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NCBI C++ ToolKit: src/algo/id_mapper/id_mapper.cpp Source File

<< iter->first << ": " \

<< iter->second.AsString() << "s"); \

<< __LINE__ << endl;

(

.length() <

.length());

(SourceAsm.

()) {

( ; LocIter; ++LocIter) {

(LocIter->Equals(

)) {

Result->

().Set().push_back(MappedLoc);

(Result->

()) {

(

.IsPacked_int() ||

.IsPacked_pnt()) {

PrimaryLoc =

(

, PrimarySpec);

Result =

(*PrimaryLoc, *Seq, Spec);

PrimaryLoc =

(

, PrimarySpec);

(*Result, Spec);

(Result !=

) {

(Result !=

) {

(Result !=

) {

HideRefSeqAcc =

;

(

->GetDesc().CanGetRelease_type() &&

->GetDesc().CanGetRelease_status() &&

HideRefSeqAcc =

;

( ; SeqIter; ++SeqIter) {

ChildIter, SeqIter->SetSequences()) {

( ; InnerIter; ++InnerIter) {

( ; IdIter; ++IdIter) {

* textseqid = IdIter->GetTextseq_Id();

(textseqid != 0) {

( ; ReplIter; ++ReplIter) {

(ReplIter->CanGetName() && !ReplIter->GetName().empty() ) {

}

(ReplIter->IsSetSequence() && ReplIter->GetSequence().IsSingle()) {

& SingleSeq = ReplIter->GetSequence().GetSingle();

(!SubName.empty() &&

( ; IdIter; ++IdIter) {

(IdIter->IsGi()) {

( (*SynIter)->IsGenbank() ||

(*SynIter)->IsRefseq() ) {

( ; IdIter; ++IdIter) {

(IdIter->IsGi()) {

DoesRecurse =

;

( ; StructIdIter; ++StructIdIter) {

(StructIdIter->Equals(TopId)) {

DoesRecurse =

;

( ; SubSeqIdIter; ++SubSeqIdIter) {

(SubSeqIdIter->Equals(TopId)) {

IsRandom =

;

( ; IdIter; ++IdIter) {

SeqHasGi =

(GenGi) ||

(RefGi);

SeqQualifies =

;

ParentQualifies =

;

SeqQualifies =

;

ParentHasGi =

(GenGi) ||

(RefGi);

ParentQualifies =

;

( ; ReplIter; ++ReplIter) {

(ReplIter->CanGetName() && ReplIter->CanGetSequence() &&

ReplIter->GetSequence().IsSingle() &&

ReplIter->GetSequence().GetSingle().CanGetSeq_id_synonyms() &&

ReplIter->GetSequence().GetSingle().CanGetStructure() ) {

& Seq = ReplIter->SetSequence().SetSingle();

NameFound =

;

NameFound =

((*it)->GetPrivate().GetSeqIdString(), ReplIter->GetName());

ChromoId->SetExternal().SetExternal() =

;

ChromoId->SetExternal().SetId().SetLocal().SetStr() = ReplIter->GetName();

SeqIter->SetSequences()

CGC_Sequence::TSeq_id_synonyms::iterator IdIter;

(IdIter =

.SetSeq_id_synonyms().begin();

IdIter !=

.SetSeq_id_synonyms().end(); ) {

((*IdIter)->IsExternal() &&

(*IdIter)->GetExternal().IsSetExternal() &&

((*IdIter)->GetExternal().GetExternal(),

)

IdIter =

.SetSeq_id_synonyms().erase(IdIter);

.SetSeq_id_synonyms().push_front(CopyId);

(LocalStr.size() == 5) {

(textseqid != 0 &&

Pre.assign(Spec.

.data(), 0, DelimPos);

(!Pre.empty() || !Post.empty()) {

(Seq.CanGetRoles()) {

SeqRole =

(SeqRole, *RoleIter);

OldRole =

(*Found->second);

(is_gb ? &tsid->GetGenbank() : &tsid->GetRefseq());

( ; IdIter; ++IdIter) {

(seq_id_alias.

