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NCBI C++ ToolKit: src/gui/objutils/report_trim.cpp Source File

(; feat_ci; ++feat_ci)

length = orig_length;

(x_IsProtLocation(feat_ci->

(), bsh, scope))

( x_AdjustLocation(new_feat->

(),length,from,to,diff) )

x_AdjustCdregionFrame(new_feat, diff);

((*codebreak)->IsSetLoc())

( x_AdjustLocation((*codebreak)->SetLoc(),length,from,to))

new_feat->

().SetCdregion().ResetCode_break();

( x_AdjustLocation(new_feat->

().SetRna().SetExt().SetTRNA().SetAnticodon(), length,from,to))

new_feat->

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

(clone_set.

())

(CClone_seq_set::Tdata::iterator clone_it = clone_set.

().begin(); clone_it != clone_set.

().end(); ++clone_it)

((*clone_it)->IsSetLocation())

( x_AdjustLocation((*clone_it)->SetLocation(), length,from,to))

(*clone_it)->ResetLocation();

((*clone_it)->IsSetSeq())

( x_AdjustLocation((*clone_it)->SetSeq(),length,from,to))

(*clone_it)->ResetSeq();

x_UpdateVariation(var, length,from,to);

CVariation_inst::TDelta::iterator delta_it = var.

().SetInstance().SetDelta().begin();

( delta_it != var.

().SetInstance().SetDelta().end())

to_delete =

;

((*delta_it)->IsSetSeq() && (*delta_it)->GetSeq().IsLoc() && x_AdjustLocation((*delta_it)->SetSeq().SetLoc(), length,from,to))

delta_it = var.

().SetInstance().SetDelta().erase(delta_it);

var.

().SetInstance().ResetDelta();

( CVariation_ref::C_Data::C_Set::TVariations::iterator var_it = var.

().SetSet().SetVariations().begin(); var_it != var.

().SetSet().SetVariations().end(); ++var_it)

x_UpdateVariation(**var_it, length,from,to);

((*con_it)->IsVariation())

x_UpdateVariation((*con_it)->SetVariation(), length,from,to);

prot_bsh.

();

diff += from - begin;

(end > length - 1)

diff += end - (length - 1);

x_AdjustLocation(loc, length, from, to, diff);

begin = interval.

();

end = interval.

();

(end < from || begin > to)

x_AdjustInt(begin, end, from, to, length, diff, strand);

interval.

(end);

(point < from || point > to)

(loc.SetPacked_int().IsSet())

vector<CPacked_seqint::Tdata::iterator> del;

(CPacked_seqint::Tdata::iterator p = loc.SetPacked_int().Set().begin(); p != loc.SetPacked_int().Set().end(); ++p)

begin = interval.

();

end = interval.

();

(end < from || begin > to)

x_AdjustInt(begin, end, from, to, length, diff, strand);

interval.

(end);

(

=0;

<del.size();

++)

CPacked_seqint::Tdata::iterator p = del[

];

loc.SetPacked_int().Set().erase(p);

(loc.SetPacked_int().Set().empty())

(loc.SetPacked_pnt().IsSetPoints())

vector<CPacked_seqpnt::TPoints::iterator> del;

(CPacked_seqpnt::TPoints::iterator p = loc.SetPacked_pnt().SetPoints().begin(); p != loc.SetPacked_pnt().SetPoints().end(); ++p)

(point < from || point > to)

(

=0;

<del.size();

++)

CPacked_seqpnt::TPoints::iterator p = del[

];

loc.SetPacked_pnt().SetPoints().erase(p);

(loc.SetPacked_pnt().SetPoints().empty())

(loc.SetMix().IsSet())

vector<CSeq_loc_mix::Tdata::iterator> del;

(CSeq_loc_mix::Tdata::iterator p = loc.SetMix().Set().begin(); p != loc.SetMix().Set().end(); ++p)

CSeq_loc &loc2 = **p;

(x_AdjustLocation(loc2, length, from,to,diff))

(

=0;

<del.size();

++)

CSeq_loc_mix::Tdata::iterator p = del[

];

loc.SetMix().Set().erase(p);

(loc.SetMix().Set().empty())

(loc.SetEquiv().IsSet())

vector<CSeq_loc_equiv::Tdata::iterator> del;

(CSeq_loc_equiv::Tdata::iterator p = loc.SetEquiv().Set().begin(); p != loc.SetEquiv().Set().end(); ++p)

CSeq_loc &loc2 = **p;

orig_diff = diff;

(x_AdjustLocation(loc2, length, from,to,orig_diff))

(p == loc.SetEquiv().Set().begin())

(

=0;

<del.size();

++)

CSeq_loc_equiv::Tdata::iterator p = del[

];

loc.SetEquiv().Set().erase(p);

(loc.SetEquiv().Set().empty())

new_offset = (orig_frame - diff) % 3;

(orig_frame < diff && new_offset != 0)

new_offset = 3 - ((diff - orig_frame) % 3);

(new_offset) {

feat->

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

new_inst->Assign(prot_bsh.

