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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/SubSource_8hpp_source.html below:

NCBI C++ ToolKit: include/objects/seqfeat/SubSource.hpp Source File

39 #ifndef OBJECTS_SEQFEAT_SUBSOURCE_HPP 40 #define OBJECTS_SEQFEAT_SUBSOURCE_HPP 80 static bool

NCBI_UseGeoLocNameForCountry(

void

);

88 static

TSubtype GetSubtypeValue(

const string

str

89

EVocabulary vocabulary = eVocabulary_raw);

93

EVocabulary vocabulary = eVocabulary_raw);

96 static bool

IsValidSubtypeName(

const string

str

97

EVocabulary vocabulary = eVocabulary_raw);

99 static bool

IsMultipleValuesAllowed(TSubtype);

102 static bool

NeedsNoText (

const

TSubtype& subtype);

105 static bool

IsDiscouraged (

const

TSubtype subtype);

110 static void

IsCorrectDateFormat(

const string

& date_string,

bool

& bad_format,

bool

& in_future);

112

eDateFormatFlag_ok = 0,

113

eDateFormatFlag_bad_format = 1,

114

eDateFormatFlag_in_future = 2,

115

eDateFormatFlag_out_of_order = 4

117 static size_t

CheckDateFormat(

const string

& date_string);

119 static string

GetCollectionDateProblem (

const string

& date_string);

121 static bool

IsCollectionDateAfterTime(

const string

& collection_date, time_t

bool

& bad_format);

122 static bool

IsCollectionDateAfterTime(

const CDate

& collection_date, time_t

);

123 static bool

IsCollectionDateAfterTime(

const CDate

& collection_date,

CTime

& ctime);

125 static bool

IsISOFormatTime(

const string

& orig_time,

int

& hour,

int

min

int

& sec,

bool

require_time_zone =

true

);

126 static bool

IsISOFormatDateOnly(

const string

& date);

127 static bool

IsISOFormatDate (

const string

& orig_date);

128 static CRef<CDate>

GetDateFromISODate(

const string

& orig_date);

134 static bool

IsDayValueOkForMonth(

int

day,

int

month,

int

year);

181 static string

FixDateFormat(

const string

& orig_date);

182 static string

FixDateFormat(

const string

& orig_date,

bool

month_first,

bool

& month_ambiguous);

183 static void

DetectDateFormat(

const string

& orig_date,

bool

& ambiguous,

bool

&day_first);

184 static void

IsCorrectLatLonFormat (

string

lat_lon,

bool

& format_correct,

bool

& precision_correct,

185 bool

& lat_in_range,

bool

& lon_in_range,

186 double

& lat_value,

double

& lon_value);

187 static string

FixLatLonFormat (

string

orig_lat_lon,

bool

guess =

false

);

188 static string

MakeLatLon(

double

lat_value,

double

lon_value,

int

lat_precision = 2,

int

lon_precision = 2);

189 static string

FixLatLonPrecision(

const string

orig

);

192

eLatLonCountryErr_None = 0,

196

eLatLonCountryErr_Value

208 static string

ValidateLatLonCountry (

const string

& countryname,

string

& lat_lon,

bool check_state

, ELatLonCountryErr& errcode);

210 static bool

IsValidSexQualifierValue (

const string

value

);

211 static string

FixSexQualifierValue (

const string

value

);

213 static bool

IsAltitudeValid (

const string

value

);

214 static string

FixAltitude (

const string

value

);

216 static bool

IsPlasmidNameValid(

const string

value

const string

& taxname);

217 static bool

IsChromosomeNameValid(

const string

value

const string

& taxname);

218 static bool

IsLinkageGroupNameValid(

const string

value

const string

& taxname);

219 static bool

IsSegmentValid(

const string

value

);

220 static bool

IsEndogenousVirusNameValid(

const string

value

);

223 static string

FixDevStageCapitalization(

const string

value

);

224 static string

FixCellTypeCapitalization(

const string

value

);

225 static string

FixIsolationSourceCapitalization(

const string

value

);

226 static string

FixTissueTypeCapitalization(

const string

value

);

227 static string

FixLabHostCapitalization(

const string

value

);

