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NCBI C++ ToolKit: include/gui/objutils/macro_biodata_iter.hpp Source File

(

)

= 0;

(

intent) { m_DeleteObject = intent; }

GetChoiceType(

& field_name,

& choice_type)

;

vector<string>&

()

{

m_Taxnames; }

objects::CSeq_entry_Handle

()

{

m_Seh; }

objects::CSeq_submit&

(

)

{

*m_SeqSubmit; }

(

objects::CSeq_submit& submit) { m_SeqSubmit.Reset(&submit); }

SetTableToApply(

&

,

match_col,

&

,

merge_de,

split_firstcol,

convert_multi,

merge_firstcols,

multiple_sp_only);

& GetTableName()

;

FindInTable(

vector<string>& strs,

case_sensitive =

);

GetUnMatchedTableEntries(

&

);

TopLevelObject()

;

objects::CObject_id::TId& MaxFeatureId();

SetHugeContext(

shared_ptr<CHugeMacroContext>&

);

: m_Seh (entry), m_DeleteObject(

), m_Modified(

), m_TableToApply(

) {}

m_Completed{

};

m_HugeData{

};

: m_Name(

), m_NrCols(0), m_SplitFlags(0){}

SetTableToApply(

&

,

match_col);

= unordered_map<string, unsigned>;

m_SplitFirstCol{

};

m_ConvertMulti{

};

m_MergeFirstCols{

};

m_MultipleSpaceOnly{

};

x_InitAndCheck(

&

,

col);

x_CacheColFromTable(

col);

(

)

;

vector<string>&

()

;

SetCreateGeneralIdFlag();

m_CreateGeneralId{

};

objects::SAnnotSelector& sel,

& feat_interval);

(

)

;

x_StepToNextFeat();

(

)

;

(

ambiguous) { m_CollDateType = (ambiguous) ? eAmbiguous_True : eAmbiguous_False; }

objects::CBioSource* x_GetBioSource();

(

)

;

m_Processed{

};

(

)

;

x_GetDescription(

& descr_name)

;

x_GetSeqId()

;

(

)

;

objects::CMolInfo* x_GetMolInfo();

(

)

;

x_StepToNextStructComment();

objects::CUser_object* x_GetDBLink();

objects::CUser_object* x_GetAutodefOptions();

(

)

;

objects::CBioseq_Handle

(

)

{

objects::CBioseq_Handle(); }

* s_MakeSeqIterator(

objects::CSeq_entry_Handle& entry, objects::CSeq_inst::EMol mol_type);

(

)

;

(

)

;

objects::CBioseq_Handle

(

)

{

objects::CBioseq_Handle(); }

(

)

;

objects::CBioseq_Handle

(

)

{

objects::CBioseq_Handle(); }

User-defined methods of the data storage class.

User-defined methods of the data storage class.

string GetValueFromTable(const CSeq_table &table, string column_name, size_t row)

CMacroBioData_AutodefOptsIter - iterates over all AutodefOptions in the seq-entry.

CMacroBioData_BioSourceIter - iterates over all biosource descriptors and features in the seq-entry.

CMacroBioData_DBLinkIter - iterates over all DBlinks in the seq-entry.

CMacroBioData_FeatIntervalIter - iterates over features within [|(left, right]|) intervals.

CMacroBioData_FeatIterBase - iterates over any type of features.

CMacroBioData_MolInfoIter - iterates over all molinfos in the seq-entry.

CMacroBioData_PubdescIter - iterates over all publication descriptors and features in the seq-entry.

CMacroBioData_SeqAlignIter - iterates over sequence alignments.

CMacroBioData_SeqIter- iterates over sequences (na and aa)

CMacroBioData_SeqSetIter- iterates over sets.

CMacroBioData_SeqdescIter- iterates over all types of sequence descriptors.

CMacroBioData_TSEntryIterBase - iterator pointing to the top seq-entry.

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 ...

