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NCBI C++ ToolKit: src/gui/objutils/macro_biodata_iter.cpp Source File

oi = nodes.front().field;

(

);

(

);

merge_del,

split_firstcol,

convert_multi,

merge_firstcols,

multiple_sp_only)

(

<<

);

(!line_reader->

()) {

(

& it : cols) {

token_it = find_if(cols.begin(), cols.end(), [](

& elem) { return !elem.empty(); });

(token_it == cols.end()) {

= cols[match_col];

= cols[0] +

+ cols[1];

cols.erase(cols.begin() + 1);

, second;

(match_col == 0) {

(match_col == 1) {

= cols[match_col - 1];

=

;

m_IdenticalItems.clear();

(line_reader.

()) {

+ m_Name,

);

(!line_reader->

()) {

(m_ConvertMulti) {

(m_MultipleSpaceOnly && m_Delimiter ==

) {

(

& it : cols) {

m_NrCols = cols.size();

(m_MergeFirstCols)

(m_SplitFirstCol) {

, second;

(!

.empty() && !second.empty())

(col >= m_NrCols) {

pos = m_CurrentPos->second;

col_it = find_if(m_TableValues.begin(), m_TableValues.end(),

[&col](

pair<size_t, TTableValues>& elem) { return elem.first == col; });

(col_it == m_TableValues.end()) {

x_CacheColFromTable(col);

it = m_TableValues.begin();

(; !found && it != m_TableValues.end(); ++it) {

(col == it->first) {

& values = it->second;

(col >= m_NrCols) {

(!line_reader->

()) {

(m_ConvertMulti) {

(

& it : cols) {

(m_MergeFirstCols) {

cols[0] = cols[0] +

+ cols[1];

cols.erase(cols.begin() + 1);

(m_SplitFirstCol) {

, second;

values.push_back(

);

values.push_back(second);

values.push_back(cols[col - 1]);

values.push_back(cols[col]);

m_TableValues.push_back(make_pair(col, values));

vector<string> values_from_data;

(

it = objs.begin(); it != objs.end() && !found; ++it) {

(

iter =

.begin(); iter !=

.end() && !found; ++iter) {

(case_sensitive) {

[&

](

pair<string, unsigned int>& elem)

{ return NStr::EqualNocase(elem.first, value); });

values_from_data.push_back(

);

(

&& it : strs) {

(case_sensitive) {

[&it](

pair<string, unsigned int>& elem)

{ return NStr::EqualNocase(elem.first, it); });

report =

;

report +=

+ it.first;

sobject.

= pscope;

subtype.append(

+

);

remove_proteins(

);

,

(!vec_tse.empty()) {

(

);

,

good_feat = [&range, left_closed, right_closed](

& feat_loc)

(left_closed ==

) {

(feat_start <= range.GetFrom()) {

(right_closed ==

) {

(feat_stop >= range.GetTo()) {

sobject.

= pscope;

subtype.append(

+

);

,

sobject.

= pscope;

.GetScope(), seq_id);

(

).append(seq_id);

remove_proteins(

);

sobject.

= pscope;

sobject.

= pscope;

;

description =

+ seq_id;

description =

;

remove_proteins(

);

m_EditedSubmitBlock->Assign(*m_OrigSubmitBlock);

m_EditedSubmitBlock;

m_OrigUserObj =

(&m_DescIter->GetUser());

(m_OrigUserObj.IsNull() &&

) {

m_OrigUserObj =

(&m_DescIter->GetUser());

m_OrigUserObj =

(&m_DescIter->GetUser());

m_FirstUserObj = m_OrigUserObj;

m_OrigUserObj.Reset();

(m_OrigUserObj.IsNull() &&

) {

(m_DescIter && ++m_DescIter) {

m_OrigUserObj =

(&m_DescIter->GetUser());

(m_OrigUserObj.IsNull()) {

m_OrigUserObj =

(&m_DescIter->GetUser());

(m_DescIter && ++m_DescIter) {

m_OrigUserObj =

(&m_DescIter->GetUser());

m_OrigUserObj.IsNull();

(m_FirstUserObj == m_OrigUserObj);

sobject.

