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NCBI C++ ToolKit: src/objects/seq/seq_align_mapper_base.cpp Source File

m_HaveStrands(

),

.m_IsSetStrand = is_set_strand;

.m_Strand = strand;

.m_IsSetStrand = is_set_strand;

.m_Strand = strand;

: m_LocMapper(loc_mapper),

m_HaveStrands(

),

m_ScoresInvalidated(

),

m_AlignFlags(eAlign_Normal)

: m_LocMapper(loc_mapper),

m_HaveStrands(

),

m_ScoresInvalidated(

),

m_AlignFlags(eAlign_Normal)

<

T,

C1,

C2>

(

C1, it, src) {

<

C1,

C2>

(

C1, it, src) {

CopyContainer<CSeq_align::TScore, TScores>(

TSegments::iterator ins_it =

dim = diag.

();

(dim != diag.

().size()) {

have_prot =

;

have_nuc =

;

CopyContainer<CDense_diag::TScores, TScores>(

(

= 0;

< dim; ++

) {

(have_prot && have_nuc) {

);

(numseg != denseg.

().size()) {

numseg =

(numseg, denseg.

().size());

CopyContainer<CDense_seg::TScores, TScores>(

have_nuc =

;

have_prot =

;

( seq_type ) {

(have_prot && have_nuc) {

);

((have_nuc || have_prot) && !unknown.

()) {

width = have_prot ? 3 : 1;

(

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

alnseg.

*= width;

seglens.reserve(sseg.size());

);

(minlen == 0 ||

== minlen) {

(maxlen == 0 ||

== maxlen) {

(minlen > maxlen) {

(minlen, maxlen);

);

(minlen != 0 && maxlen != 0) {

(minlen*3 != maxlen) {

);

(seqtype != newtype) {

);

seglens.push_back(maxlen == 0 ? -1 : maxlen);

dim = stdseg.

();

&& dim != stdseg.

().size()) {

dim =

(dim, stdseg.

().size());

seg_len = seglens[seg_idx++];

CopyContainer<CStd_seg::TScores, TScores>(

row_idx = 0;

);

have_strand =

;

( loc.

() ) {

);

(

> 0 &&

!= seg_len) {

(seg_len == -1 && seg.

== -1) {

);

(numseg != pseg.

().size()) {

numseg =

(numseg, pseg.

().size());

CopyContainer<CPacked_seg::TScores, TScores>(

(

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

have_nuc =

;

(have_nuc && seg_width == 3) {

);

alnseg.

*= seg_width;

CopyContainer<CScore_set::Tdata, TScores>(

prod_start, prod_end;

part_gen_start = gen_start;

gen_start += seg_len;

part_gen_start = gen_end;

part_prod_start = -1;

part_prod_start = prod_start;

prod_start += seg_len;

part_prod_start = prod_end;

*ex_prod_id, part_prod_start,

, ex_prod_strand);

seg_len = gen_end - gen_start;

( sparse.

().size() > 1) {

);

( sparse.

().empty() ) {

CopyContainer<CSparse_seg::TRow_scores, TScores>(

numseg =

.GetNumseg();

(numseg !=

.GetFirst_starts().size()) {

);

numseg =

(numseg,

.GetFirst_starts().size());

(numseg !=

.GetSecond_starts().size()) {

);

numseg =

(numseg,

.GetSecond_starts().size());

(numseg !=

.GetLens().size()) {

numseg =

(numseg,

.GetLens().size());

);

numseg =

(numseg,

.GetSecond_strands().size());

(width != second_width) {

);

(

.IsSetSeg_scores() ) {

CopyContainer<CSparse_align::TSeg_scores, TScores>(

(

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

.GetFirst_starts()[seg]*width,

.GetSecond_starts()[seg]*width,

( (*it)->m_ScoresInvalidated ) {

(*it)->Convert(

);

( (*it)->m_ScoresInvalidated ) {

(

row_idx = 0; row_idx <

; ++row_idx) {

TSegments::iterator seg_it =

.begin();

( ; seg_it !=

.end(); ) {

(seg_it->m_Rows.size() <=

) {

(dst_id && dst_id != seg_id &&

TSegments::iterator old_it = seg_it;

(id_it == idmap.

()) {

aln_row.

;

( rmap.

() ) {

aln_row.

;

vector< CRef<CMappingRange> > TSortedMappings;

TSortedMappings mappings;

( ; rg_it; ++rg_it) {

mappings.push_back(rg_it->second);

dst_id = mappings[0]->GetDstIdHandle();

(mappings.size() > 1) {

(TSortedMappings, it, mappings) {

((*it)->GetDstIdHandle() != dst_id) {

TSegments::iterator ins_point = seg_it;

mapped =

;

(

map_idx = 0; map_idx < mappings.size(); ++map_idx) {

(!mapping->CanMap(start, stop,

(mapping->m_Dst_id_Handle != dst_id) {

dst_id = mapping->m_Dst_id_Handle;

group_idx = mapping->m_Group;

dl = mapping->m_Src_from <= start ?