());

new_inst->ResetExt();

new_inst->SetRepr(objects::CSeq_inst::eRepr_raw);

new_inst->SetSeq_data().SetNcbieaa().Set(

);

->AddCommand(*chgInst);

( ; prot_feat_ci; ++prot_feat_ci )

new_feat->

().SetInt().SetTo(new_inst->GetLength() - 1);

->AddCommand(*chgFeat);

CSeq_loc &loc = prot_feat_ci->

();

->AddCommand(*delFeat);

->AddCommand(*chgFeat);

(; align_ci; ++align_ci)

(CBioseq::TId::const_iterator seqid = seqids.begin(); seqid != seqids.end(); ++seqid)

(

ii = 0; ii < ids.size(); ++ii) {

( ids[ii]->Match(**seqid) ) {

x_AdjustDensegAlignment(new_align,

, from, to);

->AddCommand(*chgAlign);

->AddCommand(*delAlign);

cut_len = cut_to - cut_from + 1;

(cut_to < cut_from) {

cut_len = cut_from - cut_to + 1;

x_CutDensegSegment(align,

, cut_from);

x_CutDensegSegment(align,

, cut_from + cut_len);

(seg_start < cut_from) {

(seg_start >= cut_from &&

seg_start + denseg.

()[curseg] <= cut_from + cut_len) {

align->

().SetDenseg().SetStarts()[index] = -1;

align->

().SetDenseg().SetStarts()[index] -= cut_len;

( !x_FindSegment(denseg,

, pos, foundseg, seg_start) ) {

(pos == seg_start) {

first_len = pos - seg_start;

second_len = denseg.

()[foundseg] - first_len;

second_len = pos - seg_start;

first_len = denseg.

()[foundseg] - second_len;

new_denseg->

().push_back(first_len);

new_denseg->

().push_back(second_len);

align->

().SetDenseg(*new_denseg);

(seg = 0; seg < denseg.

(); ++seg) {

(pos >= start && pos < start +

) {

new_loc->Assign(new_graph->

());

= x_AdjustLocation(*new_loc,length,from,to);

new_graph->

(*new_loc);

copy_start = graph_start;

(trim_start > graph_start) {

copy_start = trim_start;

copy_stop = graph_stop;

(trim_stop < graph_stop) {

copy_stop = trim_stop;

( src_data.

() ) {

copy_start -= graph_start;

copy_stop -= graph_start;

new_graph->

(copy_stop - copy_start + 1);

x_UpdateSeqGraphLoc(new_graph, trim_start, trim_stop, length, seqid);

(; graph_ci; ++graph_ci)

(CBioseq::TId::const_iterator seqid = seqids.begin(); seqid != seqids.end(); ++seqid)

( graph.

().GetId()->Match(**seqid) ) {

(x_TrimSeqGraphData(new_graph, graph, from, to, length, *seqid))

->AddCommand(*delGraph);

->AddCommand(*chgGraph);

( bioseq_len < 1 ) {

eResult_NoTrimNeeded;

( ! x_TestFlag(fFlags_DoNotTrimBeginning) ) {

leftmost_good_base = x_FindWhereToTrim(

seqvec, leftmost_good_base, rightmost_good_base,

( leftmost_good_base > rightmost_good_base) {

(x_IsThereGapNotAtTheEnd(bioseq_handle, 0, bioseq_len -1, bioseq_len))

eResult_NoTrimNeeded;

x_TrimToNothing( bioseq_handle );

(x_IsThereGapNotAtTheEnd(bioseq_handle, leftmost_good_base, bioseq_len -1, bioseq_len))

leftmost_good_base = 0;

( ! x_TestFlag(fFlags_DoNotTrimEnd) ) {

rightmost_good_base =

seqvec, rightmost_good_base, leftmost_good_base,

( leftmost_good_base > rightmost_good_base) {

(x_IsThereGapNotAtTheEnd(bioseq_handle, 0, bioseq_len -1, bioseq_len))

eResult_NoTrimNeeded;

x_TrimToNothing( bioseq_handle );

(x_IsThereGapNotAtTheEnd(bioseq_handle, 0, rightmost_good_base, bioseq_len))

rightmost_good_base = bioseq_len -1;

( (leftmost_good_base == 0) &&

(rightmost_good_base == (bioseq_len - 1)) )

eResult_NoTrimNeeded;

leftmost_good_base, rightmost_good_base,

left = leftmost_good_base;

right = rightmost_good_base;

eResult_SuccessfullyTrimmed;

(from == 0 && to == length - 1)

gap_inside =

;

(

pos = 1; pos < length - 1; pos++)

gap_left =

;

(

pos = 1; pos < from; pos++)

gap_right =

;

(

pos = to + 1; pos < length - 1; pos++)

gap_left || gap_right;

