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NCBI C++ ToolKit: src/objects/seqalign/Dense_seg.cpp Source File

);

num =

(numrows) * numsegs;

(starts.size() != num) {

);

(lens.size() !=

(numsegs)) {

);

(strands.size() && strands.size() != num) {

);

(widths.size() && widths.size() !=

(numrows)) {

);

);

(row < 0 || row >= dim) {

);

pos = (seg - 1) * dim +

;

((start = starts[pos]) >= 0) {

(++seg < numseg) {

((start = starts[pos]) >= 0) {

(row < 0 || row >= dim) {

);

(++seg < numseg) {

((start = starts[pos]) >= 0) {

start +

()[seg] - 1;

pos = (seg - 1) * dim +

;

((start = starts[pos]) >= 0) {

start +

()[seg] - 1;

& strands_size =

().size();

( !strands_size ) {

(strands_size < (

) dim) {

);

(row < 0 || row >= dim) {

);

= numrows * (numsegs -1);

strands_exist = !strands.empty();

numseg = 0, numrow = 0,

= 0;

(numrow = 0; numrow < numrows; numrow++) {

= strands_exist ?

(numseg = 0; numseg < numsegs; numseg++) {

start = starts[

+ numrow];

(start < min_start) {

errstr =

(

)

+

numsegs - 1 - numseg) +

lens[

? numseg : numsegs - 1 - numseg] *

(widths.size() == numrows ?

(min_start == -1) {

errstr =

(

)

list<TSignedSeqRange> delete_ranges;

(j = 0; j <

(); ++j) {

(this_start == -1) {

(

() - count_gaps > 1) {

(j = 0; j <

(); ++j) {

(this_start == -1) {

(

() - count_gaps > 1) {

list<TSignedSeqRange>::reverse_iterator iter = delete_ranges.rbegin();

list<TSignedSeqRange>::reverse_iterator end = delete_ranges.rend();

( ; iter != end; ++iter) {

(

.GetLength() == 0) {

vector<bool> can_merge(

() - 1,

);

merge_count = 0;

(j = 0; j <

(); ++j) {

( (this_start == -1 && next_start != -1)

|| (this_start != -1 && next_start == -1) ) {

can_merge[

] =

;

(this_start != -1 && next_start != -1) {

(this_start + seg_len != next_start) {

can_merge[

] =

;

can_merge[

] =

;

(can_merge[

]) {

(merge_count == 0) {

new_lens.reserve(

() - merge_count);

(

> 0 && can_merge[

- 1]) {

(j = 0; j <

(); ++j) {

new_starts[new_starts.size() -

() + j] =

new_lens.push_back(

()[

]);

(j = 0; j <

(); ++j) {

swaps_made =

;

curr_gap =

, next_gap =

;

curr_seq_row =

()+1, next_seq_row =

()+1;

(

j=0; j <

(); ++j) {

curr_seq_row =

(curr_seq_row, j);

next_seq_row =

(next_seq_row, j);

(!(curr_gap & next_gap))

(next_seq_row < curr_seq_row) {

(

j=0; j <

(); ++j) {

}

(swaps_made);

vector<bool>

(numseg,

);

remove_count = 0;

(

= 0;

< numseg; ++

) {

(j = 0; j < dim; ++j) {

(remove_count == 0) {

new_starts.reserve((numseg - remove_count) * dim);

new_lens.reserve(numseg - remove_count);

new_strands.reserve((numseg - remove_count) * dim);

(

= 0;

< numseg; ++

) {

new_lens.push_back(

()[

]);

(j = 0; j < dim; ++j) {

new_starts.push_back(

()[

* dim + j]);

new_strands.push_back(

()[

* dim + j]);

CDense_seg::TLens::iterator

=

().begin();

CDense_seg::TLens::iterator

=

().end();

(*(

++), *(--

));

(starts[

+

], starts[

+

]);