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

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

shared_ptr< objects::edit::CRemoteUpdater > m_RemoteUpdater

CMacroBioData_SeqSetIter(const objects::CSeq_entry_Handle &entry)

TPmidLookupMap m_PmidLookupMap

CMacroBioData_TSEntryIter(const objects::CSeq_entry_Handle &entry)

CConstRef< objects::CBioseq_set > m_OrigSeqSet

virtual ~CMacroBioData_MolInfoIter()

CConstRef< objects::CSeqdesc > m_FirstSeqdesc

virtual bool IsEnd(void) const =0

CConstRef< objects::CSeq_align > m_OrigSeqalign

objects::CBioseq_CI m_SeqIter

CRef< objects::CPubdesc > m_EditedPubdesc

void SetHugeDataMode(bool value)

objects::CAutoDefOptions m_AutodefOptions

objects::CSeq_entry_CI m_SeqSetIter

TDOILookupMap & SetDOILookupMap()

objects::CAlign_CI m_AlignIter

vector< pair< string, bool > > TPresent

true value for a key indicates that was present in the record

bool IsHugeDataMode() const

virtual bool IsDescriptor() const

CMacroBioData_PubdescIter & operator=(const CMacroBioData_PubdescIter &)

virtual bool IsDescriptor() const =0

objects::CSeqdesc_CI m_DescIter

objects::CBioseq_CI m_SeqIter

STableToApply(const string &file_name)

virtual ~CMacroBioData_BioSourceIter()

virtual bool IsDescriptor() const

virtual bool IsFeature() const

bool IntendToDelete() const

CMacroBioData_FeatIterBase(const CMacroBioData_FeatIterBase &)

virtual ~CMacroBioData_TSEntryIter()

CRef< objects::CSeq_feat > m_EditedFeat

const TPmidLookupMap & GetPmidLookupMap() const

virtual objects::CBioseq_Handle GetBioseqHandle(void) const =0

CConstRef< objects::CSeq_entry > m_OrigTSE

virtual bool IsDescriptor() const

objects::CSeq_entry_CI m_SeqSetIter

> provides context information

list< SResolvedField > TObs

CMacroBioData_TSEntryIter(const CMacroBioData_TSEntryIter &)

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

CMacroBioData_AutodefOptsIter(const objects::CSeq_entry_Handle &entry)

TDOILookupMap m_DOILookupMap

virtual bool IsFeature() const

vector< string > TTableValues

CMacroBioData_FeatIntervalIter & operator=(const CMacroBioData_FeatIntervalIter &)

CConstRef< objects::CSeq_feat > m_FirstFeat

const objects::CAutoDefOptions & GetAutodefOptions() const

virtual ~IMacroBioDataIter()

SFeatInterval m_FeatInterval

CMacroBioData_UserObjectIter & operator=(const CMacroBioData_UserObjectIter &)

~CMacroBioData_DBLinkIter()

CMacroBioData_SeqSetIter & operator=(const CMacroBioData_SeqSetIter &)

CConstRef< objects::CSeq_feat > m_FirstFeat

CRef< objects::CSeq_entry > m_EditedTSE

CMacroBioData_BioSourceIter & operator=(const CMacroBioData_BioSourceIter &)

virtual bool IsFeature() const

objects::CFeat_CI m_FeatIter

void SetCollDateType(bool ambiguous)

CMacroBioData_StructCommentIter & operator=(const CMacroBioData_StructCommentIter &)

CMacroBioData_SeqAlignIter(const objects::CSeq_entry_Handle &entry)

CRef< objects::CBioseq > m_EditedSeq

virtual bool IsDescriptor() const

CRef< objects::CMolInfo > m_EditedMolinfo

shared_ptr< CDoiLookupWithCache > m_DOIUpdater

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

CMacroBioData_SeqdescIter & operator=(const CMacroBioData_SeqdescIter &)

CMacroBioData_UserObjectIter(const CMacroBioData_UserObjectIter &)

CMacroBioData_MolInfoIter & operator=(const CMacroBioData_MolInfoIter &)

virtual ~CMacroBioData_SeqAlignIter()

CConstRef< objects::CSeq_feat > m_OrigFeat

CMacroBioData_StructCommentIter(const CMacroBioData_StructCommentIter &)

objects::CSeq_entry_Handle GetSEH() const

const objects::CSubmit_block & GetOrigSubmitBlock() const

virtual void BuildEditedObject()=0

Creates a copy of the object that will be edited.

