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

CollectGaps(sf.GetLocation(), sf.GetScope());

(; seq_map_ci; ++seq_map_ci)

(

= map_start;

<= map_stop; ++

) {

skip_left = 0;

TGapIntervalList::iterator it =

.begin();

(it !=

.end()) {

(it->second.first <=

&& it->second.second >=

) {

}

(it->second.first <=

.front().second + 1 && it->second.second >=

.front().second) {

.front().second = it->second.second;

TGapIntervalList::reverse_iterator rit =

.rbegin();

skip_right = 0;

(rit !=

.rend()) {

(rit->second.first <=

&& rit->second.second >=

) {

}

(rit->second.first <=

.front().first - 1 && rit->second.second >=

.front().second) {

start =

->first;

stop =

->second;

start =

->first;

stop =

->second;

start =

->first;

stop =

->second;

locs.push_back(loc2);

(locs.size() > 0) {

locs.push_back(left_loc);

reverse(locs.begin(), locs.end());

((*it)->IsSetQual() && (*it)->IsSetVal() &&

(id_label.empty() ||

((*it)->GetVal(), id_label) ||

((*it)->GetVal(), id_label +

))) {

(id_label.empty()) {

id_label = (*it)->GetVal();

(

.empty()) {

prot_seq->

().ResetExt();

prot_seq->

().SetSeq_data().SetIupacaa().Set(

);

((*id)->Which() == feat_prod.

()) {

do_replace =

;

((*id)->IsGeneral()) {

((*id)->GetGeneral().IsSetDb()) {

((*mi)->IsMolinfo()) {

((*ait)->IsFtable()) {

CSeq_annot::TData::TFtable::iterator fit = (*ait)->SetData().SetFtable().begin();

(fit != (*ait)->SetData().SetFtable().end()) {

new_prot_loc->

((*fit)->GetLocation());

complete_cut =

;

adjusted =

;

(!complete_cut && stop < orig_len - 1) {

fit = (*ait)->SetData().SetFtable().erase(fit);

new_prot_loc->

(feat_prod);

(*fit)->SetLocation().Assign(*new_prot_loc);

CCdregion::TCode_break::iterator cit = cdr.

().begin();

do_remove =

;

((*cit)->IsSetLoc()) {

(new_loc && !new_loc->

() && !new_loc->

()) {

(*cit)->SetLoc().

(*new_loc);

(new_loc && !new_loc->

() && !new_loc->

()) {

vector<CRef<CSeq_feat> > rval;

(!trim && !

) {

rval.push_back(new_feat);

cds_gap_comment =

;

vector<CRef<CSeq_loc> > locs =

(new_feat->

(), in_intron, make_partial);

(locs.size() > 0) {

comment = comment +

+ cds_gap_comment;

transcript_id_offset = 0;

transcript_id_label;

protein_id_offset = 0;

protein_id_label;

protein_seqid_offset = 0;

protein_seqid_label;

split_feat->

(*new_feat);

(*split_feat, transcript_id_offset, transcript_id_label,

);

(*split_feat, protein_id_offset, protein_id_label,

);

new_id =

(bsh, protein_seqid_offset, protein_seqid_label, create_general_only);

split_feat->

().SetWhole().Assign(*new_id);

protein_seqid_offset++;

rval.push_back(split_feat);

rval.push_back(new_feat);

rval.push_back(new_feat);

frame_adjust = frame_adjust % 3;

(frame_adjust == 0) {

(frame_adjust == 1) {

}

(frame_adjust == 2) {

(fgap->HasKnown() || fgap->HasUnknown() || fgap->HasNs()) {

gapped_feats.push_back(fgap);

(updates.size() == 0) {

(

= 1;

< updates.size();

++) {

feat.

().SetLocal().SetId(next_id);

(

= 1;

< updates.size();

++) {

((*xit)->IsSetId() && (*xit)->GetId().IsLocal() &&

(*xit)->GetId().GetLocal().IsId() &&

(*xit)->GetId().GetLocal().GetId() == search) {

(orig_id > 0 && new_id > 0 &&

.IsSetXref()) {

((*xit)->IsSetId() && (*xit)->GetId().IsLocal() &&

(*xit)->GetId().GetLocal().IsId() &&

(*xit)->GetId().GetLocal().GetId() == orig_id) {

(*xit)->SetId().SetLocal().SetId(new_id);

(updates1.size() != updates2.size()) {

(updates1.size() < 2) {

vector<CRef<CSeq_feat> >::iterator u1 = updates1.begin();

vector<CRef<CSeq_feat> >::iterator u2 = updates2.begin();

((*u1)->IsSetId() && (*u1)->GetId().IsLocal() && (*u1)->GetId().GetLocal().IsId()) {

orig_id_1 = (*u1)->GetId().GetLocal().GetId();

((*u2)->IsSetId() && (*u2)->GetId().IsLocal() && (*u2)->GetId().GetLocal().IsId()) {

orig_id_2 = (*u2)->GetId().GetLocal().GetId();

(u1 != updates1.end() && u2 != updates2.end()) {

((*u1)->IsSetId() && (*u1)->GetId().IsLocal() && (*u1)->GetId().GetLocal().IsId()) {

new_id_1 = (*u1)->GetId().GetLocal().GetId();