231 static string

AutoFix(TSubtype subtype,

const string

value

);

234 static bool

IsDeprecated(TSubtype subtype);

235 bool

IsDeprecated()

const

;

237 static bool

HasCultureNotes(

const string

value

);

238 static void

RemoveCultureNotes(

string

value

bool

is_species_level =

true

);

239 void

RemoveCultureNotes(

bool

is_species_level =

true

);

241 static string

CheckCellLine(

const string

& cell_line,

const string

& organism);

248 static string

x_ParseDateRangeWithDelimiter(

const string

& orig_date,

CTempString

delim);

249 static

vector<string> x_GetDateTokens(

const string

& orig_date);

250 static CLatLonCountryId

* x_CalculateLatLonId(

float

lat_value,

float

lon_value,

string

country,

string

province);

251 static bool

x_IsFixableIsoDate(

const string

& orig_date);

252 static string

x_RemoveIsoTime(

const string

& orig_date);

254 static int

x_GetPrecision(

const string

& num_str);

255 static string

x_FormatWithPrecision(

double val

int precision

);

257 static bool

x_GenericRepliconNameValid(

const string

value

);

258 static bool

x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules(

const string

value

const string

& taxname);

308 static bool IsValid

(

const string

& country);

309 static bool IsValid

(

const string

& country,

bool

& is_miscapitalized);

310 static bool IsValid

(

const string

& country,

bool

& is_miscapitalized,

bool

& is_null_and_virus,

bool

is_influenza_or_Sars2);

311 static bool

WasValid(

const string

& country);

312 static bool

WasValid(

const string

& country,

bool

& is_miscapitalized);

313 static string

CapitalizeFirstLetterOfEveryWord (

const string

&phrase);

314 static string

WholeCountryFix(

string

country);

315 static bool

IsSubstringOfStringInList(

const string

& phrase,

const string

& country1,

size_t

pos1);

316 static bool

ContainsMultipleCountryNames (

const string

&phrase);

317 static string

GetCorrectedCountryCapitalization(

const string

& country);

318 static string

NewFixCountry (

const string

input

bool

us_territories =

false

);

319 static bool

ChangeExtraColonsToCommas(

string

& country);

320 static string

CountryFixupItem(

const string

input

bool

capitalize_after_colon);

324 static void

ReadUSAExceptionMap (

TUsaExceptionMap

& exceptions,

const string

& filepath);

326 static void

LoadUSAExceptionMap (

const string

& exception_file );

328 static string

USAStateCleanup (

const string

& country );

331 static void

x_RemoveDelimitersFromEnds(

string

val

bool

except_paren =

false

);

332 static

vector<string> x_Tokenize(

const string

val

);

333 static void

x_FindCountryName(

const TCStringPairsMap

& fix_map,

const

vector<string>& countries,

string

& valid_country,

string

& orig_valid_country,

bool

& too_many_countries,

bool

& bad_cap);

344 CCountryExtreme

(

const string

& country_name,

int

min_x,

int

min_y,

int

max_x,

int

max_y);

356 bool

SetMinX(

int

min_x);

357 bool

SetMinY(

int

min_y);

358 bool

SetMaxX(

int

max_x);

359 bool

SetMaxY(

int

max_y);

361 bool

PreferTo(

const CCountryExtreme

* other_block,

const string

country,

const string

province,

const bool

prefer_new)

const

;

378 CCountryLine

(

const string

& country_name,

double

min_x,

double

max_x,

double

scale);

389 static int ConvertLat

(

double

scale);

390 static int ConvertLon

(

double

scale);

414 float GetLat

(

void

)

const

{

return

m_Lat; }

415 void SetLat

(

float

lat) { m_Lat = lat; }

416 float GetLon

(

void

)

const

{

return

m_Lon; }

417 void SetLon

(

float

lon) { m_Lon = lon; }

447

fProvinceMatch = (1 << 1),

448

fWaterMatch = (1 << 2),

450

fCountryClosest = (1 << 4),

451

fProvinceClosest = (1 << 5),

452

fWaterClosest = (1 << 6)

481 bool

IsCountryInLatLon(

const string

& country,

double

lat,

double

lon)

const

;