= pscope;

x_GetDescription(

);

m_EditedUserObj->Assign(*m_OrigUserObj);

oi(m_EditedUserObj, m_EditedUserObj->GetThisTypeInfo());

new_desc->

(m_EditedUserObj.GetNCObject());

(desc_it->GetUser().GetType().IsStr()

&& desc_it->GetUser().GetType().GetStr() ==

) {

&desc_it->GetUser();

(desc_it->GetUser().GetType().IsStr()

&& desc_it->GetUser().GetType().GetStr() ==

) {

&desc_it->GetUser();

(desc_it->GetUser().GetType().IsStr()

&& desc_it->GetUser().GetType().GetStr() ==

) {

&desc_it->GetUser();

sobject.

= pscope;

.GetScope(), seq_id);

description = descr_name +

+ seq_id;

description = descr_name +

;

sobject.

= pscope;

;

chgAlign->Execute();

* const_seqalign = &(*m_AlignIter);

sobject.

= pscope;

* const_bseq =

->GetCompleteBioseq().GetPointerOrNull();

sobject.

= pscope;

(

->GetCompleteSeq_entry().GetPointerOrNull() ==

sobject.

= pscope;

@ eExtreme_Positional

numerical value

static CSeq_entry_Handle GetSeq_entry_Handle(TTypeInfo type, TConstObjectPtr ptr, CScope &scope)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

void AddCommand(IEditCommand &command)

virtual void Execute()

Do the editing action.

CMacroBioData_SeqIter- iterates over sequences (na and aa)

CMacroBioData_SeqdescIter- iterates over all types of sequence descriptors.

CMacroBioData_UserObjectIter - iterates over all user objects in the seq-entry.

implements special composite command, which does not call to its internal commands when run the very ...

class CMacroExecException

@Pubdesc.hpp User-defined methods of the data storage class.

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

namespace ncbi::objects::

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

static bool GetBestId(CSeq_id_Handle, CScope &, string &)

IMacroBioDataIter - common interface of all iterators used in the editing macros The type of the iter...

CChangeUnindexedObjectCommand< objects::CSubmit_block > CChangeSubmitBlockCommand

static auto & FindOrgNames

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define DIAG_COMPILE_INFO

Make compile time diagnostic information object to use in CNcbiDiag and CException.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

void Error(CExceptionArgs_Base &args)

#define NCBI_RETHROW2(prev_exception, exception_class, err_code, message, extra)

Re-throw exception with extra parameter.

@ eUnknown

Unknown exception.

const objects::CUser_object * x_GetAutodefOptions()

void SetCreateGeneralIdFlag()

virtual string GetBestDescr() const

Used for logging.

CMacroBioData_SeqSetIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_TSEntryIter(const objects::CSeq_entry_Handle &entry)

bool m_Completed

flag to be used by actions that need to be completed only once

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

CConstRef< objects::CBioseq_set > m_OrigSeqSet

CConstRef< objects::CSeqdesc > m_FirstSeqdesc

virtual bool IsEnd(void) const =0

CConstRef< objects::CSeq_align > m_OrigSeqalign

virtual IMacroBioDataIter & Begin(void)

virtual string GetBestDescr() const

Used for logging.

objects::CBioseq_CI m_SeqIter

virtual bool IsEnd(void) const

bool SetTableToApply(const string &file_name, size_t match_col)

virtual void SetToDelete(bool intent)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual string GetBestDescr() const

Used for logging.

CMacroBioData_SeqNAIter(const objects::CSeq_entry_Handle &entry)

virtual size_t GetCount() const

bool m_MultipleSpaceOnly

when true, single space character are not considered delimiters

CRef< objects::CPubdesc > m_EditedPubdesc

void ConvertMultiSpaces(string &line, const string &delimiter)

replace any instance of 2 or more spaces with a single instance of 'delimiter'

virtual IMacroBioDataIter & Next(void)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

const objects::CMolInfo * x_GetMolInfo()

void ThrowCMacroExecException(const CDiagCompileInfo &info, CMacroExecException::EErrCode code, const string &message, const CQueryParseTree::TNode *treeNode, const CException *previous=nullptr)

Throws CMacroExecException with the specified message and error location from the TNode.

virtual const vector< string > & GetTaxnames() const

virtual IMacroBioDataIter & Begin(void)

virtual string GetBestDescr() const

Used for logging.