0 : mapping->m_Src_from - start;

= mapping->m_Src_to >= stop ?

0 : stop - mapping->m_Src_to;

);

(

= 0;

< seg.

.size(); ++

) {

lrow.

= dst_id;

stop -

- start + 1, seg.

.size(), src_reverse);

(

= 0;

< seg.

.size(); ++

) {

mapping->Map_Range(start, stop -

);

mapping->Map_Strand(

mrow.

= mapping->m_Dst_id_Handle;

left_shift += mseg.

;

start += mseg.

;

(start > stop)

;

seg.

[

].m_Id = rmap.

()->second->m_Dst_id_Handle;

(start <= stop) {

stop - start + 1, seg.

.size(), src_reverse);

(

= 0;

< seg.

.size(); ++

) {

rrow.

= dst_id;

max_rows =

.front().m_Rows.size();

(seg_it->m_Rows.size() > max_rows) {

max_rows = seg_it->m_Rows.size();

strands.reserve(max_rows);

(

r_idx = 0; r_idx < max_rows; r_idx++) {

(seg_it->m_Rows.size() <= r_idx)

;

(seg_it->m_Rows[r_idx].GetSegStart() != -1) {

strand = seg_it->m_Rows[r_idx].m_Strand;

);

.Reset(&

&

(*

->m_Id.GetSeqId()));

diag->SetIds().push_back(

);

diag->SetStarts().push_back(

->GetSegStart()/seq_width);

->m_Strand : strands[str_idx]);

diag->SetLen(seg_it->m_Len/len_width);

CloneContainer<CScore, TScores, CDense_diag::TScores>(

seg.

, diag->SetScores());

diags.push_back(diag);

CloneContainer<CScore, TScores, CDense_seg::TScores>(

(

= 0;

<

.front().m_Rows.size();

++) {

only_gaps =

;

.Reset(&

&

(*

.m_Id.GetSeqId()));

dseg.

().push_back(

);

);

dseg.

().push_back(seg_it->m_Len/len_width);

(len_width == 3) {

start =

->GetSegStart();

non_gap_count = 0;

set_frames =

;

vector< pair<TSeqPos, TSeqPos> > frames;

frames.reserve(

.size());

(seg_it->m_Rows.size() != 2) {

set_frames =

;

(r0_type == r1_type) {

set_frames =

;

set_frames =

;

start = seg_it->m_Rows[p_row].m_Start;

start_frame = start % 3;

stop_frame = (start + seg_it->m_Len) % 3;

stop_frame = 3 - stop_frame;

frames.push_back(pair<TSeqPos, TSeqPos>(start_frame, stop_frame));

std_seg->SetDim(

(seg_it->m_Rows.size()));

( !seg_it->m_Scores.empty() ) {

CloneContainer<CScore, TScores, CStd_seg::TScores>(

seg_it->m_Scores, std_seg->SetScores());

.Reset(&

&

(*

->m_Id.GetSeqId()));

std_seg->SetIds().push_back(

);

loc->

().SetId(*

);

stop = (

->m_Start + seg_it->m_Len)/width;

seg_it->m_Rows[1 - p_row];

start_frame = frames[seg_n].first;

stop_frame = frames[seg_n].second;

(start_frame, stop_frame);

( row_n == p_row ) {

(g_start < start_frame) {

std_seg->SetLoc().pop_back();

( start_frame ) {

(start >= start_frame) {

loc->

().SetFuzz_from().SetAlt().push_back(start);

start -= start_frame;

start += 3 - start_frame;

loc->

().SetFuzz_to().SetAlt().push_back(stop - 1);

loc->

().SetFrom(start);

loc->

().SetTo(stop > start ? stop - 1 : stop);

(

->m_IsSetStrand) {

loc->

().SetStrand(

->m_Strand);

std_seg->SetLoc().push_back(loc);

(seg_it ==

.begin() && non_gap_count < 2) {

( std_seg->GetLoc().empty() )

;

std_segs.push_back(std_seg);

(non_gap_count < 2 && !std_segs.empty()) {

std_segs.pop_back();

CloneContainer<CScore, TScores, CPacked_seg::TScores>(

(

= 0;

<

.front().m_Rows.size();

++) {

.Reset(&

&

(*

.m_Id.GetSeqId()));

pseg.

().push_back(

);

->m_Strand : strands[str_idx]);

pseg.

