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

22 #define THIS_FILE "xgbfeat.cpp" 32 #define THIS_MODULE this_module 36 #define ERR_FEATURE 1, 0 37 #define ERR_FEATURE_UnknownFeatureKey 1, 1 38 #define ERR_FEATURE_MissManQual 1, 2 39 #define ERR_FEATURE_QualWrongThisFeat 1, 3 40 #define ERR_FEATURE_FeatureKeyReplaced 1, 4 41 #define ERR_FEATURE_LocationParsing 1, 5 42 #define ERR_FEATURE_IllegalFormat 1, 6 43 #define ERR_QUALIFIER 2, 0 44 #define ERR_QUALIFIER_InvalidDataFormat 2, 1 45 #define ERR_QUALIFIER_Too_many_tokens 2, 2 46 #define ERR_QUALIFIER_MultiValue 2, 3 47 #define ERR_QUALIFIER_UnknownSpelling 2, 4 48 #define ERR_QUALIFIER_Xtratext 2, 5 49 #define ERR_QUALIFIER_SeqPosComma 2, 6 50 #define ERR_QUALIFIER_Pos 2, 7 51 #define ERR_QUALIFIER_EmptyNote 2, 8 52 #define ERR_QUALIFIER_NoteEmbeddedQual 2, 9 53 #define ERR_QUALIFIER_EmbeddedQual 2, 10 54 #define ERR_QUALIFIER_AA 2, 11 55 #define ERR_QUALIFIER_Seq 2, 12 56 #define ERR_QUALIFIER_BadECnum 2, 13 57 #define ERR_QUALIFIER_Cons_splice 2, 14 59 #define ParFlat_Stoken_type 1 60 #define ParFlat_BracketInt_type 2 61 #define ParFlat_Integer_type 3 62 #define ParFlat_Number_type 4 69  bool

perform_corrections);

74  bool

perform_corrections);

81  const Char

* array_string[],

86  bool

perform_corrections);

93 #define ParFlat_SPLIT_IGNORE 4 95  "citation"

,

"EC_number"

,

"rpt_type"

,

"usedin" 146  for

(TQualVector::iterator cur = quals.begin(); cur != quals.end();) {

147  const string

& qual_str = (*cur)->GetQual();

148  if

(qual_str ==

"gsdb_id"

) {

153  string

qs = qual_str;

154  if

(qs ==

"geo_loc_name"

) {

163  if

(qual_type == cur_type) {

176  if

(perform_corrections) {

177

cur = quals.erase(cur);

189  for

(

const auto

& cur : quals) {

204  if

(perform_corrections)

226  for

(

auto

& cur : quals) {

227  const string

& qual_str = cur->GetQual();

233  if

(! cur->IsSetVal()) {

237  string

val_str = cur->GetVal();

238  if

(*val_str.begin() !=

'('

) {

241  if

(*val_str.rbegin() !=

')'

) {

245

val_str = val_str.substr(1, val_str.size() - 2);

246  size_t

sep_pos = val_str.find(

','

);

247  if

(sep_pos == string::npos) {

248

cur->SetVal(val_str);

254

cur->SetVal(val_str.substr(0, sep_pos));

256  size_t offset

= sep_pos + 1;

257

sep_pos = val_str.find(

','

,

offset

);

258  while

(sep_pos != string::npos) {

264

quals.push_back(qual_new);

434  auto

val_class = QUAL_TYPE_TO_VAL_CLASS_MAP.

find

(qual_type);

435  if

(val_class == QUAL_TYPE_TO_VAL_CLASS_MAP.

end

()) {

439  return

val_class->second;

447  "EXPERIMENTAL"

,

"NOT_EXPERIMENTAL" 458  "long_terminal_repeat"

,

459  "non_LTR_retrotransposon_polymeric_tract"

,

460  "X_element_combinatorial_repeat"

,

463  "centromeric_repeat"

,

483  for

(TQualVector::iterator cur = quals.begin(); cur != quals.end();) {

484  const string

& qual_str = (*cur)->GetQual();

485  if

(qual_str ==

"gsdb_id"

) {

490  string

qs = qual_str;

491  if

(qs ==

"geo_loc_name"

) {

502  if

(perform_corrections) {

503

cur = quals.erase(cur);

515

ret =

CkQualNote

(*(*cur), error_msgs, perform_corrections);

521

ret =

CkQualText

(*(*cur),

nullptr

,

false

, error_msgs, perform_corrections);

