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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/GC__Assembly_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/genomecoll/GC_Assembly.cpp Source File

87 typedef

list<CRef<CDbtag>> TId;

89 if

((*id_it)->GetDb() ==

"GenColl"

90

(*id_it)->GetTag().IsId()) {

91

release_id = (*id_it)->GetTag().GetId();

102 typedef

list<CRef<CDbtag>> TId;

104 if

((*id_it)->GetDb() ==

"GenColl"

105

(*id_it)->GetTag().IsStr()) {

106

accession = (*id_it)->GetTag().GetStr();

122 typedef

list<CRef<CDbtag>> TId;

124 if

((*id_it)->GetDb() ==

"submitter"

125

(*id_it)->GetTag().IsStr()) {

126

submitter_id = (*id_it)->GetTag().GetStr();

142 "assembly is neither unit not set"

);

156 if

(desc && desc->CanGetName()) {

157 return

desc->GetName();

206 if

(desc && desc->IsSetDescr()) {

208 if

((*it)->IsSource()) {

209

tax_id = (*it)->GetSource().GetOrg().GetTaxId();

227 if

(desc && desc->IsSetRelease_type()) {

243 if

(desc && desc->IsSetRelease_type()) {

251 return GetName

() ==

"non-nuclear"

;

274

units.insert(units.end(),

tmp

.begin(),

tmp

.end());

278 tmp

= (**it).GetAssemblyUnits();

279

units.insert(units.end(),

tmp

.begin(),

tmp

.end());

296 switch

(

set

.GetSet_type()) {

301 if

(

set

.IsSetMore_assemblies()) {

303 set

.GetMore_assemblies()) {

304

assms.push_back(*it);

322 if

(

tmp

.insert(assm).second) {

323

assms.push_back(assm);

339 if

(seq1->GetFullAssembly()->IsTargetSetReference() &&

340

!seq2->GetFullAssembly()->IsTargetSetReference())

344 if

(seq2->GetFullAssembly()->IsTargetSetReference() &&

345

!seq1->GetFullAssembly()->IsTargetSetReference())

351 if

(seq1->GetAssemblyUnit()->IsPrimaryUnit() &&

352

!seq2->GetAssemblyUnit()->IsPrimaryUnit())

356 if

(seq2->GetAssemblyUnit()->IsPrimaryUnit() &&

357

!seq1->GetAssemblyUnit()->IsPrimaryUnit())

394 if

(it->second.size() > 1) {

395 switch

(find_option) {

398 "multiple sequences found in assembly: "

402 return

*min_element(it->second.begin(), it->second.end(),

SBestSequence

());

409 return

it->second.front();

421

sequences = it->second;

437 type

= repl->GetMoleculeType();

438 location

= repl->GetMoleculeLocation();

467 if

(target_set ==

NULL

) {

476 switch

(

set

.GetSet_type()) {

479 set

.SetPrimary_assembly().CreateHierarchy(target_set);

480 if

(

set

.IsSetMore_assemblies()) {

482 set

.SetMore_assemblies()) {

483

(*it)->CreateHierarchy(target_set);

490 set

.SetPrimary_assembly().m_TargetSet = target_set;

491 set

.SetPrimary_assembly().x_Index(*

this

);

492 if

(

set

.IsSetMore_assemblies()) {

494 set

.SetMore_assemblies()) {

495

(*it)->m_TargetSet = target_set;

503 "unknown assembly set type"

);

517 for

( ; seq_it; ++seq_it) {

525

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

526

&repl->GetSequence().GetSingle() != &this_seq) {

528

repl->GetSequence().GetSingle();

532

repl_seq.

GetSequences

().front()->GetSeqs().size() == 1 &&

533

repl_seq.