().push_back(seg_it->m_Len/len_width);

.push_back((*it)->GetDstAlign());

(last_part && last_part->Which() == part_type) {

sx_GetExonPartLength(*last_part) + part_len);

exon.

().push_back(last_part);

TSegments::const_iterator& seg,

& last_exon_partial,

partial_left =

;

partial_right =

;

(seg !=

.begin() && last_exon_partial) {

exon->SetPartial(

);

partial_left =

;

last_exon_partial =

;

prod_start = -1;

gstrand_set =

;

pstrand_set =

;

aln_protein =

;

mapped_gaps = 0;

non_gap_gen_start = 0;

non_gap_prod_start = 0;

non_gap_gen_end = 0;

non_gap_prod_end = 0;

have_non_gaps =

;

( ; seg !=

.end(); ++seg) {

(group_idx != -1 && seg->m_GroupIdx && seg->m_GroupIdx != group_idx) {

partial_right =

;

( seg->m_GroupIdx ) {

group_idx = seg->m_GroupIdx;

(seg->m_Rows.size() > 2) {

);

gend = gstart + seg->m_Len;

pend = pstart + seg->m_Len;

(gen_id != gen_row.

) {

gen_id = gen_row.

;

(prod_id != prod_row.

) {

prod_id = prod_row.

;

aln_protein =

;

);

gen_reverse =

;

prod_reverse =

;

( !gstrand_set ) {

gstrand_set =

;

(gen_strand != gen_row.

) {

);

( gstrand_set ) {

( !pstrand_set ) {

pstrand_set =

;

(prod_strand != prod_row.

) {

);

( pstrand_set ) {

last_exon_partial =

;

exon->SetPartial(

);

partial_right =

;

(prod_start >= 0 && prod_end > 0) {

(!prod_reverse) {

(pstart < prod_end) {

partial_right =

;

(pstart > prod_end) {

pins_len = pstart - prod_end;

(pend > prod_start) {

partial_right =

;

(pend < prod_start) {

pins_len = prod_start - pend;

(gen_start >= 0 && gen_end > 0) {

(gstart < gen_end) {

partial_right =

;

(gstart > gen_end) {

gins_len = gstart - gen_end;

(gend > gen_start) {

partial_right =

;

(gend < gen_start) {

gins_len = gen_start - gend;

(prod_start < 0 || prod_start > pstart) {

prod_start = pstart;

(prod_end < pend) {

(gen_start < 0 || gen_start > gstart) {

(gen_end < gend) {

( !exon->GetParts().empty() ) {

( !exon->GetParts().empty() ) {

have_non_gaps =

;

(!is_gap || !exon->GetParts().empty() || orig_ptype == ptype) {

old_size = exon->GetParts().size();

(is_gap && orig_ptype != ptype) {

mapped_gaps += exon->GetParts().size() - old_size;

non_gap_prod_start = prod_start;

non_gap_gen_start = gen_start;

non_gap_prod_end = prod_end;

non_gap_gen_end = gen_end;

( !gen_reverse ) {

gen_start += seg->m_Len;

gen_end -= seg->m_Len;

( !prod_reverse ) {

prod_start += seg->m_Len;

prod_end -= seg->m_Len;

(mapped_gaps > 0) {

(parts.size() >= mapped_gaps);

(; mapped_gaps > 0; mapped_gaps--) {

gen_start = non_gap_gen_start;

prod_start = non_gap_prod_start;

gen_end = non_gap_gen_end;

prod_end = non_gap_prod_end;

(!have_non_gaps || exon->GetParts().empty()) {

last_exon_partial =

;

(!spliced.

().empty()) {

exon->SetAcceptor_before_exon().Assign(

exon->SetDonor_after_exon().Assign(

exon->SetAcceptor_before_exon().Assign(

exon->SetDonor_after_exon().Assign(

(!gen_id && last_gen_id) {

gen_id = last_gen_id;

(!prod_id && last_prod_id) {

prod_id = last_prod_id;

exon->SetGenomic_start(gen_start);

exon->SetGenomic_end(gen_end - 1);

exon->SetGenomic_strand(gen_strand);

( aln_protein ) {

exon->SetProduct_start().SetProtpos().SetAmin(prod_start/3);

exon->SetProduct_start().SetProtpos().SetFrame(prod_start%3 + 1);

exon->SetProduct_end().SetProtpos().SetAmin((prod_end - 1)/3);

exon->SetProduct_end().SetProtpos().SetFrame((prod_end - 1)%3 + 1);

exon->SetProduct_start().SetNucpos(prod_start);

exon->SetProduct_end().SetNucpos(prod_end - 1);

exon->SetProduct_strand(prod_strand);

CloneContainer<CScore, TScores, CScore_set::Tdata>(

CloneContainer<CUser_object, CSpliced_exon::TExt, CSpliced_exon::TExt>(

spliced.

