RetroSearch Browse

) {

74 #define NCBI_USE_ERRCODE_X SNPReader 80 #define RC_NO_MORE_ALIGNMENTS RC(rcApp, rcQuery, rcSearching, rcRow, rcNotFound) 329 bool

another_vdb_table =

false

;

334

another_vdb_table =

true

;

339 if

( another_vdb_table ) {

343 "Cannot open VDB: "

<<path_or_acc,

359 for

(

size_t i

= 0;

< track_count; ++

) {

362 info

.m_Name = *cur.NAME(

);

364 info

.m_Filter.m_Filter = *cur.BITS(

);

365 info

.m_Filter.m_FilterMask = *cur.MASK(

);

368 if

( track_count == 0 ) {

387 size_t

seq_count = cur->m_Cursor.GetMaxRowId();

390 for

(

size_t i

= 0;

< seq_count; ++

) {

396 info

.m_SeqLength = *cur->LEN(

);

397 info

.m_Circular =

false

;

410 for

(

TVDBRowId row

= 1, max_row = cur->m_Cursor.GetMaxRowId();

411 row

<= max_row; ++

) {

417 if

( !

.m_PageSets.empty() ) {

425 info

.m_PageSets.push_back(pset);

436 if

( !

.m_SeqLength ) {

439 info

.m_GraphRowId = graph_row;

441

graph_row += pages * track_count;

470

CSNPDb_Impl::TTrackInfoList::const_iterator

483

CSNPDb_Impl::TSeqInfoList::const_iterator

486 string

prefix = accession+

'.'

;

491 if

( !range.second ) {

500 if

( !range.second ) {

503 size_t

index = size_t(range.first-1);

507

TSeqInfoList::const_iterator iter =

m_SeqList

.begin()+index;

513

CSNPDb_Impl::TSeqInfoList::const_iterator

519 if

( text_id->IsSetAccession() && text_id->IsSetVersion() &&

520

!text_id->IsSetName() && !text_id->IsSetRelease() ) {

521 return FindSeq

(text_id->GetAccession(), text_id->GetVersion());

540 if

( seq->GetMainSeq_id() ) {

546 size_t

seq_index = seq-

m_SeqList

.begin();

548 if

(

.m_Seq_id ) {

562 info

.m_SeqLength = *cur->LEN(seq_row);

563 info

.m_Circular =

false

;

572 TVDBRowId

max_row = cur->m_Cursor.GetMaxRowId();

580

max_row = iter->second;

585

row_before = slot.second;

590 while

( row_before+1 <

) {

592 if

( *cur->SEQ_ID_ROW_NUM(mid_row) < seq_row ) {

593

row_before = mid_row;

601 info

.m_PageSets.clear();

602 for

( ;

<= max_row; ++

) {

603 if

( *cur->SEQ_ID_ROW_NUM(

) != seq_row ) {

611 if

( !

.m_PageSets.empty() ) {

619 info

.m_PageSets.push_back(pset);

627 if

( !

.m_SeqLength ) {

634 info

.m_Seq_id = seq_id;

643 "Sequence index is out of bounds: "

646 return

seq->GetPageVDBRowRange();

652

TTrackInfoList::const_iterator track)

656 "Sequence index is out of bounds: "

661 "Filter track index is out of bounds: "

678

m_Iter(GetList().begin())

689 "Track index is out of bounds: "

690

db->GetDbPath()<<

"."

<<track_index);

699

m_Iter(db->FindTrack(name))

708 "CSNPDbTrackIterator is invalid"

);

717 m_Iter

= TList::const_iterator();

728

m_Iter(db->GetSeqInfoList().begin()),

729

m_TrackIter(db->GetTrackInfoList().begin())

740 if

( seq_index >= db->m_SeqList.size() ) {

742 "Sequence index is out of bounds: "

743

db->GetDbPath()<<

"."

<<seq_index);

746 m_Iter

= db->m_SeqList.begin()+seq_index;

757

m_Iter(db.GetNCObject().FindSeq(seq_id)),

758

m_TrackIter(db->GetTrackInfoList().begin())

764 const string

& accession,

767

m_Iter(db.GetNCObject().FindSeq(accession,

version

)),

768

m_TrackIter(db->GetTrackInfoList().begin())

783 "CSNPDbSeqIterator is invalid"

);

791 m_Iter

= CSNPDb_Impl::TSeqInfoList::const_iterator();

792 m_TrackIter

= CSNPDb_Impl::TTrackInfoList::const_iterator();

825

end += *cur->FEATURE_ROWS_COUNT(row_ids.

