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NCBI C++ ToolKit: src/objmgr/seq_table_info.cpp Source File

);

( !ret && force ) {

( !ret && force ) {

( !ret && force ) {

( !ret && force ) {

(

.GetValueType() ) {

(

.GetValueType() ) {

(

.GetValueType() ) {

(

.TryGetValue(index, value_int) ) {

setter.

(loc, value_int);

(

.TryGetValue(index, value_int8) ) {

setter.

(loc, value_int8);

(

.TryGetValue(index, value_real) ) {

setter.

(loc, value_real);

(

* ptr =

.GetStringPtr(index) ) {

(

.GetValueType() ) {

(

.TryGetValue(index, value_int) ) {

setter.

(feat, value_int);

(

.TryGetValue(index, value_int8) ) {

setter.

(feat, value_int8);

(

.TryGetValue(index, value_real) ) {

setter.

(feat, value_real);

(

* ptr =

.GetStringPtr(index) ) {

(

vector<char>* ptr =

.GetBytesPtr(index) ) {

m_Is_real_loc(

),

m_Is_simple(

),

m_Is_probably_simple(

),

m_Is_simple_point(

),

m_Is_simple_interval(

),

m_Is_simple_whole(

)

(

.IsSetField_id() ) {

( !

.IsSetField_name() ) {

( extra ==

|| extra ==

) {

( extra ==

) {

( extra ==

||

( extra ==

||

extra ==

) {

( extra ==

) {

point.

().SetGi(gi);

interval.

().SetGi(gi);

interval.

(to);

it->first.UpdateSeq_loc(loc,

, *it->second);

( it->first.IsSet(

) ) {

( !

.IsSetFeat_type() ||

(

.IsSetFeat_subtype() &&

: m_IsFeatTable(is_feat),

: m_IsFeatTable(IsGoodFeatTable(feat_table)),

(

.IsSetField_id() ) {

=

.GetField_id();

name =

.GetNameForId(

);

( !name.empty() ) {

(

.IsSetField_name() ) {

name =

.GetField_name();

=

.GetIdForName(name);

( name ==

) {

(

);

(

);

(

.IsSetField_id() ) {

=

.GetField_id();

);

( !

.IsSetField_name() ) {

(8,

<<

);

( !

.IsSetField_name() ) {

);

( !setter &&

.IsSetField_name() ) {

( name.

() ) {

(10,

);

( name[0] ==

) {

( name[0] ==

) {

( name[0] ==

) {

( name ==

) {

);

( name ==

) {

);

( name ==

) {

( name ==

) {

(

);

(

);

(

.IsSetFeat_subtype() ) {

seq_feat->

();

it->first.UpdateSeq_feat(feat,

, *it->second);

( !name.empty() && name[0] ==

) {

( !name.empty() && name[0] ==

) {

<< name.substr(2);

* value_ptr = c.first.GetStringPtr(index);

( value_ptr && !value_ptr->empty() ) {

<<

<< *value_ptr;

( name ==

) {

vector<char>* bytes = c.first.GetBytesPtr(index);

( !bytes || bytes->size() != 8 ) {

bits = *

*

(bytes->data());

&iter->second;

&iter->second;

<<field_id<<

);

<<field_name<<

);

bool IsForward(ENa_strand s)

bool IsReverse(ENa_strand s)

Annotation iterators exceptions.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

void UpdateSeq_loc(CSeq_loc &loc, size_t row, const CSeqTableSetLocField &setter) const

void UpdateSeq_feat(CSeq_feat &feat, size_t row, const CSeqTableSetFeatField &setter) const

bool GetValue(size_t row, Value &v, bool force=false) const

CConstRef< CSeq_loc > GetSeq_loc(size_t row, bool force=false) const

const vector< char > * GetBytesPtr(size_t row, bool force=false) const

bool x_ThrowUnsetValue(void) const

const string * GetStringPtr(size_t row, bool force=false) const

CConstRef< CSeq_id > GetSeq_id(size_t row, bool force=false) const

CConstRef< CSeqTable_column > m_Column

bool IsSingular(void) const

CSeqTableInfo(const CSeq_table &feat_table, bool is_feat)

static bool IsGoodFeatTable(const CSeq_table &table)

string GetLabel(size_t row) const

bool HasLabel(size_t row) const

bool IsFeatTable(void) const

TColumnsById m_ColumnsById

bool MatchBitFilter(const SAnnotSelector &sel, size_t row) const

CSeqTableLocColumns m_Location

bool x_IsSorted(void) const

TColumnsByName m_ColumnsByName

void UpdateSeq_feat(size_t row, CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const

CSeqTableColumnInfo m_Partial

SAnnotTypeSelector GetType(void) const

CConstRef< CSeq_table > m_Seq_table

vector< TColumnInfo > TExtraColumns

const CSeqTableColumnInfo * FindColumn(int field_id) const

CSeqTableLocColumns m_Product

CConstRef< CSeq_loc > m_TableLocation

TSeqPos m_SortedMaxLength

CSeqTableColumnInfo m_Disabled

TSeqPos GetSortedMaxLength(void) const

TExtraColumns m_ExtraColumns

CConstRef< CSeq_loc > GetTableLocation(void) const

void x_Initialize(const CSeq_table &table)

const CSeqTableColumnInfo & GetColumn(int field_id) const

pair< CSeqTableColumnInfo, CConstRef< TSetter > > TColumnInfo

void AddExtraColumn(const CSeqTable_column &column, const CSeqTableSetLocField *setter)

