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NCBI C++ ToolKit: src/sample/app/serial/seqannot_splicer_util.cpp Source File

->sub_contexts.clear();

(name ==

) {

}

(name ==

) {

}

(name ==

) {

}

(name ==

) {

pos = find(mapentry->second->GetData().begin(),

mapentry->second->GetData().end(),

(pos == mapentry->second->GetData().end()) {

mapentry->second->GetData().push_back(

);

pair<TSeqRef, TPosContRef>(seqid_in_annot, newcont));

seqid = find(mapentry->second->GetData().begin(),

mapentry->second->GetData().end(),

(seqid == mapentry->second->GetData().end()) {

mapentry->second->GetData().push_back(seqid_in_annot);

newvec->GetData().push_back(seqid_in_annot);

pair<CNcbiStreampos, TSeqRefContRef>(

, newvec));

(

==

) {

}

(

==

) {

list<string> flag_list;

list<string>::iterator fbegin(flag_list.begin());

list<string>::iterator fend(flag_list.end());

list<string>::iterator found_flag;

(

==

) {

}

(

==

) {

}

(

==

) {

list<string> flag_list;

list<string>::iterator fbegin(flag_list.begin());

list<string>::iterator fend(flag_list.end());

list<string>::iterator found_flag;

( !

->sub_contexts.empty()) {

->sub_contexts.pop_back();

cout << s1 <<

<< endl;

cout << s2 <<

<<

->type << endl;

cout << s2 <<

<<

->has_annots << endl;

(

->seqids.size() > 0) {

cout << s2 <<

<< endl;

(

&

:

->seqids) {

cout << s3 <<

<<

->GetSeqIdString(

) << endl;

cout << s2 <<

<< endl;

(

& sub :

->sub_contexts) {

cout << s1 <<

<< endl;

(seqid->

()) {

container_removed =

;

& seq_list(annot_in_map_iter->second->GetData());

(

& seq : seq_list) {

& annot_list(seqid_in_map->second->GetData());

seqannot = find(annot_list.begin(), annot_list.end(), annot_in_map_iter->first);

(seqannot != annot_list.end());

annot_list.erase(seqannot);

(annot_list.empty()) {

container_removed =

;

container_removed;

sai->SetStreamPos(annot_in_map->first);

& pos_list = seqid_iter->second->GetData();

( pos = pos_list.begin(); pos != pos_list.end(); pos = next_pos ) {

ncbi::TMaskedQueryRegions mask

Writing containers (SET OF, SEQUENCE OF).

void SeqAnnot_Spliced(void)

void SeqEntry_Changed(void)

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

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

Split a string using specified delimiters.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

bool IsSetData(void) const

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

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Ids

used for communication between tools

@ e_not_set

No variant selected.

@ e_Locs

used for communication between tools

Magic spell ;-) needed for some weird compilers... very empiric.

Defines NCBI C++ exception handling.

Miscellaneous common-use basic types and functionality.

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

std::istream & in(std::istream &in_, double &x_)

CSeqAnnotSplicerStats * g_Stats

void SetSeqIdChoiceMask(const string &mask)

CObjectFor< TPosCont > TPosContOb

static TAnnotToSeqIdMap s_AnnotToSeqIdMap

list< TContextPtr > TContextList

TSeqRefCont::iterator TSeqRefContIter

static TSeqIdChoiceMaskFlags s_SeqIdChoiceMask

list< CNcbiStreampos > TPosCont

bool IsSeqIdChoiceSelected(TSeqIdChoiceMaskFlags flags)

static void s_SpliceAnnotsForSeqId(unique_ptr< CObjectIStream > &sai, COStreamContainer &osc, TSeqIdToAnnotMapIter seqid_iter)

void SetSeqAnnotChoiceMask(const string &mask)