GetTo

());

860 return

unsigned(v>>32)+unsigned(v);

867 char

* dst = os.data();

868 for

(

int i

= 0;

< 8; ++

) {

869

dst[

] = char(

data

>>(8*

));

883 return

pos - pos%step;

966 auto

& gr = graph.

().SetByte();

970 count

= gr.GetValues().size();

973 auto

& gr = graph.

().SetInt();

977 count

= gr.GetValues().size();

1016 auto

& vv = graph.

().SetByte().SetValues();

1017

vv.resize(vv.size() +

);

1020 auto

& vv = graph.

().SetInt().SetValues();

1021

vv.resize(vv.size() +

);

1041 auto

& vv = graph.

().SetByte().SetValues();

1042

vv.insert(vv.end(), values, values+

);

1047 auto

& old_vv = old_data->GetValues();

1048 auto

& vv = graph.

().SetInt().SetValues();

1049 const Uint1

reinterpret_cast<const Uint1

>

(old_vv.data());

1050

vv.assign(

+old_vv.size());

1052 auto

& vv = graph.

().SetInt().SetValues();

1053

vv.insert(vv.end(), values, values+

);

1073 while

(

&& *values == 0 ) {

1078 if

( empty_before ) {

1089 if

( empty_after ) {

1137 g

.AddValue(it.GetTotalValue());

1160 if

( !it.GetTotalValue() ) {

1166 g

.AddValues(

, values.

data

()+skip_beg);

1177

TFlags

)

const 1183 return g

.FinishGraph();

1189 const string

& annot_name,

1190

TFlags

)

const 1197

annot->

SetData

().SetGraph().swap(

.FinishAnnot());

1204

TFlags

)

const 1215 return g

.FinishGraph();

1221 const string

& annot_name,

1222

TFlags

)

const 1227

annot->

SetData

().SetGraph().swap(

.FinishAnnot());

1234

TFlags

)

const 1243

TFlags

)

const 1250

feats.push_back(it.GetSeq_feat());

1252 if

( feats.empty() ) {

1261

TFlags

)

const 1271 const char

* name = 0)

1304 const char

= 0)

1311 const char

= 0)

1382

col->

SetData

().ChangeToInt8();

1409 for

(

int i

= 0;

size

; ++

) {

1426 size_t

sparse_size =

column

.values->size();

1437

to = (*

column

.values)[j++];

1440

to = (*backup_column.

values

)[

];

1442

values.push_back(to);

1456 typedef

unordered_map<CTempString, int>

TIndex

;

1467 const char

= 0)

1482

TIndex::const_iterator it =

index

.find(

);

1483 if

( it ==

index

.end() ) {

1519 const char

= 0)

1533

pair<TIndex::iterator, bool> ins =

1536

ins.first->second =

values

->size();

1537

vector<char>*

data

new

vector<char>();

1541 auto

value_index = ins.first->second;

1544 "CSNPDbSeqIterator: common bytes table is too big"

);

1546 indexes

->push_back(

int

(value_index));

1591 const string

value

)

1595 table

.SetColumns().push_back(col);

1604 table

.SetColumns().push_back(col);

1613 table

.SetColumns().push_back(col);

1622 table

.SetColumns().push_back(col);

1656 for

(

size_t i

= 0;

< range.second; ++

) {

1695

total_to += max_len-1;

1698

total_loc->

SetInt

().SetId(seq_id);

1699

total_loc->

SetInt

().SetFrom(total_from);

1700

total_loc->

SetInt

().SetTo(total_to);

1702 "Seq-table location"

1706 "Sorted, max length"

1749

vector< CRef<CSeq_annot> >

GetAnnots

(

const string

& annot_name);

1762

vector< CRef<CSeq_annot> >

1765

vector< CRef<CSeq_annot> > ret;

1766 for

(

int

k = 0; k < 2; ++k ) {

1771

ret.push_back(annot);

1787 size_t

last_index = range.second - 1;

1814 const string

& annot_name,

1816

TFlags

)

const 1832

TFlags

)

const 1840 const string

& annot_name,

1841

TFlags

)

const 1849

TFlags

)

const 1879

m_SearchMode(eSearchByOverlap)

1889

: m_SeqIter(db, ref_id)

1900

: m_SeqIter(db, ref_id)

1902 Select

(range, search_mode);

1911 Select

(range, search_mode);

1924 if

(

this

!= &iter ) {

2010 "CSNPDbPageIterator::"

<<method<<

"(): " 2011 "Invalid iterator state"

);

2017 x_CheckValid

(

"CSNPDbPageIterator::GetFirstFeatRowId"

);

2046

: m_CurrPageRowId(0),

2068 if

(

this

!= &iter ) {

2097 if

( !iter || ref_range.

