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

stop_at_stop,

cleanup_partials,

merge_abutting,

: m_Src(src), m_Target(target),

m_CdsStopAtStopCodon(stop_at_stop),

m_CdsCleanupPartials(cleanup_partials),

m_MessageListener(pMessageListener),

m_MergeAbutting(merge_abutting),

m_ExpandOverGaps(

),

m_synonym_mapper(this)

(align.GetSegs().IsDenseg()) {

m_Alignment.

(&align);

}

(align.GetSegs().IsDisc()) {

m_Alignment.Reset(&*align.CreateDensegFromDisc());

}

(align.GetSegs().IsStd()) {

m_Alignment.Reset(&*align.CreateDensegFromStdseg());

}

(align.GetSegs().IsSpliced()) {

(m_MessageListener) {

m_MessageListener->PostMessage(

eFeaturePropagationProblem_FeatureLocation));

stop_at_stop,

cleanup_partials,

merge_abutting,

expand_over_gaps,

: m_Src(src), m_Target(target),

m_CdsStopAtStopCodon(stop_at_stop),

m_CdsCleanupPartials(cleanup_partials),

m_MessageListener(pMessageListener),

m_MaxFeatId(feat_id),

m_MergeAbutting(merge_abutting),

m_ExpandOverGaps(expand_over_gaps),

m_synonym_mapper(this)

rval->

(orig_feat);

pTargetId->

(&target_label);

(

+ loc_label +

+ target_label,

rval.

(

);

vector<CRef<CSeq_feat> > rval;

rval.push_back(new_feat);

vector<CRef<CSeq_feat> > rval;

rval.push_back(new_feat);

failures.push_back(old_feat);

vector<CRef<CSeq_feat>> propagated_feats;

(

&& it : orig_feats) {

propagated_feats.push_back(new_feat);

(it->IsSetProduct()) {

propagated_feats.push_back(prot_feat);

(

&& it : propagated_feats) {

(it->IsSetXref()) {

xref_it = it->SetXref().begin();

(xref_it != it->SetXref().end()) {

((*xref_it)->IsSetId()) {

& feat_id = (*xref_it)->SetId();

xref_it = it->SetXref().erase(xref_it);

(it->GetXref().empty()) {

propagated_feats;

( seg < num_segs )

(start >= 0 && pos >= start && pos < start +

)

res = total_len + pos - start;

(start >= 0 && start > pos && left)

(start >= 0 && start +

- 1 < pos && !left)

found_len = total_len +

- 1;

( seg < num_segs )

(total_len <= pos && total_len + len > pos)

res = start + pos - total_len;

( seg < num_segs )

res = start +

- 1;

(

seg = 0; seg < num_segs; seg++)

ret->

().Assign(

);

should_be_null =

;

(

& it : loc.

().

())

(it->IsNull() != should_be_null)

should_be_null = !should_be_null;

should_be_null;

(

& it : loc.

().

())

mix->

().Set().push_back(it);

null_loc->CSeq_loc_Base::SetNull();

mix->

().Set().push_back(null_loc);

mix->

().Set().pop_back();

(source_row == -1 || target_row == -1)

new_loc->

(sourceLoc);

(start_before != start_after)

(stop_before != stop_after)

new_loc->

(targetId);

sub_partial5(

), sub_partial3(

);

align_start =

(start, source_row,

, sub_partial5, sub_partial3);

align_stop =

(stop, source_row,

, sub_partial5, sub_partial3);

(align_start < 0 || align_stop < 0)

(loc_it.

() == 0)

new_start =

(align_start, target_row,

, sub_partial5, sub_partial3);

new_stop =

(align_stop, target_row,

, sub_partial5, sub_partial3);

(new_start < 0 || new_stop < 0 || new_stop < new_start)

(loc_it.

() == 0)

loc_it.

(new_stop);

(partial5 && target)

(partial3 && target)

curLen = 0;

(

it(loc); it && curLen < truncLen; ++it) {

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

(curLen + thisLen <= truncLen) {

pTruncated->

(*pThisLoc);

pTruncated->

(*pThisLoc);

missingLen = truncLen - curLen;

(missingLen == 1) {

pPartialLoc->

().SetPoint(start);

pPartialLoc->

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

pPartialLoc->

().SetTo(start);

pPartialLoc->

().SetFrom(start);

pPartialLoc->

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

pTruncated->

(*pPartialLoc);

pTruncated->

(*pPartialLoc);

curLen += missingLen;

nuc_len = orig_len;

= nuc_len % 3;

vector_int.

().Assign(*(loc.

()));

usable_size = seq.

();

prot_len = usable_size / 3;

(

= 0;

< prot_len; ++

) {

(

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);

ambiguous =

;

((*it)->IsSetLoc()) {

& codebreak = (*it)->GetLoc();

(*it)->SetLoc(*new_codebreak);

(*it)->GetLoc().GetLabel(&loc_label);

(

+ loc_label +

+ target_label,

(!targetIsPartialStart && !origIsPartialStart) {

(!targetIsPartialStop) {

(it && *it !=

) {

newSize = 3*(it.

()+1);

feat.

().SetRna().SetExt().SetTRNA().SetAnticodon(*new_anticodon);

(

+ loc_label +

+ target_label,

feat.

