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

(loc_str.find(

) == string::npos && loc_str.find(

) == string::npos)

(

& cur : qlist) {

(cur->GetQual() != qual)

&

= cur->GetVal();

(

==

) {

optional<string> qvalue;

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

((*cur)->GetQual() != qual)

&

= (*cur)->GetVal();

(

==

) {

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

((*cur)->GetQual() != qual) {

cur = qlist.erase(cur);

= qval.find(

);

(

== string_view::npos)

(

< qval.size() && qval[

] ==

)

(

c; j < qval.size() && (c = qval[j], (c >=

&& c <=

) || (c >=

&& c <=

));)

(checkseq && qval.find(

, j) == string_view::npos)

(

& descr : descrs) {

(! descr->IsSource() || ! descr->GetSource().IsSetOrg() ||

! descr->GetSource().GetOrg().IsSetTaxname())

& org_ref = descr->GetSource().GetOrg();

(!

->IsSetSubname() || !

->IsSetSubtype())

.push_back(

->GetSubname());

(descr->GetSource().IsSetSubtype()) {

(

& subtype : descr->GetSource().GetSubtype()) {

* p =

(subtype->GetName().c_str(),

);

(p += 7; *p ==

;)

(

& entry : seq_entries) {

(bio_set->IsSetDescr())

(bioseq->IsSetDescr())

(

& descr : descrs) {

(! descr->IsGenbank())

(! descr->GetGenbank().IsSetSource())

& gb_block = descr->SetGenbank();

* pper =

;

(p[

- 1] ==

) {

(q++; *q ==

;)

vector<string>::const_iterator name =

.begin();

(name += 2; name !=

.end(); ++name) {

(

= s +

+ 1; *

==

;)

& first_name =

[0];

& second_name =

[1];

(

& entry : seq_entries) {

(bioseq->IsSetDescr())

vector<string>

;

STR_TO_REPLACE[] =

;

(!

.empty()) {

(

[0] ==

)

pos =

.find(STR_TO_REPLACE);

(pos != string::npos) {

.replace(pos,

(STR_TO_REPLACE) - 1,

);

pos =

.find(STR_TO_REPLACE);

loc_str.substr(0, 50);

string tata_save(string_view t)

void ShrinkSpaces(char *line)

static char ValidAminoAcid(string_view abbrev)

Template class for iteration on objects of class C.

#define ERR_QUALIFIER_AntiCodonLacksSequence

#define ERR_FEATURE_UnknownQualSpelling

list< CRef< objects::CSeq_entry > > TEntryList

std::list< CRef< objects::CSeqdesc > > TSeqdescList

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

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

size_t StringLen(const char *s)

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

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

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

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-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 string Sanitize(CTempString str, TSS_Flags flags=fSS_print)

Sanitize a string, allowing only specified classes of characters.

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

Case-insensitive equality of a substring with another string.

void ResetSource(void)

Reset Source data member.

const TSource & GetSource(void) const

Get the Source member data.

void SetGenome(TGenome value)

Assign a value to Genome data member.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

bool IsSetMod(void) const

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

bool IsSetOrgname(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_gb_acronym

used by taxonomy database

@ eSubtype_gb_synonym

used by taxonomy database

@ eSubtype_gb_anamorph

used by taxonomy database

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

bool DeleteQual(TQualVector &qlist, const Char *qual)

const char * ParFlat_GImod[]

string location_to_string(const CSeq_loc &loc)

static void CheckDelGbblockSourceFromDescrs(TSeqdescList &descrs, const vector< string > &names)

static void GetTaxnameNameFromDescrs(const TSeqdescList &descrs, vector< string > &names)

string CpTheQualValue(const TQualVector &qlist, const Char *qual)

bool GetGenomeInfo(CBioSource &bsp, string_view bptr)

static void GetTaxnameName(TEntryList &seq_entries, vector< string > &names)

bool SeqLocHaveFuzz(const CSeq_loc &loc)

const char * valid_organelle[]

void MaybeCutGbblockSource(TEntryList &seq_entries)

void MakeLocStrCompatible(string &str)

optional< string > GetTheQualValue(TQualVector &qlist, const Char *qual)

Uint1 GetQualValueAa(string_view qval, bool checkseq)

static void CheckDelGbblockSource(TEntryList &seq_entries, const vector< string > &names)

Int2 StringMatchIcase(const Char **array, string_view text)

void fta_StringCpy(char *dst, const char *src)

Char * StringIStr(const Char *where, const Char *what)

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

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