CMacroBioData_PubdescIter(const CMacroBioData_PubdescIter &)

const objects::CSeq_submit & GetSeqSubmit(void) const

virtual bool IsBegin(void)=0

CMacroBioData_MolInfoIter(const objects::CSeq_entry_Handle &entry)

virtual bool IsDescriptor() const

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)=0

Constructs and executes the delete command.

CMacroBioData_FeatIterBase(const objects::CBioseq_Handle &bsh, const objects::SAnnotSelector &sel, const objects::CSeq_loc &loc)

CConstRef< objects::CSeqdesc > m_OrigSeqdesc

CMacroBioData_BioSourceIter(const objects::CSeq_entry_Handle &entry)

virtual bool IsDescriptor() const

CMacroBioData_TSEntryIter & operator=(const CMacroBioData_TSEntryIter &)

ISOJTALookupMap & SetISOJTALookupMap()

virtual IMacroBioDataIter & Begin(void)=0

CMacroBioData_SeqAlignIter(const CMacroBioData_SeqAlignIter &)

SFeatInterval(const TSeqRange &range, bool left=true, bool right=true)

CMacroBioData_FeatIntervalIter(const CMacroBioData_FeatIntervalIter &)

objects::CBioseq_CI m_SeqIter

CMacroBioData_SeqdescIter(const objects::CSeq_entry_Handle &entry)

CRef< objects::CSeqdesc > m_EditedSeqdesc

unordered_map< string, unsigned > TIndex

virtual bool IsFeature() const

CConstRef< objects::CMolInfo > m_OrigMolinfo

CRef< objects::CSeq_entry > m_EditedEntry

objects::CSeqdesc_CI m_PubDescrIter

CConstRef< objects::CMolInfo > m_FirstMolinfo

CRef< CSubmitblockIter > m_SubmitBlockIter

CMacroBioData_AutodefOptsIter & operator=(const CMacroBioData_AutodefOptsIter &)

virtual void RunDeleteCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the delete command.

CConstRef< objects::CBioSource > m_OrigSource

> provides context information

void SetSeqSubmit(const objects::CSeq_submit &submit)

shared_ptr< CHugeMacroContext > m_MacroContext

CMacroBioData_DBLinkIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_SeqSetIter(const CMacroBioData_SeqSetIter &)

objects::CSeq_entry_CI m_SeqSetIter

> provides context information

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

objects::CSeq_entry_CI m_EntryIter

virtual const vector< string > & GetTaxnames() const

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

virtual bool IsFeature() const

ECollDateType m_CollDateType

virtual void x_SetDefaultObjectInfo()=0

Initializes member variable m_CurIterOI.

CMacroBioData_SeqdescIter(const CMacroBioData_SeqdescIter &)

bool m_Modified

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

virtual ~CMacroBioData_FeatIntervalIter()

CMacroBioData_SeqAlignIter & operator=(const CMacroBioData_SeqAlignIter &)

virtual ~CMacroBioData_FeatIterBase()

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

list< pair< size_t, TTableValues > > m_TableValues

objects::CFeat_CI m_PubFeatIter

virtual objects::CBioseq_Handle GetBioseqHandle(void) const

virtual IMacroBioDataIter & Next(void)=0

CRef< objects::CSeq_feat > m_EditedFeat

virtual bool IsDescriptor() const

CMacroBioData_FeatIterBase & operator=(const CMacroBioData_FeatIterBase &)

virtual SConstScopedObject GetScopedObject() const =0

Dereferences the underlying iterator.