CSeqTableColumnInfo m_Loc

ENa_strand GetStrand(size_t row) const

CSeqTable_column_info::EField_id m_BaseValue

TSeqPos GetFrom(size_t row) const

CSeq_id_Handle m_DefaultIdHandle

CConstRef< CSeq_id > GetId(size_t row) const

void SetTableKeyAndIndex(size_t row, SAnnotObject_Key &key, SAnnotObject_Index &index) const

CSeq_id_Handle GetIdHandle(size_t row) const

bool m_Is_probably_simple

vector< TColumnInfo > TExtraColumns

bool IsRealLoc(void) const

void UpdateSeq_loc(size_t row, CRef< CSeq_loc > &seq_loc, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const

CSeqTableColumnInfo m_From

pair< CSeqTableColumnInfo, CConstRef< TSetter > > TColumnInfo

TExtraColumns m_ExtraColumns

CSeqTableLocColumns(const char *field_name, CSeqTable_column_info::EField_id base_value)

CConstRef< CSeq_loc > GetLoc(size_t row) const

void SetColumn(CSeqTableColumnInfo &field, const CSeqTable_column &column)

bool AddColumn(const CSeqTable_column &column)

bool m_Is_simple_interval

CRange< TSeqPos > GetRange(size_t row) const

CSeqTableColumnInfo m_Strand

virtual void SetString(CSeq_feat &feat, const string &value) const

virtual void SetInt8(CSeq_feat &feat, Int8 value) const

virtual void SetBytes(CSeq_feat &feat, const vector< char > &value) const

virtual void SetReal(CSeq_feat &feat, double value) const

virtual void SetInt(CSeq_feat &feat, int value) const

virtual void SetInt8(CSeq_loc &loc, Int8 value) const

virtual void SetInt(CSeq_loc &loc, int value) const

virtual void SetReal(CSeq_loc &loc, double value) const

virtual void SetString(CSeq_loc &loc, const string &value) const

const vector< char > * GetBytesPtr(size_t row) const

const string * GetStringPtr(size_t row) const

CConstRef< CSeq_id > GetSeq_id(size_t row) const

CConstRef< CSeq_loc > GetSeq_loc(size_t row) const

bool IsSet(size_t row) const

void GetValue(bool &v) const

static const size_t kSkipped

size_t GetIndexAt(size_t row) const

namespace ncbi::objects::

TSeqPos GetLength(void) const

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

container_type::const_iterator const_iterator

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

static const char * str(char *buf, int n)

static const char * column

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#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.

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

TBitFilter GetFilterMask(void) const

TBitFilter GetFilterBits(void) const

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

static TThisType GetWhole(void)

#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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type size(void) const

Return the length of the represented array.

const TDefault & GetDefault(void) const

Get the Default member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

EField_id

identification of the column data in the objects described by the table known column data types posit...

const TSparse_other & GetSparse_other(void) const

Get the Sparse_other member data.

const TSparse & GetSparse(void) const

Get the Sparse member data.

const TId & GetId(void) const

Get the variant data.

bool IsSetField_name(void) const

any column can be identified by ASN.1 text locator string with omitted object type.

bool IsSetSparse_other(void) const

single value for indexes not listed in sparse table Check if a value has been assigned to Sparse_othe...

vector< CRef< CSeqTable_column > > TColumns

const THeader & GetHeader(void) const

Get the Header member data.

const TField_name & GetField_name(void) const

Get the Field_name member data.

bool IsSetData(void) const

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

bool IsSetSparse(void) const

in case not all rows contain data this field will contain sparse info Check if a value has been assig...

const TData & GetData(void) const

Get the Data member data.

bool IsSetDefault(void) const

default value for sparse table, or if row data is too short Check if a value has been assigned to Def...

@ eField_id_location

location as Seq-loc

@ eField_id_qual

field-name must be "Q.xxx", see below

@ eField_id_ext

field-name must be "E.xxx", see below

@ eField_id_location_id

location Seq-id

@ eField_id_location_strand

location strand

@ eField_id_ext_type

extra fields, see also special values for str below

@ eField_id_dbxref

field-name must be "D.xxx", see below

@ eField_id_location_to

interval to

@ eField_id_location_gi

gi

@ eField_id_product

product as Seq-loc

@ eField_id_location_fuzz_to_lim

@ eField_id_location_fuzz_from_lim

@ eField_id_data_imp_key

various data fields

@ eField_id_location_from

interval from

@ e_Int8

a set of signed 8-byte integers

@ e_Real

a set of reals, one per row

@ e_Common_bytes

a set of byte arrays with small set of possible values

@ e_Bytes

a set of byte arrays, one per row

@ e_String

a set of strings, one per row

@ e_Int

a set of 4-byte integers, one per row

@ e_Common_string

a set of string with small set of possible values

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

E_Choice

Choice variants.

virtual void Reset(void)

Reset the whole object.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ e_not_set

No variant selected.

@ e_MaxChoice

== e_Variation+1

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

void ResetFuzz_to(void)

Reset Fuzz_to data member.

ENa_strand

strand of nucleic acid

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void ResetFuzz(void)

Reset Fuzz data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void ResetStrand(void)

Reset Strand data member.

void ResetFuzz_from(void)

Reset Fuzz_from data member.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void ResetStrand(void)

Reset Strand data member.

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

NCBI_DEFINE_ERR_SUBCODE_X(12)

#define row(bind, expected)

void SetLocationIsWhole(void)

void SetLocationIsPoint(void)

void SetLocationIsInterval(void)

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