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

virtual EResult Trim(objects::CBioseq_Handle &bioseq_handle, TSignedSeqPos &left, TSignedSeqPos &right)

void x_UpdateVariation(objects::CVariation_ref &var, int length, int from, int to)

bool x_TrimSeqGraphData(CRef< objects::CSeq_graph > new_graph, const objects::CMappedGraph &orig_graph, TSeqPos trim_start, TSeqPos trim_stop, int length, const CRef< objects::CSeq_id > seqid)

bool x_IsThereGapNotAtTheEnd(objects::CBioseq_Handle bsh, TSignedSeqPos from, TSignedSeqPos to, int length)

void TrimAlignments(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to)

void AdjustAndTranslate(objects::CBioseq_Handle bsh, int length, int from, int to, CRef< CCmdComposite > command, objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

bool x_UpdateSeqGraphLoc(CRef< objects::CSeq_graph > new_graph, TSeqPos from, TSeqPos to, int length, const CRef< objects::CSeq_id > seqid)

bool x_FindSegment(const objects::CDense_seg &denseg, objects::CDense_seg::TDim row, TSeqPos pos, objects::CDense_seg::TNumseg &seg, TSeqPos &seg_start) const

void x_AdjustCdregionFrame(CRef< objects::CSeq_feat > feat, int diff)

bool x_AdjustLocation(objects::CSeq_loc &loc, int length, int from, int to, int &diff)

void TrimSeqGraphs(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to, int length)

void x_RetranslateCDS(objects::CScope &scope, CRef< CCmdComposite > command, CRef< objects::CSeq_feat > cds, const objects::CSeq_feat &old_cds)

void x_AdjustInt(int &begin, int &end, int from, int to, int length, int &diff, objects::ENa_strand strand)

void x_CutDensegSegment(CRef< objects::CSeq_align > align, objects::CDense_seg::TDim row, TSeqPos pos)

void x_AdjustDensegAlignment(CRef< objects::CSeq_align > align, objects::CDense_seg::TDim row, TSeqPos cut_from, TSeqPos cut_to)

bool x_IsProtLocation(const objects::CSeq_loc &loc, objects::CBioseq_Handle bsh, objects::CScope &scope)

SeqMap related exceptions.

namespace ncbi::objects::

static const char si[8][64]

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.

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

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void SetPartialStart(bool val, ESeqLocExtremes ext)

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

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

EResult

This indicates what happened with the trim.

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.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

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

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetProduct(void) const

bool IsProtein(void) const

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

bool IsSetClass(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

bool IsSetData(void) const

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

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const string & GetTitle(void) const

bool IsSetTitle(void) const

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

const CSeq_loc & GetLoc(void) const

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

const CSeq_graph::C_Graph & GetGraph(void) const

CSeq_graph_Handle GetSeq_graph_Handle(void) const

Get original graph handle.

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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

Check if a string ends with a specified suffix value.

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.

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.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

E_Choice Which(void) const

Which variant is currently selected.

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.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

void SetDim(TDim value)

Assign a value to Dim data member.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

vector< CRef< CSeq_id > > TIds

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

const TClone & GetClone(void) const

Get the variant data.

bool IsSetData(void) const

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

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

Tdata & Set(void)

Assign a value to data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsClone(void) const

Check if variant Clone is selected.

bool IsVariation(void) const

Check if variant Variation is selected.

bool IsSet(void) const

Check if a value has been assigned to 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 IsRna(void) const

Check if variant Rna is selected.

bool IsSetCode_break(void) const

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

bool IsSetClone_seq(void) const

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

bool IsSetFrame(void) const

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

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

ENa_strand

strand of nucleic acid

TPoint GetPoint(void) const

Get the Point member data.

TFrom GetFrom(void) const

Get the From member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

bool IsNull(void) const

Check if variant Null is selected.

@ e_Equiv

equivalent sets of locations

void SetMin(TMin value)

Assign a value to Min data member.

TByte & SetByte(void)

Select the variant.

void SetNumval(TNumval value)

Assign a value to Numval data member.

TAxis GetAxis(void) const

Get the Axis member data.

TValues & SetValues(void)

Assign a value to Values data member.

TMax GetMax(void) const

Get the Max member data.

const TByte & GetByte(void) const

Get the variant data.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

bool CanGetLoc(void) const

Check if it is safe to call GetLoc method.

void SetMax(TMax value)

Assign a value to Max data member.

TMin GetMin(void) const

Get the Min member data.

const TValues & GetValues(void) const

Get the Values member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void Reset(void)

Reset the whole object.

@ eClass_nuc_prot

nuc acid and coded proteins

list< CRef< CSeq_id > > TId

const TInstance & GetInstance(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

TConsequence & SetConsequence(void)

Assign a value to Consequence data member.

const TDelta & GetDelta(void) const

Get the Delta member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetConsequence(void) const

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

const TData & GetData(void) const

Get the Data member data.

bool IsInstance(void) const

Check if variant Instance is selected.

bool IsSet(void) const

Check if variant Set is selected.

bool IsSetVariations(void) const

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

bool IsSetData(void) const

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

#define EDIT_EACH_CODEBREAK_ON_CDREGION(Itr, Var)

#define ERASE_CODEBREAK_ON_CDREGION(Itr, Var)

ERASE_CODEBREAK_ON_CDREGION.

#define row(bind, expected)

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

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