(row1 >=

() || row1 < 0 ||

row2 >=

() || row2 < 0) {

);

(

= 0;

< idxStop;

+=

()) {

(

= 0;

< idxStop;

+=

()) {

(seg = 0; seg <

() && !found; ++seg) {

(pos >= start && pos < start +

) {

+

(row < 0 || row >=

()) {

);

);

(startOffset, stopOffset);

(startSeg, stopSeg);

start += startOffset;

(seg == startSeg) {

(seg == stopSeg) {

new_ds->

(

(rows.size()));

new_ds->

().reserve(rows.size());

(*row < 0 || *row >= dim) {

new_ds->

().push_back(id_copy);

(

segnum = 0; segnum < numseg; ++segnum) {

idx = segnum * dim + *

;

(

== 0)

;

++seg, pos +=

()) {

);

++seg, pos +=

()) {

}

(++seq_loc_i);

(ttl_loc_len < row_stop + 1) {

errstr(

);

errstr +=

;

errstr +=

;

errstr +=

;

idx = loc_plus ?

: (numsegs - 1) * numrows +

;

seg = loc_plus ? 0 : numsegs - 1;

(loc_plus ? seg <

() : seg >= 0) {

(starts[idx] == -1) {

idx += numrows; seg++;

idx -= numrows; seg--;

((loc_plus == row_plus ?

starts[idx] : ttl_loc_len - starts[idx] - lens[seg])

> len_so_far + loc_len) {

);

(loc_plus == row_plus) {

()[idx] += start - len_so_far;

start - len_so_far + ttl_loc_len - starts[idx] - lens[seg];

(lens[seg] >

) {

);

(loc_plus ? seg : seg + 1),

()[loc_plus ? seg + 1 : seg] = len_diff;

temp_starts(numrows, -1);

(

row_i = 0, tmp_idx = seg * numrows;

row_i < numrows; ++row_i, ++tmp_idx) {

(this_start != -1) {

temp_starts[row_i] = this_start;

(

== row_i) {

temp_starts[row_i] = start;

temp_starts[row_i] +=

;

this_start += len_diff;

len_so_far += loc_len;

(loc_plus ? seg + 1 : seg) * numrows,

temp_starts.begin(), temp_starts.end());

(strands.size()) {

strands.begin(), strands.begin() + numrows);

((len_diff = lens[seg] -

) > 0) {

idx += numrows; seg++;

idx -= numrows; seg--;

idx += numrows; seg++;

idx -= numrows; seg--;

( !ignore_strand ) {

(loc_plus != row_plus) {

(!strands.size()) {

(seg = 0, idx =

;

seg <

(); seg++, idx += numrows) {

strands_exist = !strands.empty();

vector<TNumseg> extra_segs;

new_ds->

(numrows);

new_numsegs = numsegs;

new_ids.resize(numrows);

new_ids[

] = id;

vector<TSignedSeqPos> expected_positions;

expected_positions.resize(numrows, -1);

.resize(numrows,

);

(strands_exist) {

idx = 0, new_idx = 0, extra_idx = 0;

(seg = 0; seg < numsegs; seg++) {

(expected_pos >= 0) {

extra_len = start - expected_pos;

extra_len = expected_pos - start -

;

(extra_len < 0) {

errstr(

);

errstr +=

;

}

(extra_len > 0) {

extra_segs.push_back(seg);

extra_lens.push_back(extra_len);

extra_starts.resize(extra_idx + numrows, -1);

extra_starts[extra_idx +

] =

extra_idx += numrows;

expected_pos = start +

;

expected_pos = start;

new_numsegs = numsegs + extra_numsegs;

new_lens.resize(numsegs + extra_numsegs);

new_starts.resize(numrows * new_numsegs);

(seg = 0, new_seg = 0, extra_seg = 0,

idx = 0, new_idx = 0, extra_idx = 0;