()) {

(seq_id_alias->IsSetPublic()) {

(seq_id_alias->IsSetGpipe()) {

(seq_id_alias->IsSetGi()) {

(!(*TagIter)->CanGetSeqs()) {

(!(*TagIter)->CanGetSeqs()) {

( ; syn_id_iter; ++syn_id_iter) {

( syn_id_iter->Equals(Id)) {

(seq_id_alias.

()) {

(&seq_id_alias->GetPublic());

(&seq_id_alias->GetGpipe());

(&seq_id_alias->GetGi());

& Private = (*it)->GetPrivate();

HasId =

;

(seq_id_alias.

()) {

((seq_id_alias->CanGetPublic() && alias_is_public) ||

(seq_id_alias->CanGetGpipe() && alias_is_gpipe) ||

(seq_id_alias->CanGetGi() && alias_is_gi)

((*it)->GetExternal().GetExternal() == Spec.

) {

((Parent ==

|| Parent ==

)) {

(seq_id_alias.

()) {

(seq_id_alias->IsSetPublic() && seq_id_alias->GetPublic().Equals(Id)) {

(seq_id_alias->IsSetGpipe() && seq_id_alias->GetGpipe().Equals(Id)) {

(seq_id_alias->IsSetGi() && seq_id_alias->GetGi().Equals(Id)) {

(*it)->GetPrivate().Equals(Id)

(Start !=

) {

& Private = (*it)->GetPrivate();

(Start !=

) {

objects::CGC_Assembly& Assembly,

Found->second;

(

<<

<< Id.AsFastaString());

(Assembly.IsAssembly_set()) {

(Assembly.IsUnit()) {

((*MolIter)->GetSequence().IsSingle()) {

& Parent = (*MolIter)->GetSequence().GetSingle();

!(*ChildIter)->CanGetSeqs()

((*SeqIter)->GetSeq_id().Equals(Id)) {

(IdIter->Equals(Id)) {

(IdStr.find(

) !=

)

(IdStr.find(

) !=

)

Start =

(IdStr, *ChromoIter);

End = Start + ChromoIter->length()-1;

((Start > 0 &&

(IdStr[Start-1])) ||

(End+1 < IdStr.length() &&

(IdStr[End+1])) )) {

Found->second;

Result->

(SourceLoc);

( ; IdIter; ++IdIter) {

IdIter->

(*DestId);

( ; PartIter; ++PartIter) {

((*IdIter)->Equals(*PartIter)) {

Result->

(SourceLoc);

(Result->

(SourceLoc))

Result =

(*Result, Spec);

(Result->

(SourceLoc)) {

(Result->

(SourceLoc)) {

Result =

(*Result, Spec);

Result =

(*Result, Spec);

(

.IsMix()) {

(

.IsPacked_int()) {

(

.IsInt()) {

(

.IsPnt()) {

Int.

().Assign(

.GetPnt().GetId());

Int.

(

.GetPnt().GetPoint());

(!Seq->CanGetStructure()) {

& DeltaExt = Seq->GetStructure();

(DeltaSeq.

()) {

(Intersect.

()) {

(Intersect == GapRange) {

(Intersect == LocRange) {

(Intersect == LocRange) {

(!Intersect.

()) {

(First != Second) {

NcbiOnly)

Seq = Found->second;

(seq_id_alias.

()) {

(seq_id_alias->IsSetPublic()) {

Synonyms.push_back(

(&seq_id_alias->GetPublic()));

(seq_id_alias->IsSetGpipe()) {

Synonyms.push_back(

(&seq_id_alias->GetGpipe()));

(seq_id_alias->IsSetGi()) {

Synonyms.push_back(

(&seq_id_alias->GetGi()));

& Private = (*it)->GetPrivate();

Synonyms.push_back(

(&Private));

list< CConstRef<CSeq_id> >::iterator Inner = Outer;

( ; Inner != Synonyms.end(); ) {

( (*Outer)->Equals(**Inner) ) {

Inner = Synonyms.erase(Inner);

Role(e_Role_NotSet),

CGencollIdMapper::SIdSpec::operator

()

(!(Primary == Other.

