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NCBI C++ ToolKit: src/algo/align/util/patch_sequence.cpp Source File

list< CRef<CSeq_align> > singleton_list;

singleton_list.push_back(alignment);

);

->SetLoc().Assign(loc);

(gap_size > tail) {

);

CDelta_ext::Tdata::const_iterator delta_it =

(; current_pos < loc_start+patch_boundary; ++delta_it) {

current_pos += (*delta_it)->IsLiteral()

? (*delta_it)->GetLiteral().GetLength()

: (*delta_it)->GetLoc().GetTotalRange().GetLength();

(!is_right_tail || current_pos > loc_start+patch_boundary) {

((*delta_it)->IsLiteral()

&& (*delta_it)->GetLiteral().GetSeq_data().IsGap())

(current_pos == loc_start+patch_boundary) {

inserted_gap = *delta_it;

inserted_gap->GetLiteral().GetLength();

patch_boundary += previous_gap_size;

patch_boundary -= previous_gap_size;

length_change -= previous_gap_size

- inserted_gap->GetLiteral().GetLength();

);

+

(current_pos > loc_start+patch_boundary) {

length_change -= current_pos - loc_start - patch_boundary;

current_pos -= (*delta_it)->GetLoc().GetTotalRange().GetLength();

length_change -= loc_start + patch_boundary - current_pos;

patch_boundary = current_pos-loc_start;

inserted_gap->SetLiteral().SetLength(50000);

inserted_gap->SetLiteral().SetSeq_data().SetGap()

inserted_gap->SetLiteral().SetSeq_data().SetGap()

length_change += 50000;

);

);

);

(!old_alignment) {

old_alignment = alignment;

<<

<< (*it2)->GetSeqStart(1)

<<

<< (*it2)->GetSeqStop(1));

total_covered += covered_range;

);

old_alignment = alignment;

TCoverMap::const_iterator next_patch = cover_map.begin();

current_pos = 0, next_pos = 0;

((*it)->IsLiteral()) {

next_pos += (*it)->GetLiteral().GetLength() + next_gap_change;

(next_pos > next_patch->first.GetFrom()) {

+ next_patch->second->GetSeq_id(0).AsFastaString()

);

target_loc.

((*it)->GetLoc());

current_pos = next_pos;

(; next_patch != cover_map.end() &&

next_pos > next_patch->first.GetFrom(); ++next_patch)

(!patch_sequence) {

aligned_patch_range = next_patch->second->GetSeqRange(0);

(aligned_patch_range.

() < patch_length)

);

);

((*seg_it)->GetSeqStrand(1) != patch_strand) {

pair<TSeqPos,TSeqPos> patch_tail(

aligned_patch_range.

(),

patch_length - aligned_patch_range.

());

temp = patch_tail.first;

patch_tail.first = patch_tail.second;

patch_tail.second = temp;

unaligned_left_length =

next_patch->first.GetFrom() - current_pos;

(unaligned_left_length) {

(patch_tail.first) {

);

unaligned_left_length,

patch_tail.first, inserted_gap,

length_change,

);

patched_contents.insert(it,

patched_contents.insert(it, inserted_gap);

}

(patch_tail.first) {

(it == patched_contents.begin() ||

!(*--it)->IsLiteral() ||

!(*it)->GetLiteral().GetSeq_data().IsGap())

+

);

(*it)->GetLiteral().GetLength();

length_change -= previous_gap_size

- (*it)->GetLiteral().GetLength();

(next_pos < next_patch->

.GetToOpen()) {

it = patched_contents.erase(it);

current_pos = next_pos;

next_pos += (*it)->IsLiteral()

? (*it)->GetLiteral().GetLength()

: (*it)->GetLoc().GetTotalRange().GetLength();

(!(*it)->IsLoc()) {

+

);

target_loc.

((*it)->GetLoc());

it = patched_contents.erase(it);

length_change -= next_patch->first.GetLength();

(*patch_id, 0, patch_length-1, patch_strand));

inserted_patch->SetLoc(*patch_loc);

patched_contents.insert(it, inserted_patch);

length_change += patch_length;

next_patch->first.GetToOpen() - current_pos;

(current_pos + length_to_replace < next_pos) {

(patch_tail.second) {

);

patch_tail.second, inserted_gap,

length_change,

);

patched_contents.insert(it, inserted_gap);

target_loc.

(scaffold_remainder->GetLoc());

patched_contents.insert(it, scaffold_remainder);

}

(patch_tail.second) {

(it == patched_contents.end() ||

!(*it)->IsLiteral() ||

!(*it)->GetLiteral().GetSeq_data().IsGap())

+

);

(*it)->GetLiteral().GetLength();

length_change -= next_gap_change =

previous_gap_size - (*it)->GetLiteral().GetLength();

current_pos += length_to_replace;

}

(exception &e) {

<<

<< e.what() <<

);

list< CRef<CSeq_align> > new_alignments;

(*align_it != next_patch->second) {

new_alignments.push_back(*align_it);

(new_alignments.empty()) {

(next_patch == cover_map.end()) {

(patched_seq->

() && length_change) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

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 IntersectingWith(const TRange &r) const

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

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

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.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

void Info(CExceptionArgs_Base &args)

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.

string AsString(void) const

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.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

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

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,...

@ 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.

bool CanGetInst_Repr(void) const

TSeqPos GetBioseqLength(void) const

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

TInst_Repr GetInst_Repr(void) const

const TInst & GetInst(void) const

void Reset(void)

Reset reference object.

position_type GetLength(void) const

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

TFrom GetFrom(void) const

Get the From member data.

bool IsDisc(void) const

Check if variant Disc is selected.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

TFrom GetFrom(void) const

Get the From member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsInt(void) const

Check if variant Int is selected.

void SetLength(TLength value)

Assign a value to Length data member.

const TGap & GetGap(void) const

Get the variant data.

void SetExt(TExt &value)

Assign a value to Ext data member.

TType GetType(void) const

Get the Type member data.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ eRepr_delta

sequence made by changes (delta) to others

@ eType_clone

Deprecated. Used only for AGP 1.1.

static set< CSeq_id_Handle > s_NovelPatches

static void s_ProcessIntraScaffoldTail(CBioseq_Handle patch_sequence, CBioseq_Handle scaffold, TSeqPos loc_start, TSeqPos &patch_boundary, TSeqPos tail_length, CRef< CDelta_seq > &inserted_gap, TSignedSeqPos &length_change, bool is_right_tail)

void AddNovelPatch(const CSeq_id_Handle &idh)

static CRef< CDelta_seq > s_SubLocDeltaSeq(const CSeq_loc &loc, TSeqPos start, TSeqPos length=0)

static void s_SubtractTail(CSeq_literal &gap, TSeqPos tail)

CRef< CSeq_inst > PatchTargetSequence(CRef< CSeq_align > alignment, CScope &scope)

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