virtual ~CMacroBioData_PubdescIter()

CMacroBioData_SeqIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_SeqIter(const CMacroBioData_SeqIter &)

virtual size_t GetCount() const

virtual ~CMacroBioData_SeqdescIter()

CObjectInfo GetEditedObject()

CConstRef< objects::CSeq_submit > m_SeqSubmit

objects::CBioseq_CI m_SeqIter

TIndex::const_iterator m_CurrentPos

virtual void SetToDelete(bool intent)

virtual bool IsFeature() const =0

bool GetCreateGeneralIdFlag() const

shared_ptr< CISOJTALookupWithCache > m_ISOJTAUpdater

CConstRef< objects::CPubdesc > m_OrigPubdesc

ECollDateType GetCollDateType() const

CMacroBioData_AutodefOptsIter(const CMacroBioData_AutodefOptsIter &)

CMacroBioData_PubdescIter(const objects::CSeq_entry_Handle &entry)

objects::CFeat_CI m_SrcFeatIter

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)

Constructs and executes the editing command.

virtual string GetBestDescr() const =0

Used for logging.

CConstRef< objects::CBioseq > m_OrigSeq

CMacroBioData_DBLinkIter(const CMacroBioData_DBLinkIter &)

TPmidLookupMap & SetPmidLookupMap()

ISOJTALookupMap m_ISOJTALookupMap

objects::CSeqdesc_CI m_SrcDescrIter

CRef< objects::CBioSource > m_EditedSource

CRef< objects::CSeq_align > m_EditedSeqalign

virtual bool IsFeature() const

CConstRef< objects::CBioSource > m_FirstSource

CRef< objects::CBioseq_set > m_EditedSeqSet

STableToApply m_TableToApply

virtual void RunEditCommand(CMacroCmdComposite *cmd_composite)=0

Constructs and executes the editing command.

CMacroBioData_DBLinkIter & operator=(const CMacroBioData_DBLinkIter &)

IMacroBioDataIter(const objects::CSeq_entry_Handle &entry)

virtual ~CMacroBioData_SeqSetIter()

CMacroBioData_BioSourceIter(const CMacroBioData_BioSourceIter &)

CConstRef< objects::CPubdesc > m_FirstPubdesc

bool IsSetSeqSubmit(void) const

objects::CFeat_CI m_FeatIter

CMacroBioData_UserObjectIter(const objects::CSeq_entry_Handle &entry)

CMacroBioData_SeqIter & operator=(const CMacroBioData_SeqIter &)

void SetOutputStream(CNcbiOstream *str)

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

CConstRef< objects::CSeq_feat > m_OrigFeat

virtual bool IsFeature() const

TIndex m_Index

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

CNcbiOstream & GetOutputStream() const

objects::CAutoDefOptions & SetAutodefOptions()

objects::CSubmit_block & GetEditedSubmitBlock() const

~CMacroBioData_StructCommentIter()

CMacroBioData_MolInfoIter(const CMacroBioData_MolInfoIter &)

CConstRef< objects::CUser_object > m_OrigUserObj

virtual ~CMacroBioData_UserObjectIter()

bool m_DeleteObject

indicates the intention to delete the underlying object

virtual ~CMacroBioData_SeqIter()

CRef< objects::CUser_object > m_EditedUserObj

~CMacroBioData_AutodefOptsIter()

vector< string > m_Taxnames

bool IsSetOutputStream() const

CMacroBioData_StructCommentIter(const objects::CSeq_entry_Handle &entry)

objects::CSeq_entry_Handle m_Seh

bool HasBeenCompleted() 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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

int TSplitFlags

Bitwise OR of ESplitFlags.

#define NCBI_GUIOBJUTILS_EXPORT

Defines to provide correct exporting from DLLs in Windows.

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

static const char delimiter[]

static CS_CONTEXT * context

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