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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cds__fix_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/edit/cds_fix.cpp Source File

(cbr.GetAa().Which()) {

= cbr.GetAa().GetNcbi8aa();

= cbr.GetAa().GetNcbi8aa();

seqData.push_back(cbr.GetAa().GetNcbieaa());

except_len = (dna_len - 1) % 3;

except_len = (dna_len - 2) % 3;

except_len = dna_len % 3;

except_len = dna_len % 3;

(except_len == 0) {

codon_loc->

().SetId(*new_id);

codon_loc->

().SetFrom(stop);

codon_loc->

().SetTo(stop + except_len - 1);

codon_loc->

().SetFrom(stop - except_len + 1);

codon_loc->

().SetTo(stop);

cbr->

().SetNcbieaa(

);

cbr->

().Assign(*codon_loc);

cds.

().SetCdregion().SetCode_break().push_back(cbr);

alt_start =

;

add->

().SetTo(stop - 1);

add->

().SetFrom(stop + 1);

overhang->

().SetId().Assign(*loc.

());

overhang->

().SetFrom(0);

overhang->

().SetTo(stop - 1);

overhang->

().SetFrom(stop + 1);

(vec[0] ==

) {

(

> 1 && vec[1] ==

) {

(

> 2 && vec[2] ==

) {

(except_len > 0) {

(vec[0] !=

) {

}

(

> 1 && vec[1] !=

) {

(vec[0] !=

&& vec[0] !=

) {

extended =

;

(except_len > 0) {

(except_len == 0) {

added_code_break =

;

(

(orig_comment, comment) == string::npos) {

added_code_break =

;

extended || added_code_break;

(partial5 && partial3) {

}

(partial5) {

}

(partial3) {

any_change =

;

((partial5 && !prot_5) || (!partial5 && prot_5)

|| (partial3 && !prot_3) || (!partial3 && prot_3)) {

any_change =

;

new_feat->

(*(

->GetSeq_feat()));

((*it)->IsMolinfo()) {

beh.

().Set().push_back(new_molinfo_desc);

(

.IsSetName() &&

.GetName().size() > 0) {

prot_nm =

.GetName().front();

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

(best_len == 0 ||

< best_len) {

mrna = &(mrna_find->GetOriginalFeature());

new_mrna->

().SetRna().SetExt().SetName(prot_nm);

found3 =

;

found5 =

;

*overlap_loc = &cd_loc;

(exon_start >= gene_start && exon_stop <= gene_stop)

exon_found =

;

(exon_start < mrna_start )

(exon_stop > mrna_stop)

has_xref =

;

((*it)->IsSetId() && (*it)->GetId().IsLocal() && (*it)->GetId().GetLocal().IsId()) {

(bioseqGenCode > 0) {

->SetId(bioseqGenCode);

this_len = it.GetRange().GetLength();

(

+ this_len <= new_len) {

new_loc->

(*this_loc);

new_loc->

(*this_loc);

len_wanted = new_len -

;

(len_wanted == 1) {

partial_loc->

().SetPoint(start);

partial_loc->

().SetFrom(start - len_wanted + 1);

partial_loc->

().SetTo(start);

partial_loc->

().SetFrom(start);

partial_loc->

().SetTo(start + len_wanted - 1);

new_loc->

(*partial_loc);

new_loc->

(*partial_loc);

(pos != string::npos) {

len_wanted = 3 * (pos + 1);

(len_wanted > 0) {

= orig_len;

vector_loc->

().SetId().Assign(*(loc.

()));

vector_loc->

().SetFrom(0);

vector_loc->

().SetTo(stop +

- 1);

vector_loc->

().SetFrom(stop -

+ 1);

usable_size = seq.