GetSequences

().front()->GetSeqs().front() == &this_seq &&

534

repl->GetSequence().GetSingle().GetSeq_id()

554 if

(these_ids.

insert

(idh).second) {

580 if

(

GetUnit

().IsSetOther_sequences()) {

582 SetUnit

().SetOther_sequences()) {

594 set

.SetPrimary_assembly().x_Index(root);

595 if

(

set

.IsSetMore_assemblies()) {

597 set

.SetMore_assemblies()) {

598

(*it)->x_Index(root);

671 x_Index

(seq, **

, (*it)->GetState());

703 x_Index

(seq, **

, (*it)->GetState());

719 x_Index

(seq, **

, (*it)->GetState());

764 "Unexpected subset in call to CGC_Assembly::GetMolecules()"

);

772 bool

invalid_data =

false

;

775 for

( ; sequence_it; ++sequence_it, ++

count

) {

776 if

(sequence_it->GetSeq_id().IsGi() && !sequence_it->IsSetRoles() ) {

777

invalid_data =

true

;

782 bool

fits_role =

false

;

786 else if

(sequence_it->IsSetRoles()) {

801 "GC-Sequence.roles is not set in the current assembly; " 802 "please re-extract GC-Assembly"

);

811 s_Extract

(

set

.GetPrimary_assembly(), molecules, subset);

812 if

(

set

.IsSetMore_assemblies()) {

814 set

.GetMore_assemblies()) {

826

molecules.resize(

set

.IsSetMore_assemblies()

827

set

.GetMore_assemblies().

size

() + 1 : 1);

828

vector< list< CConstRef<CGC_Sequence> > >::iterator unit_it = molecules.begin();

829 s_Extract

(

set

.GetPrimary_assembly(), *unit_it++, subset);

830 if

(

set

.IsSetMore_assemblies()) {

832 set

.GetMore_assemblies()) {

857

molecules.front().clear();

884 if

(

IsUnit

() &&

GetUnit

().GetFullAssembly().GetPointer() !=

this

) {

891 "IsTargetSetReference() called on target set"

);

User-defined methods of the data storage class.

static bool s_RoleFitsSubset(int role, CGC_Assembly::ESubset subset)

static void s_Extract(const CGC_Assembly &assm, list< CConstRef< CGC_Sequence > > &molecules, CGC_Assembly::ESubset subset)

Molecule Extraction Routines.

User-defined methods of the data storage class.

string GetFileSafeDisplayName() const

Get file-safe version of full label for assmebly.

CConstRef< CGC_Assembly > GetFullAssembly() const

Access the most specific full assembly the assembly unit belongs to This is needed because assemblies...

CGC_Assembly * m_Assembly

string GetDisplayName() const

Get full display name of assembly unit.

list< CConstRef< CGC_Assembly > > TFullAssemblies

string GetAccession() const

Retrieve the accession for this assembly.

bool IsOrganelle() const

Is this a non-nuclear assembly unit?

void CreateHierarchy(CGC_Assembly *target_set=NULL)

Generate the internal up-pointers.

TTaxId GetTaxId() const

Retrieve the tax-id for this assembly.

CGC_AssemblyUnit::TClass GetUnitClass() const

If this is an assembly unit, get unit class.

string x_GetSubmitterId() const

string GetName() const

Retrieve the name of this assembly.

TFullAssemblies GetFullAssemblies() const

Retrieve a list of all full assemblies contained in this assembly Note that, if the assembly is a ful...

list< CConstRef< CGC_AssemblyUnit > > TAssemblyUnits

string GetBestIdentifier() const

Either accession or submitter-provided id.

string GetFileSafeName() const

Retrieve the file-safe version of assembly name, if available; othwreise default to standard name.

TAssemblyUnits GetAssemblyUnits() const

Retrieve a list of all assembly units contained in this assembly.

void PreWrite() const

PreWrite() / PostRead() handle events for indexing of local structures.

bool IsTargetSetReference() const

Is this assembly the reference assembly of the target set, or part of it?

bool IsGenBank() const

Is this assembly a GenBank assembly?

void GetMoleculesByUnit(vector< TSequenceList > &molecules, ESubset subset) const

Retrieve a subset of molecules separately for each unit, in the same order in which the units are ret...

void Find(const CSeq_id_Handle &id, TSequenceList &sequences) const

Find all references to a given sequence within an assembly.

