigitPos = tempString.find_first_not_of(

);

(notDigitPos != string_view::npos) {

accessionLength += notDigitPos;

accessionLength = length - current_col;

(notDigitPos == string_view::npos || tempString[notDigitPos] !=

) {

accession =

(line.c_str() + current_col, accessionLength);

current_col += accessionLength;

(! linein.empty()) {

line{ linein };

length = line.size();

current_col = 0;

(current_col < length) {

(

(line[current_col]) || line[current_col] ==

) {

(

(line[current_col])) {

string_view tempString(line.c_str() + current_col,

(length - current_col));

not_digit_pos = tempString.find_first_not_of(

);

num_digits = (not_digit_pos == string_view::npos) ?

(length - current_col) : not_digit_pos;

current_token.

=

(line.c_str() + current_col, num_digits);

tokens.push_back(current_token);

current_col += num_digits;

skip_new_token =

;

(line[current_col]) {

(

closing_quote_pos = line.find(

, current_col + 1);

closing_quote_pos == string::npos) {

= closing_quote_pos - current_col + 1;

current_token.

=

(line.c_str() + current_col,

);

current_col =

(

, current_col, line);

current_col =

(

, current_col, line);

current_col =

(

, current_col, line);

(current_col < length - 3) &&

(line[current_col + 3] ==

||

line[current_col + 3] ==

||

line[current_col + 3] ==

||

line[current_col + 3] ==

)) {

current_token.

=

;

tokens.push_back(current_token);

(;

(line[current_col]); current_col++)

current_col =

(

, current_col, line);

current_col =

(

, current_col, line);

skip_new_token =

;

(current_col < length - 1 && line[current_col + 1] ==

) {

tokens.push_back(current_token);

(current_col < length - 1) {

(line[current_col + 1] ==

) {

tokens.push_back(current_token);

tokens.push_back(current_token);

(current_col < length - 1) {

(line[current_col + 1] ==

) {

(current_col == length - 1 || line[current_col + 1] !=

) {

(current_col < length - 1 && line[current_col + 1] ==

) {

(current_col < length - 1) {

(line[current_col + 1] ==

) {

(! skip_new_token) {

tokens.push_back(current_token);

(current_token != end(tokens)) {

(current_token == end(tokens)) {

par_msg =

+ to_string(paren_count) +

;

(current_token != end(tokens)) {

interval.

(range - 1);

.SetGeneral().SetTag().SetId(0);

it =

(current_it);

gapsize_it = it++;

current_it =

(it);

strange_sin_dot =

;

end_it = end(tokens);

strange_sin_dot =

;

(! strange_sin_dot) {

(currentPt == end_it) {

numPt =

(currentPt->data.c_str()) - 1;

(num_found != 1) {

one_of_ok =

;

at_end_one_of =

;

numPt =

(currentPt->data.c_str()) - 1;

(one_of_ok && ! at_end_one_of && currentPt != end_it) {

(currentPt->choice) {

at_end_one_of =

;

(! one_of_ok && ! at_end_one_of) {

(! at_end_one_of && currentPt != end_it) {

at_end_one_of =

;

end_it = end(tokens);

(accver && currentPt->data.find(

) >= currentPt->data.size() - 1) {

new_id =

(

(currentPt->data));

(currentPt == end_it) {

}

(! seq_ids.empty()) {

new_id->

(*(*seq_ids.begin()));

(currentPt == end_it) {

(currentPt->choice) {

ret->SetInt().SetFuzz_from(*new_fuzz);

ret->SetInt().SetId(*new_id);

(ret->SetInt().SetFrom(), ret->SetInt().SetFuzz_from(), keep_rawPt, currentPt, tokens, numErrors,

);

ret->SetInt().ResetFuzz_from();

(ret->GetInt().GetFrom(), *new_id, keep_rawPt, numErrors, tokens, currentPt);

(currentPt != end_it) {

in_caret =

;

(currentPt->choice) {

(ret->GetInt().IsSetFuzz_from()) {

(currentPt == end_it) {

(ret->GetInt().IsSetFuzz_from()) {

(ret->SetInt().SetTo(), ret->SetInt().SetFuzz_to(), keep_rawPt, currentPt, tokens, numErrors,

);

ret->SetInt().ResetFuzz_to();

(ret->GetInt().GetTo(), *new_id, keep_rawPt, numErrors, tokens, currentPt);

to = ret->GetInt().GetTo();

(point.

() + 1 == to) {

point.