().push_back(exon);

& last_exon_partial,

& single_gen_id,

& single_gen_str,

& single_prod_id,

& single_prod_str,

& partial)

TSegments::const_iterator seg = sub_align.

.begin();

(seg != sub_align.

.end()) {

added_exon = sub_align.

(spliced, seg, ex_gen_id, ex_prod_id,

ex_gen_strand, ex_prod_strand, last_exon_partial,

last_gen_id, last_prod_id);

partial = partial || last_exon_partial;

last_gen_id = ex_gen_id;

single_gen_id &= gen_id == ex_gen_id;

prod_id = ex_prod_id;

single_prod_id &= prod_id == ex_prod_id;

(gen_strand == ex_gen_strand);

gen_strand = ex_gen_strand;

(prod_strand == ex_prod_strand);

prod_strand = ex_prod_strand;

single_gen_id =

;

single_gen_str =

;

single_prod_id =

;

single_prod_str =

;

partial =

;

last_exon_partial =

;

(gen_row, prod_row);

last_exon_partial, gen_id, last_gen_id, single_gen_id,

gen_strand, single_gen_str,

prod_id, last_prod_id, single_prod_id,

prod_strand, single_prod_str,

last_exon_partial, gen_id, last_gen_id, single_gen_id,

gen_strand, single_gen_str,

prod_id, last_prod_id, single_prod_id,

prod_strand, single_prod_str,

ex_gen_reverse =

;

ex_prod_reverse =

;

( exon->IsSetGenomic_strand() ) {

ex_gen_reverse =

(exon->GetGenomic_strand());

( exon->IsSetProduct_strand() ) {

ex_prod_reverse =

(exon->GetProduct_strand());

gen_start = exon->GetGenomic_start();

gen_end = exon->GetGenomic_end();

(exon->GetProduct_start().IsProtpos());

(exon->GetProduct_end().IsProtpos());

prod_start = exon->GetProduct_start().GetProtpos().GetAmin()*3

+ exon->GetProduct_start().GetProtpos().GetFrame() - 1;

prod_end = exon->GetProduct_end().GetProtpos().GetAmin()*3

+ exon->GetProduct_end().GetProtpos().GetFrame() - 1;

(exon->GetProduct_start().IsNucpos());

(exon->GetProduct_end().IsNucpos());

prod_start = exon->GetProduct_start().GetNucpos();

prod_end = exon->GetProduct_end().GetNucpos();

(

(exon->GetParts().front()->Which()) ) {

( ex_gen_reverse ) {

( ex_prod_reverse ) {

exon->SetParts().pop_front();

exon->SetGenomic_start(gen_start);

exon->SetGenomic_end(gen_end);

exon->SetProduct_start().SetProtpos().SetAmin(prod_start/3);

exon->SetProduct_start().SetProtpos().SetFrame(prod_start%3 + 1);

exon->SetProduct_end().SetProtpos().SetAmin(prod_end/3);

exon->SetProduct_end().SetProtpos().SetFrame(prod_end%3 + 1);

exon->SetProduct_start().SetNucpos(prod_start);

exon->SetProduct_end().SetNucpos(prod_end);

exon = spliced.

().back();

ex_gen_reverse =

;

ex_prod_reverse =

;

( exon->IsSetGenomic_strand() ) {

ex_gen_reverse =

(exon->GetGenomic_strand());

( exon->IsSetProduct_strand() ) {

ex_prod_reverse =

(exon->GetProduct_strand());

gen_start = exon->GetGenomic_start();

gen_end = exon->GetGenomic_end();

(exon->GetProduct_start().IsProtpos());

(exon->GetProduct_end().IsProtpos());

prod_start = exon->GetProduct_start().GetProtpos().GetAmin()*3

+ exon->GetProduct_start().GetProtpos().GetFrame() - 1;

prod_end = exon->GetProduct_end().GetProtpos().GetAmin()*3

+ exon->GetProduct_end().GetProtpos().GetFrame() - 1;

(exon->GetProduct_start().IsNucpos());

(exon->GetProduct_end().IsNucpos());

prod_start = exon->GetProduct_start().GetNucpos();

prod_end = exon->GetProduct_end().GetNucpos();

(

(exon->GetParts().back()->Which()) ) {

( ex_gen_reverse ) {

( ex_prod_reverse ) {

exon->SetParts().pop_back();

exon->SetGenomic_start(gen_start);

exon->SetGenomic_end(gen_end);

exon->SetProduct_start().SetProtpos().SetAmin(prod_start/3);

exon->SetProduct_start().SetProtpos().SetFrame(prod_start%3 + 1);

exon->SetProduct_end().SetProtpos().SetAmin(prod_end/3);

exon->SetProduct_end().SetProtpos().SetFrame(prod_end%3 + 1);

exon->SetProduct_start().SetNucpos(prod_start);

exon->SetProduct_end().SetNucpos(prod_end);

single_gen_id =

;

single_prod_id =

;