((*u2)->IsSetId() && (*u2)->GetId().IsLocal() && (*u2)->GetId().GetLocal().IsId()) {

new_id_2 = (*u2)->GetId().GetLocal().GetId();

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 AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

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

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

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

CBioseq_set_EditHandle –.

pair< EGapIntervalType, pair< size_t, size_t > > TGapInterval

CSeq_feat_Handle m_Feature

static void x_AdjustFrame(CCdregion &cdregion, TSeqPos frame_adjust)

bool x_UsableInterval(const TGapInterval &interval, bool unknown_length, bool known_length, bool ns)

TIntervalList m_InsideGaps

void CalculateRelevantIntervals(bool unknown_length, bool known_length, bool ns=false)

bool IsRelatedByCrossRef(const CFeatGapInfo &other) const

void x_AdjustCodebreaks(CSeq_feat &feat)

@ eGapIntervalType_unknown

vector< CRef< CSeq_feat > > AdjustForRelevantGapIntervals(bool make_partial, bool trim, bool split, bool in_intron, bool create_general_only=false)

void x_AdjustOrigLabel(CSeq_feat &feat, size_t &id_offset, string &id_label, const string &qual)

void CollectGaps(const CSeq_loc &feat_loc, CScope &scope)

void x_AdjustAnticodons(CSeq_feat &feat)

bool ShouldRemove() const

void Trim(CSeq_loc &loc, bool make_partial, CScope &scope)

TIntervalList m_RightGaps

vector< CRef< CSeq_loc > > TLocList

CSeq_feat_Handle GetFeature() const

static CRef< CBioseq > AdjustProteinSeq(const CBioseq &seq, const CSeq_feat &feat, const CSeq_feat &orig_cds, CScope &scope)

TLocList Split(const CSeq_loc &orig, bool in_intron, bool make_partial)

CSeq_feat_EditHandle –.

namespace ncbi::objects::

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

bool s_IsRelated(const CSeq_feat &f1, CObject_id::TId search)

TGappedFeatList ListGappedFeatures(CFeat_CI &feat_it, CScope &scope)

void s_ReplaceFeatureIdXref(CSeq_feat &f, CObject_id::TId orig_id, CObject_id::TId new_id)

void s_FixPartial(CSeq_feat &feat)

void ProcessForTrimAndSplitUpdates(CSeq_feat_Handle cds, vector< CRef< CSeq_feat > > updates)

void FixFeatureIdsForUpdatePair(vector< CRef< CSeq_feat > > &updates1, vector< CRef< CSeq_feat > > &updates2)

void FixFeatureIdsForUpdates(CSeq_feat &feat, CObject_id::TId &next_id)

vector< CRef< CFeatGapInfo > > TGappedFeatList

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

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

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

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

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.

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 ResetStrand(void)

Reset the strand on this location.

void SetPartialStart(bool val, ESeqLocExtremes ext)

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

CRef< CSeq_loc > Intersect(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

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

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

TSeqPos LocationOffset(const CSeq_loc &outer, const CSeq_loc &inner, EOffsetType how=eOffset_FromStart, CScope *scope=0)

returns (TSeqPos)-1 if the locations don't overlap

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

@ eOffset_FromStart

For positive-orientation strands, start = left and end = right; for reverse-orientation strands,...

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.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eLocationToProduct

Map from the feature's location to product.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

CBioseq_EditHandle AttachBioseq(CBioseq &seq, int index=-1) const

Attach a bioseq.

const CSeqFeatData & GetData(void) const

void Remove(void) const

Remove the feature from Seq-annot.

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

virtual const CSeq_loc & GetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

CSeqMap::ESegmentType GetType(void) const

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

static CConstRef< CSeqMap > GetSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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

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

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.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsSetDb(void) const

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

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

TId GetId(void) const

Get the variant data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

void SetAnticodon(TAnticodon &value)

Assign a value to Anticodon data member.

bool IsSetExt(void) const

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

void ResetAnticodon(void)

Reset Anticodon data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetComment(void) const

Check if a value has been assigned to Comment 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.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetCode_break(void)

Reset Code_break data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

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.

bool IsLocal(void) const

Check if variant Local is selected.

const TData & GetData(void) const

Get the Data member data.

void SetId(TId &value)

Assign a value to Id data member.

void SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

const TRna & GetRna(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

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.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

bool IsEmpty(void) const

Check if variant Empty is selected.

const TWhole & GetWhole(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsNull(void) const

Check if variant Null is selected.

@ e_not_set

No variant selected.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetDescr(void) const

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

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_annot > > TAnnot

@ eRepr_raw

continuous sequence

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

@ eSplitLocOption_split_in_intron

@ eSplitLocOption_make_partial

@ eSplitLocOption_split_in_exon

void SplitLocationForGap(CSeq_loc &loc1, CSeq_loc &loc2, size_t start, size_t stop, const CSeq_id *seqid, unsigned int options=eSplitLocOption_make_partial|eSplitLocOption_split_in_exon)

void SeqLocAdjustForTrim(CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted)

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

static Uint4 letter(char c)

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