(extra_numsegs) {

( ; size_t(extra_seg) < extra_segs.size() && extra_segs[extra_seg] == seg; ++new_seg, ++extra_seg) {

new_lens[new_seg] = extra_lens[extra_seg];

(

= 0;

< numrows; ++

, ++new_idx, ++extra_idx) {

new_starts[new_idx] = extra_starts[extra_idx];

new_lens[new_seg] = lens[seg];

new_starts[new_idx++] = starts[idx++];

(strands_exist) {

(new_seg = 0; new_seg < new_numsegs; new_seg++) {

(

= 0;

< numrows;

++, new_idx++) {

& transcript )

query_strand_specific =

subj_strand_specific =

(!query_strand_specific || !subj_strand_specific) {

string::const_iterator ib = transcript.begin();

string::const_iterator ie = transcript.end();

string::const_iterator ii = ib;

seg_type;

* badsymerr =

;

c = ii != ie ? *ii++ : 0;

(c ==

|| c ==

) {

(c ==

) {

(c ==

) {

);

(

((

) c)) {

(seg_type == 0 && (c ==

|| c ==

)) {

(seg_type == 1 && c ==

) {

(seg_type == 2 && c ==

) {

starts.push_back(seg_type == 1? (

)-1: query_start + query_close);

strands.push_back(query_strand);

starts.push_back(seg_type == 2? (

)-1: subj_start + subj_close);

strands.push_back(subj_strand);

0: seg_len = pos1 - start1;

;

1: seg_len = pos2 - start2;

;

2: seg_len = pos1 - start1;

;

lens.push_back(seg_len);

(c ==

|| c ==

){

(c ==

) {

(c ==

) {

(!

((

) c)) {

);

(ii < ie &&

((

)(*ii))) {

= 10*

+ *ii -

;

0: pos1 +=

; pos2 +=

;

;

1: pos2 +=

;

;

2: pos1 +=

;

;

starts.push_back(seg_type == 1? (

)-1: query_start + query_close);

strands.push_back(query_strand);

starts.push_back(seg_type == 2? (

)-1: subj_start + subj_close);

strands.push_back(subj_strand);

0: seg_len = pos1 - start1;

;

1: seg_len = pos2 - start2;

;

2: seg_len = pos1 - start1;

;

lens.push_back(seg_len);

+

(

seg = 0; seg <

(); seg++) {

(

(start) < from) {

(start +

> to) {

);

ret->

(to - 1);

(plus_len >= minus_len*2) {

(plus_len*2 < minus_len) {

ds.

().reserve(numseg);

( bad_alloc&

) {

( bad_alloc&

) {

DefaultRead(

, member);

.FindMember(

);

x_GetMember().SetLocalReadHook(

, hook);

x_GetMember().SetGlobalReadHook(hook);

( bad_alloc&

) {

DefaultRead(

, member);

.FindMember(

);

x_GetMember().SetLocalReadHook(

, hook);

x_GetMember().SetGlobalReadHook(hook);

( bad_alloc&

) {

DefaultRead(

, member);

.FindMember(

);

x_GetMember().SetLocalReadHook(

, hook);

x_GetMember().SetGlobalReadHook(hook);

#define ASSERT_CONSISTENCY()

NCBI_PARAM_DECL(bool, OBJECTS, DENSE_SEG_RESERVE)

NCBI_PARAM_DEF_EX(bool, OBJECTS, DENSE_SEG_RESERVE, true, eParam_NoThread, OBJECTS_DENSE_SEG_RESERVE)

bool IsReverse(ENa_strand s)

static char * s_Reserve(size_t size, CSimpleBufferT< char > &buffer)

static void SetHook(CObjectIStream &in)

static void SetGlobalHook(void)

static CObjectTypeInfoMI x_GetMember(void)

void ReadClassMember(CObjectIStream &in, const CObjectInfoMI &member)

This method will be called at approriate time when the object of requested type is to be read.

void ReadClassMember(CObjectIStream &in, const CObjectInfoMI &member)