().SetRna().SetExt().SetTRNA().ResetAnticodon();

prot_feat->

(orig_prot);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const CSeq_id & GetSeq_id(TDim row) const

CMessageListener_Basic * m_MessageListener

vector< CRef< CSeq_feat > > PropagateFeatureList(const vector< CConstRef< CSeq_feat >> &orig_feats)

Propagates a feature list from the source sequence The propagated protein feature is stored right aft...

TSignedSeqPos SeqPosToAlignPos(TSignedSeqPos pos, CDense_seg::TDim row, bool left, bool &partial5, bool &partial3)

void x_CdsCleanupPartials(CSeq_feat &cds, bool origIsPartialStart)

CRef< CSeq_loc > x_MapLocation(const CSeq_loc &sourceLoc, const CSeq_id &targetId)

map< CObject_id::TId, CObject_id::TId > m_FeatIdMap

CConstRef< CSeq_align > m_Alignment

CRef< CSeq_loc > CreateRowSeq_loc(const CSeq_align &align, CDense_seg::TDim row)

CRef< CSeq_loc > MakeOrdered(const CSeq_loc &loc)

CRef< CSeq_loc > x_TruncateToStopCodon(const CSeq_loc &loc, unsigned int truncLen)

CFeaturePropagator(CBioseq_Handle src, CBioseq_Handle target, const CSeq_align &align, bool stop_at_stop=true, bool cleanup_partials=true, bool merge_abutting=true, CMessageListener_Basic *pMessageListener=nullptr, CObject_id::TId *feat_id=nullptr)

void x_CdsStopAtStopCodon(CSeq_feat &cds)

bool IsOrdered(const CSeq_loc &loc)

vector< CRef< CSeq_feat > > PropagateAllReportFailures(vector< CConstRef< CSeq_feat > > &)

@ eFeaturePropagationProblem_CodeBreakLocation

@ eFeaturePropagationProblem_AnticodonLocation

@ eFeaturePropagationProblem_FeatureLocation

void x_PropagatetRNA(CSeq_feat &feat, const CSeq_id &targetId)

void x_CdsMapCodeBreaks(CSeq_feat &feat, const CSeq_id &targetId)

void x_PropagateCds(CSeq_feat &feat, const CSeq_id &targetId, bool origIsPartialStart)

CObject_id::TId * m_MaxFeatId

CSynonymMapper m_synonym_mapper

vector< CRef< CSeq_feat > > PropagateAll()

CRef< CSeq_feat > Propagate(const objects::CSeq_feat &orig_feat)

CRef< CSeq_feat > ConstructProteinFeatureForPropagatedCodingRegion(const CSeq_feat &orig_cds, const CSeq_feat &new_cds)

bool m_CdsStopAtStopCodon

TSignedSeqPos AlignPosToSeqPos(TSignedSeqPos pos, CDense_seg::TDim row, bool left, bool &partial5, bool &partial3)

CRef< CSeq_loc > x_ExtendToStopCodon(CSeq_feat &feat)

CDense_seg::TDim FindRow(const CSeq_align &align, CBioseq_Handle bsh)

bool m_CdsCleanupPartials

static const CTrans_table & GetTransTable(int id)

Default implementation of IMessageListener: collects all messages posted.

Default IMessage implementation: text and severity only.

ESubtype GetSubtype(void) const

CRef< CSeq_align > CreateDensegFromDisc(SSeqIdChooser *SeqIdChooser=0) const

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

namespace ncbi::objects::

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

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

CRef< CSeq_align > AsDiscSeg() const

Convert this alignment to a discontinuous segment.

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

const_iterator end() const

const_iterator find(const key_type &key) const

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

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

@ eDiag_Error

Error message.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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 EPostResult PostMessage(const IMessage &message)

Post new message to the listener.

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

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void SetPacked_int(TPacked_int &v)

void SetFrom(TSeqPos from)

Set the range from position.

void SetTo(TSeqPos to)

Set the range to position.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

void Delete(void)

Delete current element, and make iterator to point to the next element.

ENa_strand GetStrand(void) const

Get the location's 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

size_t GetPos(void) const

Get iterator's position.

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.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

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.

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

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

size_t GetSize(void) const

Get number of ranges.

TRange GetRange(void) const

Get the range.

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.

ENa_strand GetStrand(void) const

void GetLabel(string *label) const

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

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

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.

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.

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.

TInst_Length GetInst_Length(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetPos(void) const

void SetCoding(TCoding coding)

const_iterator begin(void) const

void Reset(void)

Reset reference object.

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 StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsId(void) const

Check if variant Id is selected.

TId & SetId(void)

Select the variant.

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.

bool IsSetExt(void) const

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

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetStrands(void) const

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

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

TDim GetDim(void) const

Get the Dim member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsDisc(void) const

Check if variant Disc is selected.

bool IsSpliced(void) const

Check if variant Spliced is selected.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

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 ResetCode_break(void)

Reset Code_break data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsLocal(void) const

Check if variant Local is selected.

TLocal & SetLocal(void)

Select the variant.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void SetId(TId &value)

Assign a value to Id data member.

const TCode & GetCode(void) const

Get the Code member data.

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.

void ResetProduct(void)

Reset Product data member.

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 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_three

reading frame

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetTo(TTo value)

Assign a value to To data member.

bool IsMix(void) const

Check if variant Mix is selected.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

bool IsSetPoints(void) const

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

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

const TWhole & GetWhole(void) const

Get the variant data.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

const TPoints & GetPoints(void) const

Get the Points member data.

bool IsNull(void) const

Check if variant Null is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

#define row(bind, expected)

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