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual bool IsEnd(void) const

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual IMacroBioDataIter & Next(void)

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

objects::CSeq_entry_CI m_SeqSetIter

bool FindInTable(const CMQueryNodeValue::TObs &objs, bool case_sensitive=true)

virtual IMacroBioDataIter & Begin(void)

void x_StepToNextStructComment()

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

objects::CAlign_CI m_AlignIter

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

objects::CSeqdesc_CI m_DescIter

objects::CBioseq_CI m_SeqIter

virtual bool IsBegin(void)

bool m_MergeFirstCols

when true, merges first two columns to form the seq-id match field

virtual string GetBestDescr() const

Used for logging.

bool GetValueFromTable(size_t col, string &value)

CRef< objects::CSeq_feat > m_EditedFeat

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual bool IsBegin(void)

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual bool IsEnd(void) const

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

CConstRef< objects::CSeq_entry > m_OrigTSE

objects::CSeq_entry_CI m_SeqSetIter

> provides context information

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

list< SResolvedField > TObs

virtual IMacroBioDataIter & Next(void)

const objects::CBioSource * x_GetBioSource()

CConstRef< objects::CSubmit_block > m_OrigSubmitBlock

CMacroBioData_FeatIterBase(const objects::CSeq_entry_Handle &entry, const objects::SAnnotSelector &sel)

CMacroBioData_AutodefOptsIter(const objects::CSeq_entry_Handle &entry)

virtual bool IsDescriptor() const

string GetValueFromTable(size_t col)

vector< string > TTableValues

void SetTableToApply(const string &file_name, size_t match_col, const string &delimiter, bool merge_de, bool split_firstcol, bool convert_multi, bool merge_firstcols, bool multiple_sp_only)

static CMacroBioData_SeqIter * s_MakeSeqIterator(const objects::CSeq_entry_Handle &entry, objects::CSeq_inst::EMol mol_type)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual string GetBestDescr() const

Used for logging.

CConstRef< objects::CSeq_feat > m_FirstFeat

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

virtual string GetBestDescr() const

Used for logging.

virtual string GetBestDescr() const

Used for logging.

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual IMacroBioDataIter & Next(void)

SFeatInterval m_FeatInterval

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

CSubmitblockIter(CConstRef< objects::CSeq_submit > seqsubmit)

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual IMacroBioDataIter & Begin(void)

CConstRef< objects::CSeq_feat > m_FirstFeat

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual IMacroBioDataIter & Begin(void)

CRef< objects::CSeq_entry > m_EditedTSE

virtual string GetBestDescr() const

Used for logging.

virtual bool IsBegin(void)

virtual IMacroBioDataIter & Next(void)

objects::CFeat_CI m_FeatIter

virtual IMacroBioDataIter & Begin(void)

virtual bool IsBegin(void)

virtual IMacroBioDataIter & Begin(void)

CMacroBioData_SeqAlignIter(const objects::CSeq_entry_Handle &entry)

CRef< objects::CBioseq > m_EditedSeq

virtual IMacroBioDataIter & Begin(void)

CRef< objects::CMolInfo > m_EditedMolinfo

virtual IMacroBioDataIter & Begin(void)

virtual string GetBestDescr() const

Used for logging.

bool m_HugeData

indicates that the data is large and some macros should take that into account (for example: taxlooku...

CConstRef< objects::CSeq_feat > m_OrigFeat

void GetPrimitiveObjectInfos(CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)

virtual string GetBestDescr() const

Used for logging.

const string & GetTableName() const

virtual IMacroBioDataIter & Begin(void)

virtual bool IsBegin(void)

objects::CObject_id::TId & MaxFeatureId()

void RunCommand(CRef< CCmdComposite > cmd, CMacroCmdComposite *cmd_composite)

Method for executing a specific command.