( single_gen_id ) {

( single_prod_id ) {

( mapped_it->

() ) {

mapped_it->

(**it);

.push_back(mapped_it);

( single_gen_id ) {

(*it)->ResetGenomic_id();

( gen_id && !(*it)->IsSetGenomic_id() ) {

( single_prod_id ) {

(*it)->ResetProduct_id();

( prod_id && !(*it)->IsSetProduct_id() ) {

(*it)->SetProduct_id(

&

(*prod_id.

()));

( single_gen_str ) {

(*it)->ResetGenomic_strand();

( single_prod_str ) {

(*it)->ResetProduct_strand();

(

.IsSetPoly_a() ) {

(

.IsSetProduct_length() ) {

(!partial &&

.IsSetModifiers()) {

CloneContainer<CScore, TScores, CSparse_seg::TRow_scores>(

sparse.

().push_back(aln);

(seg->m_Rows.size() > 2) {

);

(first_start < 0 || second_start < 0) {

(first_idh != first_row.

) {

);

first_idh = first_row.

;

(second_idh != second_row.

) {

);

second_idh = second_row.

;

first_width = first_prot ? 3 : 1;

second_width = second_prot ? 3 : 1;

len_width = (first_prot || second_prot) ? 3 : 1;

aln->SetFirst_starts().push_back(first_start/first_width);

aln->SetSecond_starts().push_back(second_start/second_width);

aln->SetLens().push_back(seg->m_Len/len_width);

(aln->IsSetSecond_strands() ||

(

= aln->SetSecond_strands().size();

< s;

++) {

aln->SetSecond_strands().push_back(

(first_strand)

? second_strand :

(second_strand));

(scores_group == -2) {

scores_group = seg->m_ScoresGroupIdx;

(scores_group != seg->m_ScoresGroupIdx) {

(scores_group >= 0) {

CloneContainer<CScore, TScores, CSparse_align::TSeg_scores>(

start_seg)

TSegments::const_iterator start_seg_it =

.begin();

(

s = 0; s < start_seg && start_seg_it !=

.end();

s++, start_seg_it++) {

(start_seg_it ==

.end()) {

num_rows = start_segment.

.size();

last_seg =

.size() - 1;

vector<CSeq_id_Handle> ids;

ids.resize(num_rows);

(

= 0;

< num_rows;

++) {

TSegments::const_iterator seg_it = start_seg_it;

seg_idx = start_seg;

( ; seg_idx <= last_seg && seg_it !=

.end();

seg_idx++, seg_it++) {

(seg_it->m_Rows.size() != num_rows) {

last_seg = seg_idx - 1;

(last_id && last_id !=

.m_Id) {

last_seg = seg_idx - 1;

last_id =

.m_Id;

ids[

] =

.m_Id;

seg_start =

.GetSegStart();

seg_stop = seg_start == -1 ? -1 : seg_start + seg_it->m_Len;

(seg_start != -1) {

(

.m_IsSetStrand ) {

strands[

] =

.m_Strand;

last_seg = seg_idx - 1;

(seg_stop > left) {

last_seg = seg_idx - 1;

(seg_start < right) {

last_seg = seg_idx - 1;

(last_seg >= start_seg);

(

= 0;

< num_rows;

++) {

dseg.

().push_back(

);

vector<size_t> segs_per_row(num_rows, 0);

non_empty_segs = 0;

cur_seg = start_seg;

(TSegments::const_iterator it = start_seg_it; it !=

.end();

(cur_seg > last_seg) {

only_gaps =

;

(

= 0;

< it->m_Rows.size();

++) {

segs_per_row[

]++;

(only_gaps)

;

dseg.

().push_back(it->m_Len/len_width);

start =

->GetSegStart();

(non_empty_segs == 0) {

(vector<size_t>,

, segs_per_row) {

last_seg + 1;

(!dseg)

;

.push_back(dseg);

have_prot =

;

have_nuc =

;

(have_prot && have_nuc)

;

(

= 0;

< seg->m_Rows.size(); ++

) {

(

>= strands.size()) {

(

.GetSegStart() == -1) {

(

.m_IsSetStrand ) {

strands[

] =

.m_Strand;

( !