TSeqIdToAnnotMap::iterator TSeqIdToAnnotMapIter

TAnnotToSeqIdMap::const_iterator TAnnotToSeqIdMapCIter

static TContextListIter s_ContextSequenceIter

void CurrentContextContainsSeqAnnots(void)

static CNcbiStreampos s_AnnotPos

ESerialDataFormat GetFormat(const string &name)

static void s_DeleteContext(TContextPtr context)

static TContextPtr s_RootContextPtr

stack< TContextPtr > TContextPtrStack

static TSeqAnnotChoiceMaskFlags s_SeqAnnotChoiceMask

TAnnotToSeqIdMap::iterator TAnnotToSeqIdMapIter

void SeqAnnotMapSeqId(TSeqRef seqid_in_annot)

CRef< TPosContOb > TPosContRef

void ResetSeqEntryProcessing(void)

struct SContext_tag SContext

set< TSeqRef, PPtrLess< TSeqRef > > TContextSeqIds

static TSeqAnnotChoiceMaskFlags s_GetSeqAnnotChoiceMask(const CSeq_annot *annot)

CRef< TSeqRefContOb > TSeqRefContRef

TContextList::iterator TContextListIter

void SeqAnnotSet_Pre(CObjectIStream &in)

static TContextPtrStack s_ContextPtrStack

static TSeqIdToAnnotMap s_SeqIdToAnnotMap

static bool s_RemoveAnnot(TAnnotToSeqIdMapIter annot_in_map_iter)

CObjectFor< TSeqRefCont > TSeqRefContOb

static TContextPtr s_CurrentContextPtr

void AddSeqIdToCurrentContext(TSeqRef id)

static TSeqIdChoiceMaskFlags s_GetSeqIdChoiceMask(const CSeq_id *seqid)

static bool s_SpliceAnnot(unique_ptr< CObjectIStream > &sai, COStreamContainer &osc, TAnnotToSeqIdMapIter annot_in_map)

map< TSeqRef, TPosContRef, PPtrLess< TSeqRef > > TSeqIdToAnnotMap

static TContextList s_ContextSequence

TSeqIdToAnnotMap::const_iterator TSeqIdToAnnotMapCIter

TPosCont::iterator TPosContIter

map< CNcbiStreampos, TSeqRefContRef > TAnnotToSeqIdMap

struct SContext_tag * TContextPtr

bool IsSeqAnnotChoiceSelected(TSeqAnnotChoiceMaskFlags flags)

list< TSeqRef > TSeqRefCont

void ContextStart(CObjectIStream &in, EContextType type)

void ProcessSeqEntryAnnot(unique_ptr< CObjectIStream > &sai, COStreamContainer &osc)

unsigned int TSeqAnnotChoiceMaskFlags

Binary OR of "ESeqAnnotChoiceMaskFlags".

@ fSIMF_Gpipe

Internal NCBI genome pipeline processing ID.

@ fSIMF_General

for other databases

@ fSIMF_Tpg

Third Party Annot/Seq Genbank.

@ fSIMF_Giim

Geninfo import id.

@ fSIMF_NotSet

No variant selected.

@ fSIMF_Gi

GenInfo Integrated Database.

@ fSIMF_Pdb

PDB sequence.

@ fSIMF_Named_annot_track

Internal named annotation tracking ID.

@ fSIMF_Tpe

Third Party Annot/Seq EMBL.

@ fSIMF_Gibbsq

Geninfo backbone seqid.

@ fSIMF_Other

for historical reasons, 'other' = 'refseq'

@ fSIMF_Tpd

Third Party Annot/Seq DDBJ.

@ fSIMF_Gibbmt

Geninfo backbone moltype.

ncbi::CRef< ncbi::objects::CSeq_id > TSeqRef

unsigned int TSeqIdChoiceMaskFlags

Binary OR of "ESeqIdChoiceMaskFlags".

@ fSAMF_Ids

used for communication between tools

@ fSAMF_Locs

used for communication between tools

@ fSAMF_NotSet

No variant selected.

TContextList sub_contexts

static CS_CONTEXT * context

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