CMacroBioData_MolInfoIter(const objects::CSeq_entry_Handle &entry)

CConstRef< objects::CSeqdesc > m_OrigSeqdesc

CMacroBioData_BioSourceIter(const objects::CSeq_entry_Handle &entry)

virtual bool IsBegin(void)

virtual bool IsEnd(void) const

bool GetFieldsByName(CMQueryNodeValue::TObs *results, const CObjectInfo &oi_i, const string &field_name)

Resolve existing dot qualified ASN.1 name (field_name) starting from the object information instance ...

objects::CBioseq_CI m_SeqIter

virtual bool IsBegin(void)

virtual IMacroBioDataIter & Next(void)

CMacroBioData_SeqdescIter(const objects::CSeq_entry_Handle &entry)

CRef< objects::CSeqdesc > m_EditedSeqdesc

CConstRef< objects::CMolInfo > m_OrigMolinfo

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

CRef< objects::CSeq_entry > m_EditedEntry

objects::CSeqdesc_CI m_PubDescrIter

CConstRef< objects::CMolInfo > m_FirstMolinfo

CRef< CSubmitblockIter > m_SubmitBlockIter

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

CConstRef< objects::CBioSource > m_OrigSource

> provides context information

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

virtual IMacroBioDataIter & Next(void)

shared_ptr< CHugeMacroContext > m_MacroContext

virtual IMacroBioDataIter & Next(void)

CMacroBioData_DBLinkIter(const objects::CSeq_entry_Handle &entry)

virtual bool IsBegin(void)

bool GetChoiceType(const string &field_name, string &choice_type) const

returns choice type string for a given identifier field_name

virtual bool IsDescriptor() const

virtual bool IsBegin(void)

objects::CSeq_entry_CI m_SeqSetIter

> provides context information

objects::CSeq_entry_CI m_EntryIter

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual IMacroBioDataIter & Next(void)

map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > m_ProductToCDS

virtual string GetBestDescr() const

Used for logging.

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual void x_SetDefaultObjectInfo()=0

Initializes member variable m_CurIterOI.

virtual bool IsEnd(void) const

CRef< objects::CSubmit_block > BuildEditedObject()

bool m_Modified

indicates whether the edited object has been modified. When it's TRUE, call RunEditCommand()

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual bool IsBegin(void)

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual bool IsBegin(void)

const objects::CUser_object * x_GetDBLink()

NStr::TSplitFlags m_SplitFlags

virtual IMacroBioDataIter & Begin(void)

virtual bool IsEnd(void) const

TPresent m_State

to report values of the matching field that are present in the table, but not present in the data

CConstRef< objects::CUser_object > m_FirstUserObj

string m_Delimiter

< number of actual columns in the table

virtual bool IsBegin(void)

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

objects::CFeat_CI m_PubFeatIter

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

string x_GetSeqId() const

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

CRef< objects::CSeq_feat > m_EditedFeat

virtual IMacroBioDataIter & Next(void)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

CMacroBioData_SeqIter(const objects::CSeq_entry_Handle &entry)

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

CConstRef< objects::CSeq_submit > m_SeqSubmit

virtual IMacroBioDataIter & Begin(void)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

objects::CBioseq_CI m_SeqIter

TIndex::const_iterator m_CurrentPos

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

virtual bool IsFeature() const

virtual string GetBestDescr() const

Used for logging.

virtual bool IsFeature() const

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual bool IsEnd(void) const

bool TopLevelObject() const

virtual bool IsEnd(void) const

virtual IMacroBioDataIter & Begin(void)

CConstRef< objects::CPubdesc > m_OrigPubdesc

virtual IMacroBioDataIter & Next(void)

CMacroBioData_SeqAAIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_PubdescIter(const objects::CSeq_entry_Handle &entry)

void SetHugeContext(const shared_ptr< CHugeMacroContext > &context)

objects::CFeat_CI m_SrcFeatIter

virtual void BuildEditedObject()

Creates a copy of the object that will be edited.

bool x_CacheColFromTable(size_t col)

CConstRef< objects::CBioseq > m_OrigSeq

string GetUnMatchedTableEntries(int &count)

objects::CSeqdesc_CI m_SrcDescrIter

virtual bool IsEnd(void) const

CRef< objects::CBioSource > m_EditedSource

CRef< objects::CSeq_align > m_EditedSeqalign

CConstRef< objects::CBioSource > m_FirstSource

CRef< objects::CBioseq_set > m_EditedSeqSet

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

STableToApply m_TableToApply

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

virtual IMacroBioDataIter & Begin(void)

virtual IMacroBioDataIter & Next(void)

