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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fcleanup_8cpp_source.html below:

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

(

& desc : seq_set.

().

()) {

(desc->IsSource()) {

(bioseq->IsSetDescr()) {

(TSeqdescList::iterator desc = descrs.begin(); desc != descrs.end(); ++desc) {

((*desc)->IsSource()) {

seq_set.

().Set().push_back(*desc);

(! prot_ref.

() || prot_ref.

().empty() || (prot_ref.

().size() == 1 && prot_ref.

().front() ==

)) {

(TQualVector::iterator qual = feat.

().begin(); qual != feat.

().end(); ++qual) {

((*qual)->IsSetQual() && (*qual)->GetQual() ==

&& (*qual)->IsSetVal()) {

prot_ref.

().push_back((*qual)->GetVal());

sz = ranges.size();

(

= 1;

< sz; ++

) {

(ranges[

].

!= ranges[

- 1].second && ranges[

].

!= ranges[

- 1].second + 1) {

new_int->

(to);

(

->IsSetFuzz_from()) {

(

->IsSetFuzz_to()) {

vector<pair<TSeqPos, TSeqPos>> ranges;

(

& cur_loc : locs) {

(cur_loc->IsInt()) {

ranges.push_back(make_pair(interval.

(), interval.

()));

(! first_interval) {

first_interval = &interval;

first_interval = &interval;

(! last_interval) {

last_interval = &interval;

last_interval = &interval;

}

(cur_loc->IsPnt()) {

(! first_interval) {

(ranges.begin(), ranges.end());

(first_interval, last_interval, ranges.front().first, ranges.back().second, loc);

vector<pair<TSeqPos, TSeqPos>> ranges;

(

& interval : ints) {

ranges.push_back(make_pair(interval->GetFrom(), interval->GetTo()));

(ranges.begin(), ranges.end());

& scope = entryHandle.

();

protein_id_counter = 99;

(

cds_it(entryHandle, sel); cds_it; ++cds_it) {

pCds = cds_it->GetSeq_feat();

(! pCds->IsSetProduct()) {

pNewCds->Assign(*pCds);

(scope.GetBioseqHandle(pNewCds->GetLocation()), protein_id_counter, idLabel,

);

pNewCds->SetProduct().SetWhole().Assign(*pProteinId);

pCdsEditHandle.

(*pNewCds);

}

(pCds->GetProduct().GetId() &&

scope.Exists(*pCds->GetProduct().GetId())) {

protHandle = scope.GetBioseqHandle(pCds->GetProduct());

protName =

;

(

& entry : seq_entries) {

.ExtendedCleanup(*entry);

gene_set =

;

(feat->IsSetData() && feat->GetData().IsGene()) {

(feat->IsSetLocation()) {

& loc = feat->SetLocation();

}

(loc.

()) {

(feat->IsSetData() && feat->GetData().IsProt()) {

(! loc.

()) {

mol_info(bioseq_h, CSeqdesc::E_Choice::e_Molinfo);

&

= *ids.front();

(

.Which() == loc.

()->

()) {

@ eExtreme_Biological

5' and 3'

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

static CRef< CSeq_entry > AddProtein(const CSeq_feat &cds, CScope &scope)

static const string & GetProteinName(const CProt_ref &prot)

const CSeq_interval * GetStopInt(ESeqLocExtremes ext) const

const CSeq_interval * GetStartInt(ESeqLocExtremes ext) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

TSeqPos GetStart(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

static void LookForProductName(CSeq_feat &feat)

static NCBI_UNUSED bool IsEmptyMolInfo(const CMolInfo &mol_info)

void g_InstantiateMissingProteins(CSeq_entry_Handle entryHandle)

static void MoveSourceDescrToTop(CSeq_entry &entry)

static bool IsConversionPossible(const vector< pair< TSeqPos, TSeqPos >> &ranges)

void FinalCleanup(TEntryList &seq_entries)

static void ConvertPackedIntToInterval(CSeq_loc &loc)

static void ConvertMixToInterval(CSeq_loc &loc)

static void SetNewInterval(const CSeq_interval *first, const CSeq_interval *last, const TSeqPos &from, TSeqPos &to, CSeq_loc &loc)

list< CRef< objects::CSeq_entry > > TEntryList

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

static void cleanup(void)

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

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

static TDSRET convert(TDSSOCKET *tds, TDSICONV *conv, TDS_ICONV_DIRECTION direction, const char *from, size_t from_len, char *dest, size_t *dest_len)

unsigned int TSeqPos

Type for sequence locations and lengths.

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

Set object to copy of another one.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

void AddProteinFeature(const CBioseq &seq, const string &protein_name, const CSeq_feat &cds, CScope &scope)

AddProteinFeature A function to create a protein feature with the specified protein name.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CScope & GetScope(void) const

Get scope this handle belongs to.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

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 bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

TName & SetName(void)

Assign a value to Name data member.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetQual(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

TQual & SetQual(void)

Assign a value to Qual data member.

void ResetQual(void)

Reset Qual data member.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

void SetTo(TTo value)

Assign a value to To data member.

bool IsMix(void) const

Check if variant Mix is selected.

list< CRef< CSeq_interval > > Tdata

TPoint GetPoint(void) const

Get the Point member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

TTo GetTo(void) const

Get the To member data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetDescr(void) const

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

void SetDescr(TDescr &value)

Assign a value to Descr data member.

bool IsSetCompleteness(void) const

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

bool IsSetTechexp(void) const

explanation if tech not enough

bool IsSetBiomol(void) const

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

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_id > > TId

TBiomol GetBiomol(void) const

Get the Biomol member data.

bool IsSetTech(void) const

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

const TMolinfo & GetMolinfo(void) const

Get the variant data.

bool IsSetGbmoltype(void) const

identifies particular ncRNA Check if a value has been assigned to Gbmoltype data member.

constexpr auto sort(_Init &&init)

const CharType(& source)[N]

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