Empty

() ) {

2136 "CSNPDbGraphIterator::"

<<method<<

"(): " 2137 "Invalid iterator state"

);

2150 x_CheckValid

(

"CSNPDbGraphIterator::GetCoverageValues"

);

2195 while

( first < max_row && *m_Feat->SEQ_ID_ROW_NUM(

first

) < seq_row ) {

2219

: m_PageIter(db, ref_id, ref_pos, window, sel.m_SearchMode)

2231

: m_PageIter(db, ref_id, range, sel.m_SearchMode)

2242

: m_PageIter(seq, range, sel.m_SearchMode)

2259 if

(

this

!= &iter ) {

2300 Uint8

best_bits_count = 0;

2301

CSNPDb_Impl::TTrackInfoList::const_iterator best_track;

2313 if

( bits_count > best_bits_count ) {

2314

best_bits_count = bits_count;

2318 if

( best_bits_count ) {

2396 if

( ref_len == 0 ) {

2398 if

( ref_pos > 0 ) {

2403 TSeqPos

ref_end = ref_pos + ref_len;

2452 "CSNPDbFeatIterator::"

<<method<<

"(): " 2453 "Invalid iterator state"

);

2459 x_CheckValid

(

"CSNPDbFeatIterator::GetFeatIdPrefix"

);

2473 x_CheckValid

(

"CSNPDbFeatIterator::x_GetExtraRange"

);

2490 _ASSERT

(index < range.second);

2491 return

m_Extra

->RS_ALLELE(range.first + index);

2508 template

size_t

ValueSize>

2512 return str

.size() == ValueSize-1 &&

str

value

;

2515 #define x_SetStringConstant(obj, Field, value) \ 2516 if ( !(obj).NCBI_NAME2(IsSet,Field)() || \ 2517 !x_IsStringConstant((obj).NCBI_NAME2(Get,Field)(), value) ) { \ 2518 (obj).NCBI_NAME2(Set,Field)((value)); \ 2527 if

( !ptr || !ptr->ReferencedOnlyOnce() ) {

2548 #define ALLELE_CACHE 2578 if

(

.size() == 1 ) {

2579 switch

(

[0] ) {

2588 if

(

.size() == 0 ) {

2659

quals.assign(range.second,

null

);

2660 for

(

size_t i

= 0;

< range.second; ++

) {

2686

dbtag.

SetTag

().SetId8(feat_id);

2696 if

(

& ext_flags ) {

2707 "VariationClass"

));

2743 template

class

Values>

2748 if

( values[

] ) {

2756 template

class

TValues>

2762 TSeqPos

dst_ind = pos_index / bit_values;

2764 if

(

TSeqPos

first_offset = pos_index % bit_values ) {

2765 TSeqPos

first_count = bit_values - first_offset;

2766 if

( !bits[dst_ind] ) {

2770

src_ind += first_count;

2772 while

( src_ind < values.

size

() ) {

2773 if

( !bits[dst_ind] ) {

2774

bits[dst_ind] =

sx_HasNonZero

(values, src_ind, bit_values);

2777

src_ind += bit_values;

2798 sx_AddBits2

(bits, bit_values, pos_index, values);

2803 sx_AddBits2

(bits, bit_values, pos_index, values);

2817 Uint8

feat_per_page = total_feat_count/page_count+1;

2832 template

class

Cont>

2833 typename

Cont::value_type::TObjectType&

sx_AddNew

(Cont& cont)

2835 typename Cont::value_type

obj(

new typename

Cont::value_type::TObjectType);

2836

cont.push_back(obj);

2844

obj.

SetType

().SetStr(

"AnnotationTrack"

);

2845

obj.

AddField

(

"ZoomLevel"

, zoom_level);

2850

CSNPDbSeqIterator::TFlags

2851 const string

& annot_name,

2867

TFlags

)

const 2883 for

(

auto

: annot->GetData().GetGraph() ) {

2888

annots.push_back(annot);

2902

annots.push_back(annot);

2912

annots.push_back(annot);

2922

TFlags