void x_Index(CGC_Assembly &assm, CGC_Replicon &replicon)

indexing infrastructure

const CGC_AssemblyDesc & GetDesc() const

Retrieve the full set of assembly descriptors.

const list< CRef< CDbtag > > & x_GetId() const

string GetFileSafeDisplayName() const

Get file-safe version of full label for assmebly.

bool IsRefSeq() const

Is this assembly a RefSeq assembly?

list< CConstRef< CGC_Sequence > > TSequenceList

CGC_Assembly * m_TargetSet

TSequenceIndex m_SequenceMap

void GetMolecules(TSequenceList &molecules, ESubset subset) const

Retrieve a subset of molecules.

void CreateIndex()

Generate the Seq-id index.

void GetRepliconTypeLocRole(const CSeq_id_Handle &id, string &type, string &location, set< int > &role) const

Returns replicon type, location and role.

int GetReleaseId() const

Retrieve the release id for this assembly.

CConstRef< CGC_Assembly > GetTargetSet() const

Access the top-level target set that this assemhly belongs to.

string GetDisplayName() const

Get full label for assmebly; if this is a unit, full assembly name followed by unit name.

@ eSubmitterPseudoScaffold

CGC_AssemblyUnit * m_AssemblyUnit

CGC_Assembly * m_Assembly

CGC_Replicon * m_Replicon

CGC_Sequence * m_ParentSequence

CConstRef< CGC_Replicon > GetReplicon() const

Access the replicon the sequence belongs to.

CGC_AssemblyUnit * m_AssemblyUnit

CGC_Assembly * m_Assembly

CGC_TaggedSequences::TState m_ParentRel

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

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const char location[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define NCBI_THROW(exception_class, err_code, message)

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

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CGC_Sequence > > TSeqs

const TUnit & GetUnit(void) const

Get the variant data.

bool IsSingle(void) const

Check if variant Single is selected.

const TDesc & GetDesc(void) const

Get the Desc member data.

TClass GetClass(void) const

Get the Class member data.

list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms

bool IsAssembly_set(void) const

Check if variant Assembly_set is selected.

const TFilesafe_name & GetFilesafe_name(void) const

Get the Filesafe_name member data.

TSequences & SetSequences(void)

Assign a value to Sequences data member.

bool IsSetFilesafe_name(void) const

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

const TDesc & GetDesc(void) const

Get the Desc member data.

const TPrimary_assembly & GetPrimary_assembly(void) const

Get the Primary_assembly member data.

void SetSequence(TSequence &value)

Assign a value to Sequence data member.

const TSeq_id_synonyms & GetSeq_id_synonyms(void) const

Get the Seq_id_synonyms member data.

list< CRef< CGC_TaggedSequences > > TSequences

const TAssembly_set & GetAssembly_set(void) const

Get the variant data.

list< CRef< CGC_Replicon > > TMols

bool IsSetSequences(void) const

placed: populated both on chromosome and scaffold levels unlocalized: populated on chromosome level C...

const TSequence & GetSequence(void) const

Get the Sequence member data.

TUnit & SetUnit(void)

Select the variant.

const TSequences & GetSequences(void) const

Get the Sequences member data.

bool IsUnit(void) const

Check if variant Unit is selected.

list< CRef< CGC_Assembly > > TMore_assemblies

list< CRef< CGC_Sequence > > TSet

TAssembly_set & SetAssembly_set(void)

Select the variant.

bool IsSetSeq_id_synonyms(void) const

Other known identifiers: Local / gpipe-satellite / genbank / refseq Check if a value has been assigne...

list< CRef< CGC_TaggedSequences > > TOther_sequences

const TId & GetId(void) const

Get the Id member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

@ 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

@ eSet_type_full_assembly

full-assembly: set of asm-units

@ eSet_type_assembly_set

set of full-assemblies stopper

list< CRef< CSeqdesc > > Tdata

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

bool operator()(const CConstRef< CGC_Sequence > &seq1, const CConstRef< CGC_Sequence > &seq2) const

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