&&

Alias == Other.

&&

Role == Other.

&&

Result +=

;

(TypedChoice) {

Result +=

;

Result +=

;

Result +=

;

Result +=

;

Result +=

;

Result +=

;

Result +=

;

Result += External +

+

;

RoleTop =

;

(Guessed.

) {

RoleTop = (Top == Guessed.

);

RoleTop = (Role == Guessed.

);

(Guessed.

&& RoleTop );

Alias == Guessed.

&&

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

the sequence(s) representing this molecule in the case of 2L and 2R - the molecule is represented by ...

CConstRef< CSeq_id > GetSubmitterName() const

CConstRef< CSeq_id > GetSynonymSeq_id(CGC_TypedSeqId::E_Choice type, CGC_SeqIdAlias::E_AliasTypes) const

bool HasRole(int Role) const

CGC_TaggedSequences::TState GetParentRelation() const

Access the relationship to the parent.

CConstRef< CGC_Sequence > GetParent() const

Access the parent sequence of this sequence.

bool Guess(const objects::CSeq_loc &Loc, SIdSpec &Spec) const

TSeqLocMapperRef m_UpMapper

CGencollIdMapper(CConstRef< objects::CGC_Assembly > SourceAsm)

CConstRef< objects::CSeq_id > x_ApplyPatternToId(CConstRef< objects::CSeq_id > Id, const SIdSpec &Spec) const

void x_StripPseudoSeq(objects::CGC_Sequence &Seq)

CRef< objects::CSeq_loc > x_Map_Up(const objects::CSeq_loc &SourceLoc, const objects::CGC_Sequence &Seq, const SIdSpec &Spec) const

E_Gap x_Merge_E_Gaps(E_Gap First, E_Gap Second) const

CConstRef< objects::CSeq_id > x_GetIdFromSeqAndSpec(const objects::CGC_Sequence &Seq, const SIdSpec &Spec) const

int x_GetRole(const objects::CGC_Sequence &Seq) const

CConstRef< objects::CSeq_id > x_FixImperfectId(CConstRef< objects::CSeq_id > Id, const SIdSpec &Spec) const

void x_PrioritizeIds(void)

CConstRef< objects::CGC_Sequence > x_FindParentSequence(const objects::CSeq_id &Id, const objects::CGC_Assembly &Assembly, int Depth=0) const

bool CanMeetSpec(const objects::CSeq_loc &Loc, const SIdSpec &Spec) const

bool x_DoesSeqContainSyn(const objects::CGC_Sequence &Seq, const objects::CSeq_id &Id) const

void x_AddSeqToMap(const objects::CSeq_id &Id, CConstRef< objects::CGC_Sequence > Seq)

TSeqLocMapperRef m_DownMapper_Shallow

TAccToVerMap m_AccToVerMap

CRef< objects::CSeq_loc > x_Map_OneToOne(const objects::CSeq_loc &SourceLoc, const objects::CGC_Sequence &Seq, const SIdSpec &Spec) const

void x_BuildSeqMap(const objects::CGC_Assembly &assm)

vector< string > m_Chromosomes

void x_RecursiveSeqFix(objects::CGC_Sequence &Seq)

bool x_NCBI34_Guess(const objects::CSeq_id &Id, SIdSpec &Spec) const

bool x_IsFuzzyIdInAssembly(const objects::CSeq_id &Id) const

CRef< objects::CSeq_loc > x_Map_Down(const objects::CSeq_loc &SourceLoc, const objects::CGC_Sequence &Seq, const SIdSpec &Spec) const

void x_RemoveHiddenAccessions(objects::CGC_Sequence &Seq)

bool x_IsExactIdInAssembly(const objects::CSeq_id &Id) const

TSeqLocMapperRef m_DownMapper_Deep

void x_FillGpipeTopRole(objects::CGC_Sequence &Seq)