557

ret =

CkQualEcnum

(*(*cur), error_msgs, perform_corrections);

605  if

((*cur)->IsSetVal() && ! (*cur)->GetVal().empty()) {

610  if

(perform_corrections) {

619

cur = quals.erase(cur);

648  size_t

comma = caa.find(

','

);

649  if

(comma != string::npos) {

650

caa = caa.substr(0, comma);

656  while

(*

str

!=

'\0'

&& (*

str

==

' '

|| *

str

==

')'

))

659  if

(*

str

==

'\0'

) {

697  while

(*

str

==

' '

)

707  while

(*

str

!=

'\0'

&& (*

str

==

','

|| *

str

==

' '

))

713  while

(*

str

==

' '

)

717  string

aa(

str

, eptr);

771  bool

has_embedded =

false

;

774

retval =

CkQualText

(cur, &has_embedded,

true

, error_msgs, perform_corrections);

778  string

val_str = cur.

GetVal

();

779

std::replace(val_str.begin(), val_str.end(),

'\"'

,

'\''

);

801  for

(bptr =

value

; *bptr !=

'\0'

;) {

802  for

(; *bptr !=

'/'

&& *bptr !=

'\0'

; bptr++)

806  for

(++bptr, ptr = bptr; *bptr !=

'='

&& *bptr !=

' '

&& *bptr !=

'\0'

; bptr++)

809  string

qual(ptr, bptr);

833  bool

perform_corrections)

841

*has_embedded =

false

;

851  if

(perform_corrections) {

860  while

(*

str

!=

'\0'

&& (*

str

==

' '

|| *

str

==

'\"'

)) {

863  if

(*(

str

- 1) ==

'\"'

) {

868  for

(bptr =

str

; *

str

!=

'\0'

&& *

str

!=

'\"'

;

str

++)

872  while

(*

str

!=

'\0'

&& (*

str

==

' '

|| *

str

==

'\"'

))

875  if

(*

str

!=

'\0'

) {

881  string value

(bptr, eptr);

910  const Char

* eptr =

nullptr

;

915  while

(*

str

==

' '

)

922  while

(*

str

!=

'\0'

&& (*

str

==

','

|| *

str

==

' '

))

928  while

(*

str

==

' '

)

932  string

aa(

str

, eptr);

983  for

(bptr =

str

; *

str

!=

'\0'

&& *

str

!=

' '

;

str

++)

987  while

(*

str

!=

'\0'

&& *

str

==

' '

)

990  if

(*

str

==

'\0'

) {

991  string msg

(bptr, eptr);

993  for

(

Int2 i

= 0;

i

< totalstr; ++

i

) {

1030

retval =

CkQualText

(cur,

nullptr

,

false

, error_msgs, perform_corrections);

1035  while

(*

str

!=

'\0'

&& (*

str

==

' '

|| *

str

==

'\"'

))

1038  for

(; *

str

!=

'\0'

&& *

str

!=

'\"'

;

str

++)

1066  const Char

* yes_or_no =

"not \'YES\', \'NO\' or \'ABSENT\'"

;

1083  for

(; *

str

==

' '

;

str

++)

1085  for

(; *

str

==

','

;

str

++)

1087  for

(; *

str

==

' '

;

str

++)

1104  if

(*

str

==

')'

) {

1106  while

(*

str

!=

'\0'

&& (*

str

==

' '

|| *

str

==

')'

))

1112

bptr =

"extra characters"

;

1162  bool

token_there =

false

;

1168  if

(*

str

!=

'\0'

) {

1169

token_there =

true

;

1171  if

(! token_there) {

1178  for

(bptr =

str

; *

str

!=

'\0'

&& *

str

!=

' '

;

str

++)

1182  while

(*

str

!=

'\0'

&& *

str

==

' '

)

1185  if

(*

str

==

'\0'

) {

1187  string

token(bptr, eptr);

1197  if

(*

str

==

'\0'

) {

1216

bptr =

"Invalid [integer] format"

;

1219

bptr =

"Not an integer number"

;

1222

bptr =

"Invalid format"

;

1226

bptr =

"Bad qualifier value"

;

1260  return "NULL value"

;

1261  if

(*

str

==

'['

) {

1269  if

(*

str

!=

']'

) {

1273  if

(*

str

!=

'\0'

) {

1294  if

(*

str

!=

'\0'

) {

1308  bool

range =

true

,

label

=

true

;

1314  if

(*

str

==

'.'

&& *(

str

+ 1) ==

'.'

