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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/graphread_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/readers/sra/graphread.cpp Source File

use_vdb_index =

(VDBGRAPH, USE_VDB_INDEX)::GetDefault();

!use_vdb_index;

another_vdb =

;

<<path,

last_row = curs->m_Cursor.GetMaxRowId();

(

<<

);

( *seq_id ==

.m_SeqId ) {

.m_SeqLength = start +

;

( !

.m_SeqId.empty() ) {

.m_SeqId = *seq_id;

( !

.m_SeqId.empty() ) {

.m_RowLast = last_row;

.m_SeqId = *seq_id;

.m_RowSize = *curs->LEN(

);

( range.second > 1 ) {

+= range.second-1;

ret = curs->m_GR_ZOOM_Q100;

*iter->second;

curs =

();

(

.

() ) {

.m_RowFirst = first_row;

first_len = *curs->LEN(first_row);

.m_RowSize = first_len;

(first_row == range.first);

( range.second > 1 ) {

last_row = first_row + range.second - 1;

.m_RowLast = last_row;

last_len = *curs->LEN(last_row);

.m_SeqLength = last_start + last_len;

.m_RowLast = first_row;

.m_SeqLength = first_start + first_len;

*iter->second;

* text_id = seq_id->GetTextseq_Id();

curs =

();

( !range.second ) {

first_row = range.first;

.m_Seq_id_Handle = idh;

.m_RowFirst = first_row;

first_len = *curs->LEN(first_row);

.m_RowSize = first_len;

( range.second > 1 ) {

last_row = first_row + range.second - 1;

.m_RowLast = last_row;

last_len = *curs->LEN(last_row);

.m_SeqLength = last_start + last_len;

.m_RowLast = first_row;

.m_SeqLength = first_start + first_len;

);

<

DstVector,

SrcVector>

(DstVector& dst,

SrcVector& src)

dst.reserve(src.size());

(

SrcVector, it, src ) {

( !annot_name.empty() ) {

TValue kMinIntValue =

;

TValue kMaxIntValue =

;

TValue kMinByteValue = 0;

TValue kMaxByteValue =

;

(

index = pos%row_size/step;

++index, pos += step ) {

TValue v = values[index];

switch_to_real =

;

switch_to_real = v < kMinIntValue;

switch_to_real = v > kMaxIntValue;

( switch_to_real && int_vv ) {

real_graph = &graph->

().SetReal();

int_vv->push_back(

(v));

real_vv->push_back(

(v));

pos < (

-

.m_RowFirst+1)*row_size ) {

);

( min_v >= kMinByteValue && max_v <= kMaxByteValue ) {

numval = int_vv->size();

byte_graph->SetAxis(0);

byte_graph->SetMin(

(min_v));

byte_graph->SetMax(

(max_v));

(byte_graph->SetValues(), *int_vv);

graph->

().SetByte(*byte_graph);

( real_graph ) {

numval = real_vv->size();

real_graph->

(

(min_v));

real_graph->

(

(max_v));

numval = int_vv->size();

int_graph->

(

(min_v));

int_graph->

(

(max_v));

graph->

(1./scale);

( numval >

(

) ) {

);

TValue kMinIntValue =

;

TValue kMaxIntValue =

;

TValue min_v = 0, max_v = 0;

( ; pos < range.

(); ++

, pos += row_size ) {

TValue v = vv_arr[off+

];

->SetFeat_type(0);

->SetColumns().push_back(col_id);

col_id->

().SetField_name(

);

->SetColumns().push_back(col_id);

->SetColumns().push_back(col_pos);

->SetColumns().push_back(col_span);

col_span->

().SetField_name(

);

->SetColumns().push_back(col_val);

col_val->

().SetField_name(

);

TValue cur_v = vv[0];

( min_v < kMinIntValue || max_v > kMaxIntValue ) {

arr_pos.push_back(cur_i+range.

());

arr_span.push_back(

-cur_i);

arr_vv.push_back(

(cur_v));

arr_pos.push_back(cur_i+range.

());

arr_span.push_back(

-cur_i);

arr_vv.push_back(

(cur_v));

arr_pos.push_back(cur_i+range.

());

arr_span.push_back(

-cur_i);

arr_vv.push_back(

(cur_v));

arr_pos.push_back(cur_i+range.

());

arr_span.push_back(

-cur_i);

arr_vv.push_back(

(cur_v));

->SetColumns().push_back(col_step);

col_step->

().SetField_name(

);

( arr_pos.size() >

(

) ) {

);

->SetNum_rows(

(arr_pos.size()));

( !cursor.m_NUM_SWITCHES ) {

TValue kMinIntValue =

;

TValue kMaxIntValue =

;

TValue kMinByteValue = 0;

TValue kMaxByteValue =

;

TValue min_v = 0, max_v = 0;

( ; pos < range.

(); ++

, pos += row_size ) {

switches += *cursor.NUM_SWITCHES(

.m_RowFirst+

);

TValue v = cursor.GR_Q100(

.m_RowFirst+

);

table_value_size =

min_v < kMinIntValue || max_v > kMaxIntValue?

(double):

(

);

graph_value_size =

min_v < kMinByteValue || max_v > kMaxByteValue? table_value_size: 1;

(table_value_size+2*

(

))*switches;

graph_value_size*values;

table_size < graph_size;

( range.

() ) {

seq_table_is_smaller;

& annot_name,

( range0.

() ) {

( !annot_name.empty() ) {

annot->

().Set().push_back(desc);

);

obj.

().SetStr(

);

obj.

(

,

(step));

obj.