TChildToParentMap m_ChildToParentMap

bool x_IsParentSequence(const objects::CSeq_id &Id, const objects::CGC_Sequence &Parent) const

CConstRef< objects::CSeq_id > x_NCBI34_Map_IdFix(CConstRef< objects::CSeq_id > SourceId) const

CRef< objects::CSeq_loc > Map(const objects::CSeq_loc &Loc, const SIdSpec &Spec) const

CConstRef< objects::CGC_Sequence > x_FindChromosomeSequence(const objects::CSeq_id &Id, const SIdSpec &Spec) const

void x_FillChromosomeIds(void)

CConstRef< objects::CGC_Assembly > GetInternalGencoll(void) const

void x_Init_SeqLocMappers(void) const

CRef< objects::CGC_Assembly > m_Assembly

E_Gap x_IsLoc_Int_InAGap(const objects::CSeq_interval &Int) const

void GetSynonyms(const objects::CSeq_id &BaseId, list< CConstRef< objects::CSeq_id > > &Synonyms, bool NcbiOnly=true) const

E_Gap IsLocInAGap(const objects::CSeq_loc &Loc) const

bool x_MakeSpecForSeq(const objects::CSeq_id &Id, const objects::CGC_Sequence &Seq, SIdSpec &Spec) const

int x_CanSeqMeetSpec(const objects::CGC_Sequence &Seq, const SIdSpec &Spec, int Level=0) const

TSeqPos GetLength(void) const

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define LOG_POST(message)

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

void Warning(CExceptionArgs_Base &args)

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

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

Override Assign() to incorporate cache invalidation.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void Assign(const CTypeIteratorBase &it)

@ eSeqMap_Down

map from a segmented bioseq to segments

@ eSeqMap_Up

map from segments to the top level bioseq

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

bool IsNull(void) const THROWS_NONE

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

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

bool IsNull(void) const THROWS_NONE

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

TThisType IntersectionWith(const TThisType &r) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Check if a string ends with a specified suffix value.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Replace occurrences of a substring within a 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 bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another 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.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTo(TTo value)

Assign a value to To data member.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

bool CanGetSequences(void) const

Check if it is safe to call GetSequences method.

bool CanGetSeq_id(void) const

Check if it is safe to call GetSeq_id method.

E_Choice

Choice variants.

bool CanGetPrimary_assembly(void) const

Check if it is safe to call GetPrimary_assembly method.

bool IsGenbank(void) const

Check if variant Genbank is selected.

list< CRef< CGC_Sequence > > TSeqs

const TId & GetId(void) const

Get the Id member data.

TGenbank & SetGenbank(void)

Select the variant.

const TUnit & GetUnit(void) const

Get the variant data.

const TStructure & GetStructure(void) const

Get the Structure member data.

bool IsSingle(void) const

Check if variant Single is selected.

bool CanGetSeq_id_synonyms(void) const

Check if it is safe to call GetSeq_id_synonyms method.

TRefseq & SetRefseq(void)

Select the variant.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

bool IsSetMols(void) const

collections of molecules for this assembly Check if a value has been assigned to Mols data member.

TSeq_id_synonyms & SetSeq_id_synonyms(void)

Assign a value to Seq_id_synonyms data member.

list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms

bool IsAssembly_set(void) const

Check if variant Assembly_set is selected.