484 const string

& province =

kEmptyStr

)

const

;

486 double

range,

double

& distance);

487 bool

IsClosestToLatLon(

const string

& country,

double

lat,

double

lon,

488 double

range,

double

& distance)

const

;

489 bool

HaveLatLonForRegion(

const string

& country)

const

;

490 bool

DoCountryBoxesOverlap(

const string

& country1,

const string

& country2)

const

;

491 const CCountryExtreme

* IsNearLatLon(

double

lat,

double

lon,

double

range,

493 const string

& country,

494 const string

& province =

kEmptyStr

)

const

;

496 static int

AdjustAndRoundDistance (

double

distance,

double

scale);

497 int

AdjustAndRoundDistance (

double

distance)

const

;

502

fNegateLat = (1 << 1),

503

fNegateLon = (1 << 2),

508 void

x_InitFromDefaultList(

const char

const

*list,

int

num);

509 bool

x_InitFromFile(

const string

& filename);

517 size_t

x_GetLatStartIndex (

int

const

;

518 const CCountryExtreme

* x_FindCountryExtreme (

const string

& country)

const

;

double ErrorDistance(double latA, double lonA, double scale)

static string GetSubtypeName(const CSubSource &qual)

map< string, string, PNocase > TUsaExceptionMap

CStaticPairArrayMap< const char *, const char *, PCase_CStr > TCStringPairsMap

string GetLevel0(void) const

string GetCountry(void) const

string GetLevel1(void) const

CCountryExtreme * GetBlock(void) const

const string & GetCountry(void) const

CCountryExtreme * m_Block

double GetLat(void) const

void SetBlock(CCountryExtreme *block)

static int ConvertLat(double y, double scale)

double GetMaxLon(void) const

int x_ConvertLat(double y)

double GetMinLon(void) const

CCountryLine(const string &country_name, double y, double min_x, double max_x, double scale)

int x_ConvertLon(double x)

static int ConvertLon(double x, double scale)

int GetClaimedDistance(void) const

string GetClosestProvince(void) const

void SetFullGuess(string guess)

void SetWaterDistance(int dist)

int GetWaterDistance(void) const

void SetClaimedDistance(int dist)

string GetFullGuess(void) const

void SetClosestCountry(string closest)

string GetClaimedFull(void) const

void SetClosestFull(string closest)

string GetClosestWater(void) const

void SetGuessProvince(string guess)

void SetLandDistance(int dist)

int TClassificationFlags

Bitwise OR of "EClassificationFlags".

string GetGuessCountry(void) const

void SetClosestWater(string closest)

string GetGuessWater(void) const

void SetGuessWater(string guess)

string GetClosestFull(void) const

void SetClosestProvince(string closest)

void SetClaimedFull(string claimed)

int GetLandDistance(void) const

string GetClosestCountry(void) const

string GetGuessProvince(void) const

void SetGuessCountry(string guess)

TCountryExtremeList m_CountryExtremes

int TLatLonAdjustFlags

Bitwise OR of "ELatLonAdjustFlags".

double GetScale(void) const

TCountryExtremeList::const_iterator TCountryExtremeList_iter

TCountryLineList m_CountryLineList

TCountryLineList m_LatLonSortedList

TCountryLineList::const_iterator TCountryLineList_iter

vector< CCountryLine * > TCountryLineList

vector< CCountryExtreme * > TCountryExtremeList

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

@ eLatLonCountryErr_State

@ eLatLonCountryErr_Water

@ eLatLonCountryErr_Country

CSubSource(const CSubSource &value)

CSubSource & operator=(const CSubSource &value)

static string GetCollectionDateProblem(const string &date_string, bool &is_null_and_virus, bool is_influenza_or_Sars2)

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

static void check_state(const char name[], prfunc print, int erc)

static char line1[1024 *16]

static char line2[1024 *16]

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

string GetLabel(const CSeq_id &id)

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQFEAT_EXPORT

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

TName & SetName(void)

Assign a value to Name data member.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const GenericPointer< typename T::ValueType > T2 value

Defines: CTimeFormat - storage class for time format.

static bool FixCapitalization(string &name, bool apostroph)

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