(

,

);

annot->

().Set().push_back(desc);

( !(content &

) ) {

step, *curs, curs->m_GR_Q0 , 0);

step, *curs, curs->m_GR_Q10 , 10);

step, *curs, curs->m_GR_Q50 , 50);

step, *curs, curs->m_GR_Q90 , 90);

step, *curs, curs->m_GR_Q100, 100);

annot->

().SetGraph().push_back(graph);

);

obj.

().SetStr(

);

obj.

(

,

(step));

obj.

(

,

);

annot->

().Set().push_back(desc);

( !(content &

) ) {

step, *curs, curs->m_GR_ZOOM_Q0 , 0);

step, *curs, curs->m_GR_ZOOM_Q10 , 10);

step, *curs, curs->m_GR_ZOOM_Q50 , 50);

step, *curs, curs->m_GR_ZOOM_Q90 , 90);

step, *curs, curs->m_GR_ZOOM_Q100, 100);

annot->

().SetGraph().push_back(graph);

as_table =

;

obj.

().SetStr(

);

obj.

(

,

);

annot->

().Set().push_back(desc);

1, *curs, curs->m_GRAPH, -1);

annot->

().SetGraph().push_back(graph);

@ eNotFoundTable

DB table not found.

virtual TErrCode GetErrCode(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

CVDBTableIndex m_LookupIndex

CRef< SGraphTableCursor > Graph(void)

bool HasMidZoomGraphs(void)

CVDBObjectCache< SGraphTableCursor > m_Graph

TSeqInfoMapBySeq_id m_SeqMapBySeq_id

CVDBGraphDb_Impl(CVDBMgr &mgr, CTempString path, ELookupType lookup_type=eLookupDefault)

SSeqInfo GetSeqInfoAtRow(TVDBRowId row)

void Put(CRef< SGraphTableCursor > &curs)

bool LookupIsInMemory() const

SSeqInfo GetSeqInfo(const CSeq_id_Handle &seq_id)

TSeqInfoMapByFirstRow m_SeqMapByFirstRow

const CVDBTable & GraphTable(void)

virtual ~CVDBGraphDb_Impl(void)

list< SSeqInfo > TSeqInfoList

CVDBGraphDb_Impl::SSeqInfo m_Info

bool x_SeqTableIsSmaller(COpenRange< TSeqPos > range, SGraphTableCursor &cursor) const

CVDBGraphDb_Impl & GetDb(void) const

bool SeqTableIsSmaller(COpenRange< TSeqPos > range) const

CRef< CSeq_graph > x_MakeGraph(const string &annot_name, CSeq_loc &loc, const SSeqInfo &info, const COpenRange< TSeqPos > &range, TSeqPos step, SGraphTableCursor &cursor, CVDBColumn &column, int level) const

CVDBGraphSeqIterator & operator++(void)

CRef< CSeq_table > x_MakeTable(const string &annot_name, CSeq_loc &loc, const SSeqInfo &info, const COpenRange< TSeqPos > &range, SGraphTableCursor &cursor) const

CVDBGraphSeqIterator(void)

CRef< CSeq_annot > GetAnnot(COpenRange< TSeqPos > range, const string &annot_name=kEmptyStr, TContentFlags content=fDefaultContent) const

const SSeqInfo & GetInfo(void) const

TVDBRowIdRange Find(const string &value) const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

The NCBI C++ standard methods for dealing with std::string.

static const char * column

NCBI_DEFINE_ERR_SUBCODE_X(1)

NCBI_PARAM_DECL(bool, VDBGRAPH, USE_VDB_INDEX)

static void sx_Assign(DstVector &dst, const SrcVector &src)

NCBI_PARAM_DEF_EX(bool, VDBGRAPH, USE_VDB_INDEX, true, eParam_NoThread, VDBGRAPH_USE_VDB_INDEX)

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.

#define ERR_POST(message)

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

#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)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

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.

TObjectType & GetNCObject(void) const

Get object.

#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

TThisType & SetFrom(position_type from)

position_type GetTo(void) const

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

position_type GetFrom(void) const

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

Convert int 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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

void SetType(TType &value)

Assign a value to Type data member.

void SetHeader(THeader &value)

Assign a value to Header data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetDefault(TDefault &value)

Assign a value to Default data member.

@ eField_id_location_id

location Seq-id

@ eField_id_location_from

interval from

bool IsSetAccession(void) const

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

TVersion GetVersion(void) const

Get the Version member data.

bool IsSetRelease(void) const

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

bool IsSetVersion(void) const

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

bool IsSetName(void) const

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

const TAccession & GetAccession(void) const

Get the Accession member data.

void SetA(TA value)

Assign a value to A data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

TValues & SetValues(void)

Assign a value to Values data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void SetNumval(TNumval value)

Assign a value to Numval data member.

void SetComp(TComp value)

Assign a value to Comp data member.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetMin(TMin value)

Assign a value to Min data member.

void SetMin(TMin value)

Assign a value to Min data member.

TValues & SetValues(void)

Assign a value to Values data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TName & SetName(void)

Select the variant.

bool IsSetData(void) const

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

TUser & SetUser(void)

Select the variant.

unsigned int

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

Definition of all error codes used in SRA C++ support libraries.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

constexpr bool empty(list< Ts... >) noexcept

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

#define NCBI_THROW2_FMT(exception_class, err_code, message, extra)

#define row(bind, expected)

SGraphTableCursor(const CVDBTable &table)

#define INIT_VDB_COLUMN(name)

pair< TVDBRowId, TVDBRowCount > TVDBRowIdRange

#define INIT_OPTIONAL_VDB_COLUMN(name)

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