();

length = usable_size / 3;

(

= 0;

< length; ++

) {

(k = 0; k < 3; ++k, ++start) {

new_loc->

(*this_loc);

new_loc->

(*this_loc);

extension = ((

+ 1) * 3) -

;

last_interval->

().SetId().Assign(*(this_loc->

()));

last_interval->

().SetFrom(this_start - extension);

last_interval->

().SetTo(this_stop);

last_interval->

().SetFrom(this_start);

last_interval->

().SetTo(this_stop + extension);

new_loc->

(*last_interval);

new_loc->

(*last_interval);

(usable_size < 3 && !new_loc) {

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

new_annot->

().SetFtable();

orig_feat = new_annot.

(feh);

(feat_list.empty())

(frame_type) {

modified =

;

(orig_frame != new_frame) {

cds.

().SetCdregion().SetFrame(new_frame);

(!product || !product.

()) {

orig_prot_seq;

tmp_cds->

().SetCdregion().SetFrame(fr);

new_prot_seq;

new_prot_seq.erase(new_prot_seq.end() - 1);

new_str = base;

id_base_hash =

(id_base);

new_str = id_base;

new_hash = id_base_hash;

(b_found || b_found_hash)

id_base_hash =

(id_base);

new_str = id_base;

new_hash = id_base_hash;

(b_found || b_found_hash)

(fall_through)

vector<CRef<CSeq_id> > ids;

(

it : bsh.

())

(it.GetSeqIdOrNull())

ids.push_back(new_id);

(ids.empty() && !bsh.

().empty())

ids.push_back(new_id);

(

it : bsh.

())

(it.GetSeqId()->IsGeneral() && it.GetSeqId()->GetGeneral().IsSetDb() &&

!it.GetSeqId()->GetGeneral().IsSkippable())

(gen_id && general_only)

found =

;

(

it : b_iter->GetId())

(it.GetSeqId()->IsGeneral() && it.GetSeqId()->GetGeneral().IsSetDb() &&

!it.GetSeqId()->GetGeneral().IsSkippable())

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

bool AddTerminalCodeBreak(CSeq_feat &cds, CScope &scope)

bool ExtendCDSToStopCodon(CSeq_feat &cds, CScope &scope)

ExtendCDSToStopCodon A function to extend a CDS location to the first in-frame stop codon in the prot...

string s_GetmRNAName(const CSeq_feat &mrna)

CRef< CSeq_loc > GetLastCodonLoc(const CSeq_feat &cds, CScope &scope)

bool SetTranslExcept(CSeq_feat &cds, const string &comment, bool strict, bool extend, CScope &scope)

SetTranslExcept A function to set a code break at the 3' end of a coding region to indicate that the ...

void ExtendStop(CSeq_loc &loc, TSeqPos len, CScope &scope)

vector< CRef< CSeq_id > > GetNewProtIdFromExistingProt(CBioseq_Handle bsh, int &offset, string &id_label)

static CRef< CSeq_id > GetNewGeneralProtId(const string &id_base, const string &db, CScope &scope, int &offset)

bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding reg...

bool DoesCodingRegionHaveTerminalCodeBreak(const CCdregion &cdr)

bool IsGeneralIdProtPresent(CSeq_entry_Handle tse)

CRef< CSeq_feat > MakemRNAforCDS(const CSeq_feat &cds, CScope &scope)

MakemRNAforCDS A function to create a CSeq_feat that represents the appropriate mRNA for a given CDS.

string s_GetProductName(const CProt_ref &prot)

CRef< CSeq_id > GetNewLocalProtId(const string &id_base, CScope &scope, int &offset)

void AdjustCDSFrameForStartChange(CCdregion &cds, int change)

static string GetIdHash(const string &str)

bool TruncateCDSAtStop(CSeq_feat &cds, CScope &scope)

TruncateCDSAtStop A function to truncate a CDS location after the first stop codon in the protein tra...

const unsigned int MAX_ID_LENGTH

TSeqPos GetLastPartialCodonLength(const CSeq_feat &cds, CScope &scope)

static CRef< CSeq_loc > TruncateSeqLoc(const CSeq_loc &orig_loc, size_t new_len)