This method will be called at approriate time when the object of requested type is to be read.

static void SetHook(CObjectIStream &in)

static void SetGlobalHook(void)

static CObjectTypeInfoMI x_GetMember(void)

static void SetHook(CObjectIStream &in)

void ReadClassMember(CObjectIStream &in, const CObjectInfoMI &member)

This method will be called at approriate time when the object of requested type is to be read.

static CObjectTypeInfoMI x_GetMember(void)

static void SetGlobalHook(void)

virtual void PreReadClassMember(CObjectIStream &in, const CObjectInfoMI &member)

Return true to invoke default reading method afterwards.

void TrimEndGaps()

Trim leading/training gaps if possible.

CRef< CDense_seg > ExtractRows(const vector< TDim > &rows) const

Extract specified rows of the alignment, in specified order.

const CSeq_id & GetSeq_id(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

CRef< CSeq_interval > CreateRowSeq_interval(TDim row) const

TSeqPos GetSeqStop(TDim row) const

void Reverse(void)

Reverse the segments' orientation.

static void SetGlobalReserveHooks(void)

void OffsetRow(TDim row, TSignedSeqPos offset)

Offset row's coords.

void RemovePureGapSegs()

Remove any segments in which every row has a gap (these can arise when ExtractRows is used)

TNumseg CheckNumSegs(void) const

void SwapRows(TDim row1, TDim row2)

Swap two rows (changing *order*, not content)

TSeqPos GetSeqStart(TDim row) const

void OrderAdjacentGaps()

Order adjacent gaps, so that the side with sequence is in row-decending order.

void FromTranscript(TSeqPos query_start, ENa_strand query_strand, TSeqPos subj_start, ENa_strand subj_strand, const string &transcript)

Initialize from pairwise alignment transcript (a string representation produced by CNWAligner)

CRef< CDense_seg > ExtractSlice(TDim row, TSeqPos from, TSeqPos to) const

Extract a slice of the alignment that includes the specified range.

TDim CheckNumRows(void) const

TNumseg x_FindSegment(TDim row, TSignedSeqPos pos) const

CRef< CDense_seg > FillUnaligned() const

Create a new dense-seg with added all unaligned pieces (implicit inserts), if any,...

void Compact()

Join adjacent mergeable segments to create a more compact alignment.

void Validate(bool full_test=false) const

void RemapToLoc(TDim row, const CSeq_loc &loc, bool ignore_strand=false)

static void SetReserveHooks(CObjectIStream &in)

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

overloaded Assign()

const TWidths & GetWidths(void) const

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

Base class for all serializable objects.

static const char si[8][64]

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

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

ESerialRecursionMode

How to assign and compare child sub-objects of serial objects.

C & SerialAssign(C &dest, const C &src, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

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

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

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

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

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

static C * Get(const CTypesIterator &it)

TMemberIndex GetMemberIndex(void) const

Get index of the member in the class.

const CObjectInfo & GetClassObject(void) const

Get containing class data.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

position_type GetLength(void) const

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to 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.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetLens(void) const

lengths in ids order within segs Check if a value has been assigned to Lens data member.

TLens & SetLens(void)

Assign a value to Lens data member.

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.

vector< ENa_strand > TStrands

TDim & SetDim(void)

Assign a value to Dim data member.

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

void SetDim(TDim value)

Assign a value to Dim data member.

vector< CRef< CSeq_id > > TIds

TDim GetDim(void) const

Get the Dim member data.

TNumseg & SetNumseg(void)

Assign a value to Numseg data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool IsSetStarts(void) const

start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStrands(void) const

Check if it is safe to call GetStrands 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.

bool IsSetIds(void) const

sequences in order Check if a value has been assigned to Ids data member.

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsWhole(void) const

Check if variant Whole is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

@ eNa_strand_both

in forward orientation

const struct ncbi::grid::netcache::search::fields::SIZE size

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define row(bind, expected)

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