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

CConstRef< objects::CPubdesc > m_FirstPubdesc

virtual IMacroBioDataIter & Begin(void)

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

objects::CFeat_CI m_FeatIter

CMacroBioData_UserObjectIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_FeatIntervalIter(const objects::CBioseq_Handle &bsh, const objects::SAnnotSelector &sel, const SFeatInterval &feat_interval)

CConstRef< objects::CSeq_feat > m_OrigFeat

TIndex m_Index

stores the match_field value and the row number where that value appears in the table

virtual string GetBestDescr() const

Used for logging.

virtual bool IsBegin(void)

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

virtual bool IsEnd(void) const

virtual bool IsEnd(void) const

virtual IMacroBioDataIter & Next(void)

virtual SConstScopedObject GetScopedObject() const

Dereferences the underlying iterator.

CConstRef< objects::CUser_object > m_OrigUserObj

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

string x_GetDescription(const string &descr_name) const

void x_InitAndCheck(const string &file_name, size_t col)

bool m_DeleteObject

indicates the intention to delete the underlying object

virtual IMacroBioDataIter & Begin(void)

virtual void x_SetDefaultObjectInfo()

Initializes member variable m_CurIterOI.

virtual IMacroBioDataIter & Next(void)

vector< string > m_Taxnames

CMacroBioData_StructCommentIter(const objects::CSeq_entry_Handle &entry)

objects::CSeq_entry_Handle m_Seh

objects::CBioseq_Handle GetBioseqForSeqFeat(const objects::CSeq_feat &f, objects::CScope &scope)

CRef< objects::CScope > scope

CConstRef< CObject > object

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

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

@ ePrimitiveValueString

string|char*|const char*

@ ePrimitiveValueInteger

(signed|unsigned) (char|short|int|long)

@ ePrimitiveValueEnum

enum

CTempString GetCurrentLine(void) const

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual Uint8 GetLineNumber(void) const =0

Returns the current line number (counting from 1, not 0).

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

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

Override Assign() to incorporate cache invalidation.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

const string & GetAlias(void) const

CObjectInfo GetPointedObject(void) const

Get data and type information of object to which this type refers.

CChoiceVariant GetCurrentChoiceVariant(void) const

Get data and type information of selected choice variant.

ETypeFamily GetTypeFamily(void) const

Get data type family.

void GetPrimitiveValueString(string &value) const

Get string data.

Int4 GetPrimitiveValueInt4(void) const

Get data as Int4.

EPrimitiveValueType GetPrimitiveValueType(void) const

Get type of primitive value.

Int8 GetPrimitiveValueInt8(void) const

Get data as Int8.

void ChangeSeqLocId(CSeq_loc *loc, bool best, CScope *scope)

Change each of the CSeq_ids embedded in a CSeq_loc to the best or worst CSeq_id accoring to the value...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

vector< CSeq_entry_Handle > TTSE_Handles

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

void Rewind(void)

Move to the first object in iterated sequence.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

TObjectType & GetNCObject(void) const

Get object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#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 list< string > & SplitByPattern(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Variation of Split() with fSplit_ByPattern flag applied by default.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert int to string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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 & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

static const char label[]

const TLocation & GetLocation(void) const

Get the Location member data.

void SetData(TData &value)

Assign a value to Data data member.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

TPub & SetPub(void)

Select the variant.

const TPub & GetPub(void) const

Get the variant data.

TSource & SetSource(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

TMolinfo & SetMolinfo(void)

Select the variant.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

Lightweight interface for getting lines of data with minimal memory copying.

Biodata iterators for macro execution.

Functions that resolve field names described in asn format.

const GenericPointer< typename T::ValueType > T2 value

Miscellaneous common-use basic types and functionality.

static const char delimiter[]

Utility macros and typedefs for exploring NCBI objects from seq.asn.

Utility macros and typedefs for exploring NCBI objects from seqset.asn.

static SLJIT_INLINE sljit_ins nr(sljit_gpr dst, sljit_gpr src)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void GetProductToCDSMap(objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

static CS_CONTEXT * context

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