TRoles & SetRoles(void)

Assign a value to Roles data member.

bool IsSetMore_assemblies(void) const

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

const TExternal & GetExternal(void) const

Get the External member data.

void ResetGpipe(void)

Reset Gpipe data member.

const TOther_sequences & GetOther_sequences(void) const

Get the Other_sequences member data.

const TPrimary_assembly & GetPrimary_assembly(void) const

Get the Primary_assembly member data.

const TSeq_id_synonyms & GetSeq_id_synonyms(void) const

Get the Seq_id_synonyms member data.

bool CanGetRoles(void) const

Check if it is safe to call GetRoles method.

list< CRef< CGC_TaggedSequences > > TSequences

const TAssembly_set & GetAssembly_set(void) const

Get the variant data.

const TMols & GetMols(void) const

Get the Mols member data.

bool IsRefseq(void) const

Check if variant Refseq is selected.

list< CRef< CGC_Replicon > > TMols

bool CanGetMols(void) const

Check if it is safe to call GetMols method.

void ResetSeq_id(void)

Reset Seq_id data member.

void SetPublic(TPublic &value)

Assign a value to Public data member.

const TSequences & GetSequences(void) const

Get the Sequences member data.

bool IsUnit(void) const

Check if variant Unit is selected.

bool CanGetStructure(void) const

Check if it is safe to call GetStructure method.

list< CRef< CGC_Assembly > > TMore_assemblies

list< CRef< CGC_Sequence > > TSet

const TSingle & GetSingle(void) const

Get the variant data.

const TPublic & GetPublic(void) const

Get the Public member data.

const TSet & GetSet(void) const

Get the variant data.

bool CanGetMore_assemblies(void) const

Check if it is safe to call GetMore_assemblies method.

const TMore_assemblies & GetMore_assemblies(void) const

Get the More_assemblies member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

@ e_not_set

No variant selected.

@ eGC_SequenceRole_top_level

@ eGC_SequenceRole_component

@ eGC_SequenceRole_scaffold

@ eGC_SequenceRole_pseudo_scaffold

@ eGC_SequenceRole_chromosome

@ eGC_SequenceRole_submitter_pseudo_scaffold

@ eState_placed

exist only within a replicon. placed sequences on higher sequence

void SetTo(TTo value)

Assign a value to To data member.

TChain GetChain(void) const

Get the Chain member data.

const TPdb & GetPdb(void) const

Get the variant data.

bool IsSetAccession(void) const

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

bool IsMix(void) const

Check if variant Mix is selected.

list< CRef< CSeq_interval > > Tdata

const TId & GetId(void) const

Get the Id member data.

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetMol(void) const

Check if it is safe to call GetMol method.

bool IsPdb(void) const

Check if variant Pdb is selected.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

TVersion GetVersion(void) const

Get the Version member data.

bool CanGetVersion(void) const

Check if it is safe to call GetVersion method.

const TMol & GetMol(void) const

Get the Mol member data.

TLocal & SetLocal(void)

Select the variant.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetVersion(void) const

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

bool CanGetChain(void) const

Check if it is safe to call GetChain method.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_not_set

No variant selected.

const TInst & GetInst(void) const

Get the Inst member data.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsLoc(void) const

Check if variant Loc is selected.

const TId & GetId(void) const

Get the Id member data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

const TLoc & GetLoc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsLiteral(void) const

Check if variant Literal is selected.

list< CRef< CDelta_seq > > Tdata

CConstRef< CGC_SeqIdAlias > s_GetSeqIdAlias_GenBankRefSeq(CConstRef< CGC_TypedSeqId > tsid)

bool s_RevStrLenSort(const string &A, const string &B)

map< string, CStopWatch > TTimerMap

bool s_DoesBioseqRecurse(const CBioseq &Bioseq)

bool s_HasMoreDigits(const string &Name, const string &Chromo)

bool s_IsNumericString(const string &A)

size_t s_CountNumeric(const string &A)

map< string, CStopWatch > TTimerMap

constexpr auto sort(_Init &&init)

bool operator==(const SIdSpec &Other) const

@ e_Role_ExcludePseudo_Top

bool IsSpecMet(const SIdSpec &Guessed) const

bool operator<(const SIdSpec &Other) const

string ToString(void) const

Selector used in CSeqMap methods returning iterators.

string ToString(const wxRect &rc)

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