.empty() ) {

(seg->m_Rows.size() < 2)

;

(++non_empty >= 2) {

( !(*sub)->x_IsEmpty() )

;

);

TSegments::iterator seg =

.begin();

vector<CSeq_id_Handle> row_ids;

( ; seg !=

.end(); ++seg) {

(row_ids.size() < seg->m_Rows.size()) {

row_ids.resize(seg->m_Rows.size());

(

= 0;

< seg->m_Rows.size();

++) {

row_ids[

] =

.m_Id;

( !row_ids[

] ) {

TSegments::iterator fwd = seg;

( ; fwd !=

.end(); ++fwd) {

(fwd->m_Rows.size() <=

)

;

row_ids[

] = fwd_row.

;

( row_ids[

] ) {

.m_Id = row_ids[

];

CloneContainer<CScore, TScores, CSeq_align::TScore>(

CloneContainer<CSeq_loc, CSeq_align::TBounds, CSeq_align::TBounds>(

CloneContainer<CObject_id, CSeq_align::TId, CSeq_align::TId>(

CloneContainer<CUser_object, CSeq_align::TExt, CSeq_align::TExt>(

row_ids.size() == 2 &&

( orig_choice ) {

unique_ptr<CSeq_align_Mapper_Base> sub(

sub->InitExon(spliced, exon);

sub.release();

(

.empty() || idx >=

.begin()->m_Rows.size() ) {

);

.begin()->m_Rows[idx].m_Id;

bool IsForward(ENa_strand s)

bool IsReverse(ENa_strand s)

ENa_strand Reverse(ENa_strand s)

bool SameOrientation(ENa_strand a, ENa_strand b)

Seq-loc and seq-align mapper exceptions.

Class used to map seq-alignments.

CSeq_loc_Mapper_Base & m_LocMapper

void x_PushExonPart(CRef< CSpliced_exon_chunk > &last_part, CSpliced_exon_chunk::E_Choice part_type, int part_len, CSpliced_exon &exon) const

void x_ConvToDstDisc(CRef< CSeq_align > &dst) const

CSeq_align::C_Segs::TDendiag TDendiag

void x_GetDstSparse(CRef< CSeq_align > &dst) const

CRef< CSeq_align > GetDstAlign(void) const

Create mapped alignment.

CSeq_align_Mapper_Base(const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper)

void Convert(void)

Map the whole alignment through the linked seq-loc mapper.

bool x_HaveMixedStrand(void) const

void x_InvalidateScores(SAlignment_Segment *seg=NULL)

void x_GetDstDenseg(CRef< CSeq_align > &dst) const

void x_GetDstDisc(CRef< CSeq_align > &dst) const

vector< CRef< CSeq_align_Mapper_Base > > TSubAligns

void x_FillKnownStrands(TStrands &strands) const

bool x_GetDstExon(CSpliced_seg &spliced, TSegments::const_iterator &seg, CSeq_id_Handle &gen_id, CSeq_id_Handle &prod_id, ENa_strand &gen_strand, ENa_strand &prod_strand, bool &last_exon_partial, const CSeq_id_Handle &last_gen_id, const CSeq_id_Handle &last_prod_id) const

SAlignment_Segment & x_InsertSeg(TSegments::iterator &where, int len, size_t dim, bool reverse)

void InitExon(const CSpliced_seg &spliced, const CSpliced_exon &exon)

bool x_IsEmpty(void) const

void x_ConvertRow(size_t row)

bool x_HaveMixedSeqTypes(void) const

void x_GetDstDendiag(CRef< CSeq_align > &dst) const

CConstRef< CSpliced_exon > m_OrigExon

vector< ENa_strand > TStrands

CRef< CSeq_align > m_DstAlign

~CSeq_align_Mapper_Base(void)

void x_GetDstSplicedSubAlign(CSpliced_seg &spliced, const CSeq_align_Mapper_Base &sub_align, bool &last_exon_partial, CSeq_id_Handle &gen_id, CSeq_id_Handle &last_gen_id, bool &single_gen_id, ENa_strand &gen_strand, bool &single_gen_str, CSeq_id_Handle &prod_id, CSeq_id_Handle &last_prod_id, bool &single_prod_id, ENa_strand &prod_strand, bool &single_prod_str, bool &partial) const

void x_ConvertAlign(size_t *row)

void x_GetDstStd(CRef< CSeq_align > &dst) const

CConstRef< CSeq_align > m_OrigAlign

TScoresGroups m_GroupScores

CSeq_align::C_Segs::TStd TStd

ssize_t x_GetPartialDenseg(CRef< CSeq_align > &dst, size_t start_seg) const

void x_Init(const CSeq_align &align)

const CSeq_id_Handle & GetRowId(size_t idx) const

Get seq-id for the given row.

virtual CSeq_align_Mapper_Base * CreateSubAlign(const CSeq_align &align)

void x_GetDstPacked(CRef< CSeq_align > &dst) const

void x_GetDstSpliced(CRef< CSeq_align > &dst) const

CSeq_id_Handle x_ConvertSegment(TSegments::iterator &seg_it, size_t row)

SAlignment_Segment & x_PushSeg(int len, size_t dim, ENa_strand strand=eNa_strand_unknown)

list< SAlignment_Segment > TSegments

CSeq_loc_Mapper_Base –.