) {

1323  if

(*

str

!=

'\0'

) {

1334  if

(*

str

==

'\0'

) {

1340  if

(*

str

!=

'\0'

) {

1344  if

(range ||

label

) {

static char ValidAminoAcid(string_view abbrev)

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

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

EQualifier

List of available qualifiers for feature keys.

@ eQual_environmental_sample

@ eQual_recombination_class

@ eQual_UniProtKB_evidence

@ eQual_culture_collection

@ eQual_ribosomal_slippage

@ eQual_calculated_mol_wt

@ eQual_metagenome_source

@ eQual_mobile_element_type

@ eQual_artificial_location

const TQualifiers & GetMandatoryQualifiers(void) const

Get the list of all mandatory qualifiers for the feature.

static EQualifier GetQualifierType(CTempString qual)

convert qual string to enumerated value

static CTempString GetQualifierAsString(EQualifier qual)

Convert a qualifier from an enumerated value to a string representation or empty if not found.

const_iterator end() const

const_iterator find(const key_type &key) const

bool StringEquNI(const char *s1, const char *s2, size_t n)

#define FtaErrPost(sev, level,...)

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

char Char

Alias for char.

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

Case-insensitive equality of a substring with another string.

@ eTrunc_End

Truncate trailing whitespace only.

static const char label[]

const TVal & GetVal(void) const

Get the Val member data.

void SetQual(const TQual &value)

Assign a value to Qual data member.

bool IsSetQual(void) const

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

void SetVal(const TVal &value)

Assign a value to Val data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetVal(void) const

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

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

const GenericPointer< typename T::ValueType > T2 value

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

#define ParFlat_Stoken_type

#define ERR_QUALIFIER_Pos

static int CkQualMatchToken(CGb_qual &cur, bool error_msgs, const Char *array_string[], Int2 totalstr)

int XGBFeatKeyQualValid(CSeqFeatData::ESubtype subtype, TQualVector &quals, bool error_msgs, bool perform_corrections)

static int CkQualPosaa(CGb_qual &cur, bool error_msgs)

#define ERR_QUALIFIER_MultiValue

static const Char * CkNumberType(const Char *str)

static int CkQualPosSeqaa(CGb_qual &cur, bool error_msgs, string &aa, const Char *eptr)

#define ERR_FEATURE_QualWrongThisFeat

#define ERR_QUALIFIER_UnknownSpelling

static int CkQualText(CGb_qual &cur, bool *has_embedded, bool from_note, bool error_msgs, bool perform_corrections)

const Char * ParFlat_IntOrString[]

#define ParFlat_Number_type

const Char * ParFlat_LRBString[]

#define ERR_QUALIFIER_SeqPosComma

#define ParFlat_SPLIT_IGNORE

static const Char * CkLabelType(const Char *str)

#define ERR_QUALIFIER_Too_many_tokens

#define ERR_QUALIFIER_BadECnum

static int CkQualSeqaa(CGb_qual &cur, bool error_msgs)

#define ERR_FEATURE_MissManQual

static ETokenClass GetQualifierClass(CSeqFeatData::EQualifier qual_type)

static Int2 GBQualSplit(const Char *qual)

static int CkQualNote(CGb_qual &cur, bool error_msgs, bool perform_corrections)

#define ParFlat_Integer_type

#define ERR_QUALIFIER_EmptyNote

static int CkQualEcnum(CGb_qual &cur, bool error_msgs, bool perform_corrections)

const Char * GBQual_names_split_ignore[4]

static const Char * CkBracketType(const Char *str)

static int CkQualTokenType(CGb_qual &cur, bool error_msgs, Uint1 type)

static bool ScanEmbedQual(const Char *value)

#define ParFlat_BracketInt_type

static const Char * this_module

#define ERR_QUALIFIER_InvalidDataFormat

const Char * ParFlat_RptString[]

#define ERR_QUALIFIER_Seq

static int GBQualSemanticValid(TQualVector &quals, bool error_msgs, bool perform_corrections)

static int SplitMultiValQual(TQualVector &quals)

static int CkQualSite(CGb_qual &cur, bool error_msgs)

#define ERR_QUALIFIER_Xtratext

#define ERR_QUALIFIER_Cons_splice

const Char * ParFlat_ExpString[]

#define GB_FEAT_ERR_SILENT

std::vector< CRef< objects::CGb_qual > > TQualVector

#define GB_FEAT_ERR_REPAIRABLE

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