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

unsigned char GetCodeBreakCharacter(const CCode_break &cbr)

TSeqPos ExtendLocationForTranslExcept(CSeq_loc &loc, CScope &scope)

static CRef< CSeq_id > GetGeneralOrLocal(CSeq_id_Handle hid, CScope &scope, int &offset, bool fall_through)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

bool DoesCodingRegionEndWithStopCodon(const CSeq_feat &cds, CScope &scope)

bool DemoteCDSToNucSeq(CSeq_feat_Handle &orig_feat)

string GetIdHashOrValue(const string &base, int offset)

bool IsOverhangOkForTerminalCodeBreak(const CSeq_feat &cds, CScope &scope, bool strict)

Checksum and hash calculation classes.

static ECdsFrame s_GetFrameFromName(const string &name)

static bool s_SetCDSFrame(CSeq_feat &cds, ECdsFrame frame_type, CScope &scope)

static CCdregion::TFrame s_FindMatchingFrame(const CSeq_feat &cds, CScope &scope)

int GetGenCode(int def=1) const

static const CTrans_table & GetTransTable(int id)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

ESubtype GetSubtype(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

static Uint8 CityHash64(const CTempString str)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

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

Set object to copy of another one.

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

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

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

@ eContent

Untagged human-readable accession or the like.

@ eBoth

Type and content, delimited by a vertical bar.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

bool IsReverseStrand(void) const

Return true if all ranges have reverse strand.

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

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

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

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

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end o...

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

bool AdjustForCDSPartials(const CSeq_feat &cds, CSeq_entry_Handle seh)

AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the...

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

Int8 TestForOverlap64(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)

64-bit version of TestForOverlap() Check if the two locations have ovarlap of a given type.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ eOverlap_CheckIntervals

2nd is a subset of 1st with matching boundaries

@ eOverlap_CheckIntRev

1st is a subset of 2nd with matching boundaries

CConstRef< CSeq_feat > GetOverlappingmRNA(const CSeq_loc &loc, CScope &scope)

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

TClass GetClass(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

void SetDescr(TDescr &v) const

void Remove(void) const

Remove current annot.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsProtein(void) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Length GetInst_Length(void) const

bool IsSetClass(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_feat_EditHandle TakeFeat(const CSeq_feat_EditHandle &handle) const

CSeq_annot_EditHandle GetAnnot(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

const TId & GetId(void) const

CConstRef< CSeq_annot > GetSeq_annotCore(void) const

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void SetCoding(TCoding coding)

const_iterator begin(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

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

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsId(void) const

Check if variant Id is selected.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId GetId(void) const

Get the variant data.

bool IsSetOrgname(void) const

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

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

void SetAa(TAa &value)

Assign a value to Aa data member.

bool IsSetComment(void) const

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

void ResetPartial(void)

Reset Partial data member.

bool IsSetData(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

list< CRef< CCode_break > > TCode_break

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

const TRna & GetRna(void) const

Get the variant data.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

void SetFrame(TFrame value)

Assign a value to Frame data member.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsSetFrame(void) const

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

bool IsSetLocation(void) const

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

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

@ e_Ncbi8aa

NCBI8aa code.

@ e_Ncbieaa

ASCII value of NCBIeaa code.

TGeneral & SetGeneral(void)

Select the variant.

bool IsGeneral(void) const

Check if variant General is selected.

TLocal & SetLocal(void)

Select the variant.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ eClass_nuc_prot

nuc acid and coded proteins

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetCompleteness(void) const

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

list< CRef< CSeqdesc > > Tdata

const TSource & GetSource(void) const

Get the variant data.

bool IsSetBiomol(void) const

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

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

const TFtable & GetFtable(void) const

Get the variant data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const TData & GetData(void) const

Get the Data member data.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, size_t pos, CScope *scope)

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define FOR_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

FOR_EACH_SEQFEATXREF_ON_SEQFEAT EDIT_EACH_SEQFEATXREF_ON_SEQFEAT.

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