CSpliced_seg_modifier –.

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const char * bounds[]

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.

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 ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

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

Set object to copy of another one.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

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

const CSeq_id * GetId(void) const

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

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

ESeqType GetSeqTypeById(const CSeq_id_Handle &idh) const

Methods for getting sequence types, use cached types (m_SeqTypes) if possible.

const TIdMap & GetIdMap() const

void SetSeqTypeById(const CSeq_id_Handle &idh, ESeqType seqtype) const

Methods for setting sequence types.

bool x_IsSetMiscFlag(EMiscFlags flag) const

static TSeqPos sx_GetExonPartLength(const CSpliced_exon_chunk &part)

CRef< CMappingRanges > m_Mappings

const CSeq_id_Handle & x_GetPrimaryId(const CSeq_id_Handle &synonym) const

TIdMap::const_iterator TIdIterator

void x_AdjustSeqTypesToProt(const CSeq_id_Handle &idh)

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

const_iterator begin(void) const

#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.

TFrom GetFrom(void) const

Get the From member data.

const TScores & GetScores(void) const

Get the Scores member data.

bool IsSetProduct_strand(void) const

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

const TDonor_after_exon & GetDonor_after_exon(void) const

Get the Donor_after_exon member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TId & GetId(void) const

Get the Id member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

TModifiers & SetModifiers(void)

Assign a value to Modifiers data member.

TId & SetId(void)

Assign a value to Id data member.

bool IsSetProduct_type(void) const

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

TScore & SetScore(void)

Assign a value to Score data member.

vector< CRef< CSeq_loc > > TLoc

const TScores & GetScores(void) const

Get the Scores member data.

TRow_scores & SetRow_scores(void)

Assign a value to Row_scores data member.

bool IsProtpos(void) const

Check if variant Protpos is selected.

E_Choice

Choice variants.

TLens & SetLens(void)

Assign a value to Lens data member.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsSetBounds(void) const

regions of sequence over which align was computed Check if a value has been assigned to Bounds data m...

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetParts(void) const

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

list< CRef< CStd_seg > > TStd

TPresent & SetPresent(void)

Assign a value to Present data member.

bool IsSetId(void) const

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

bool IsSetStrands(void) const

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

TProduct_ins & SetProduct_ins(void)

Select the variant.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

E_Choice

Choice variants.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

bool IsSetProduct_strand(void) const

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TDim GetDim(void) const

Get the Dim member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

bool IsSetScores(void) const

score for each seg Check if a value has been assigned to Scores data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

const TAcceptor_before_exon & GetAcceptor_before_exon(void) const

Get the Acceptor_before_exon member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

TDiag & SetDiag(void)

Select the variant.

bool IsSetAcceptor_before_exon(void) const

splice sites Check if a value has been assigned to Acceptor_before_exon data member.

TExons & SetExons(void)

Assign a value to Exons data member.

void SetProduct_strand(TProduct_strand value)

Assign a value to Product_strand data member.

const TIds & GetIds(void) const

Get the Ids member data.

TScores & SetScores(void)

Assign a value to Scores data member.

TScores & SetScores(void)

Assign a value to Scores data member.

bool IsSetScores(void) const

score for each segment Check if a value has been assigned to Scores data member.

TNumseg GetNumseg(void) const

Get the Numseg member data.

void SetProduct_length(TProduct_length value)

Assign a value to Product_length data member.

TLen GetLen(void) const

Get the Len member data.

void SetDim(TDim value)

Assign a value to Dim data member.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TRows & SetRows(void)

Assign a value to Rows data member.

void SetDim(TDim value)

Assign a value to Dim data member.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool IsSetStrands(void) const

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

void SetDim(TDim value)

Assign a value to Dim data member.

bool IsSetGenomic_strand(void) const

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_str...

const TScores & GetScores(void) const

Get the Scores member data.

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

void SetType(TType value)

Assign a value to Type data member.

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

void ResetDonor_after_exon(void)

Reset Donor_after_exon data member.

TMismatch & SetMismatch(void)

Select the variant.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

const TSpliced & GetSpliced(void) const

Get the variant data.

bool IsSetIds(void) const

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

TIds & SetIds(void)

Assign a value to Ids data member.