().SetRange().SetMax(to);

ret->GetInt().GetFrom() == ret->GetInt().GetTo() &&

! ret->GetInt().IsSetFuzz_from() &&

! ret->GetInt().IsSetFuzz_to()) {

add_nulls =

;

current_token = currentPt;

did_complement =

;

end_it = end(tokens);

(current_token->choice) {

(currentPt == end_it) {

(currentPt == end_it) {

retval =

(keep_rawPt, parenPt, currentPt, tokens, numErrors, seq_ids, accver);

did_complement =

;

(currentPt != end_it) {

(currentPt, end_it, retval,

);

(currentPt, end_it, retval,

);

retval =

(keep_rawPt, currentPt, tokens, numErrors, seq_ids, accver);

}

(in_sites && currentPt != end_it);

(! numErrors && ! did_complement && retval &&

(currentPt == end_it) {

(currentPt == end_it) {

(! numErrors && currentPt != end_it) {

(currentPt != end_it &&

(currentPt == end_it)

(retval->

())

retval->

().AddSeqLoc(*next_loc);

retval->

().Add(*next_loc);

(retval->

())

retval->

().AddSeqLoc(*null_loc);

retval->

().Add(*null_loc);

(currentPt == end_it) {

retval->

().Assign(*(*seq_ids.begin()));

ret =

(keep_rawPt, parenPt, currentPt, tokens, numErrors, seq_ids, accver);

(currentPt == end(tokens)) {

(

,

keep_rawPt =

;

(tokens.empty()) {

head_token = tokens.begin();

current_token = head_token;

end_it = tokens.end();

paren_count = 0;

(current_token != end_it) {

(current_token->choice) {

ret =

(keep_rawPt, paren_count, current_token, tokens, numErrors, seq_ids, accver);

(

, tokens, current_token);

ret =

(keep_rawPt, current_token, tokens, numErrors, seq_ids, accver);

ret =

(keep_rawPt, paren_count, current_token, tokens, numErrors, seq_ids, accver);

}

(in_sites && current_token != end_it);

std::list< CRef< objects::CSeq_id > > TSeqIdList

int fta_atoi(string_view sv)

void Nlm_ErrSetContext(const char *module, const char *fname, int line)

void Nlm_ErrPostStr(ErrSev sev, int lev1, int lev2, string_view str)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void SetNull(void)

Override all setters to incorporate cache invalidation.

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

Get reverse complement of the seq-loc (?)

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Truncate whitespace in a string (in-place)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eNocase

Case insensitive compare.

void SetMin(TMin value)

Assign a value to Min data member.

TRange & SetRange(void)

Select the variant.

TMin GetMin(void) const

Get the Min member data.

void SetMax(TMax value)

Assign a value to Max data member.

TLim & SetLim(void)

Select the variant.

TMax GetMax(void) const

Get the Max member data.

const TRange & GetRange(void) const

Get the variant data.

@ eLim_tl

space to left of position

@ e_not_set

No variant selected.

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsMix(void) const

Check if variant Mix is selected.

TPoint GetPoint(void) const

Get the Point member data.

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

void SetFrom(TFrom value)

Assign a value to From data member.

virtual void Reset(void)

Reset the whole object.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetFuzz_from(void) const

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

bool IsPnt(void) const

Check if variant Pnt is selected.

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

Miscellaneous common-use basic types and functionality.

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

static void xgbparse_error(string_view front, TTokenConstIt head, TTokenConstIt end_it)

static void do_xgbparse_error(string_view msg, string_view details)

static CRef< CSeq_loc > xgbloc_ver(bool &keep_rawPt, int &parenPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static void sConvertIntToPoint(CSeq_loc &loc)

static void xlex_error_func(string_view msg, const string &line, unsigned int current_col)

static CRef< CSeq_loc > xgbint_ver(bool &keep_rawPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static int xgbparselex_ver(string_view linein, TTokens &tokens, bool accver)

static void xgbgap(TTokenIt &current_it, TTokenConstIt end_it, CRef< CSeq_loc > &loc, bool unknown)

static void xfind_one_of_num(list< STokenInfo > &tokens)

list< STokenInfo > TTokens

static void * xgbparse_range_data

static CRef< CSeq_loc > XGapToSeqLocEx(Int4 range, bool unknown)

static void xgbparse_better_be_done(int &numErrors, TTokenIt current_token, const TTokens &tokens, bool &keep_rawPt, int paren_count)

static int sGetAccession(string &accession, unsigned int &current_col, const string &line, bool accver)

static string xgb_unparse(TTokenConstIt head, TTokenConstIt end_it)

TTokens::const_iterator TTokenConstIt

static CRef< CSeq_loc > xgbreplace_ver(bool &keep_rawPt, int &parenPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static void xgbload_number(TSeqPos &numPt, CInt_fuzz &fuzz, bool &keep_rawPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, int take_which)

void xinstall_gbparse_error_handler(X_gbparse_errfunc new_func)

const char * unkseqlitdbtag

void xinstall_gbparse_range_func(void *data, X_gbparse_rangefunc new_func)

static void xgbcheck_range(TSeqPos num, const CSeq_id &id, bool &keep_rawPt, int &numErrors, const TTokens &tokens, TTokenConstIt current)

TTokens::iterator TTokenIt

static unsigned advance_to(const char c, unsigned current_pos, const string &line)

static X_gbparse_errfunc Err_func

CRef< CSeq_loc > xgbparseint_ver(string_view raw_intervals, bool &keep_rawPt, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static X_gbparse_rangefunc Range_func

#define ERR_FEATURE_LocationParsing_validatr

static size_t sParseAccessionPrefix(string_view accession)

Int4(* X_gbparse_rangefunc)(void *, const objects::CSeq_id &id)

void(* X_gbparse_errfunc)(string_view, string_view)

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