TDim GetDim(void) const

Get the Dim member data.

list< CRef< CSpliced_seg_modifier > > TModifiers

const TLens & GetLens(void) const

Get the Lens member data.

list< CRef< CSeq_loc > > TBounds

bool IsGenomic_ins(void) const

Check if variant Genomic_ins is selected.

const TPacked & GetPacked(void) const

Get the variant data.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

TExt & SetExt(void)

Assign a value to Ext data member.

bool IsSetScores(void) const

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

bool IsSetGenomic_strand(void) const

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

const TStd & GetStd(void) const

Get the variant data.

const TScores & GetScores(void) const

Get the Scores member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TIds & GetIds(void) const

Get the Ids member data.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

void SetPoly_a(TPoly_a value)

Assign a value to Poly_a data member.

TDim GetDim(void) const

Get the Dim member data.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TDendiag & GetDendiag(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool IsSetStrands(void) const

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

const TPresent & GetPresent(void) const

Get the Present member data.

TGenomic_ins & SetGenomic_ins(void)

Select the variant.

void ResetAcceptor_before_exon(void)

Reset Acceptor_before_exon data member.

TType GetType(void) const

Get the Type member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

TParts & SetParts(void)

Assign a value to Parts data member.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TRow_scores & GetRow_scores(void) const

Get the Row_scores member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

list< CRef< CSpliced_exon_chunk > > TParts

TMatch & SetMatch(void)

Select the variant.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetGenomic_strand(TGenomic_strand value)

Assign a value to Genomic_strand data member.

bool IsSpliced(void) const

Check if variant Spliced is selected.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

list< CRef< CSeq_align > > Tdata

const TSparse & GetSparse(void) const

Get the variant data.

TIds & SetIds(void)

Assign a value to Ids data member.

bool IsSetGenomic_id(void) const

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

bool IsProduct_ins(void) const

Check if variant Product_ins is selected.

const TScore & GetScore(void) const

Get the Score member data.

TBounds & SetBounds(void)

Assign a value to Bounds data member.

TDim GetDim(void) const

Get the Dim member data.

const TScores & GetScores(void) const

Get the Scores member data.

const TRows & GetRows(void) const

Get the Rows member data.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

const TDisc & GetDisc(void) const

Get the variant data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

TStrands & SetStrands(void)

Assign a value to Strands data member.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsSetScores(void) const

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

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsSetDonor_after_exon(void) const

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

bool IsSetRow_scores(void) const

per-row scores Check if a value has been assigned to Row_scores data member.

TLens & SetLens(void)

Assign a value to Lens data member.

const TBounds & GetBounds(void) const

Get the Bounds member data.

bool IsSetGenomic_id(void) const

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

bool IsSetScores(void) const

scores for this exon Check if a value has been assigned to Scores data member.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_not_set

No variant selected.

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

@ eType_partial

mapping pieces together

@ eProduct_type_transcript

ENa_strand

strand of nucleic acid

const TPnt & GetPnt(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrand(void) const

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

bool IsSetStrand(void) const

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

bool IsWhole(void) const

Check if variant Whole is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

@ e_Empty

to NULL one Seq-id in a collection

unsigned int

A callback function used to compare two keys in a database.

Definition of all error codes used in objects libraries.

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

constexpr auto sort(_Init &&init)

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

bool IsExonGap(CSpliced_exon_chunk::E_Choice chunk_type)

void CopyContainer(const C1 &src, C2 &dst)

void SetPartLength(CSpliced_exon_chunk &part, CSpliced_exon_chunk::E_Choice ptype, TSeqPos len)

void CloneContainer(const C1 &src, C2 &dst)

#define row(bind, expected)

Single row of a single alignment segment.

ENa_strand m_Strand

Strand value.

TSeqPos m_Start

kInvalidSeqPos means gap

CSeq_id_Handle m_Id

Row's seq-id.

int GetSegStart(void) const

Get segment start or -1 if it's a gap.

bool m_IsSetStrand

Is strand set for the row?

bool SameStrand(const SAlignment_Row &r) const

Check if the query row has the same strand orientation.

bool m_Mapped

Flag indicating mapped rows.

void SetMapped(void)

Mark the row as mapped.

Structure to hold information about a single alignment segment.

vector< SAlignment_Row > TRows

TRows m_Rows

Segment rows.

SAlignment_Row & CopyRow(size_t idx, const SAlignment_Row &src_row)

Create a copy of the given row, store is to this segment as row number 'idx'.

TScores m_Scores

Scores for this segment.

ssize_t m_ScoresGroupIdx

Group of scores.

bool m_HaveStrands

Do at least some rows have strand set?

int m_Len

Segment length.

SAlignment_Row & GetRow(size_t idx)

Get row data with the given index.

SAlignment_Row & AddRow(size_t idx, const CSeq_id &id, int start, bool is_set_strand, ENa_strand strand)

Add new row.

int m_GroupIdx

Group of segments (e.g.

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