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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/table__data__gcassembly_8cpp_source.html below:

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

82

vector< CConstRef<CGC_Sequence> >

m_Seqs

;

102  "GenBank Accession"

,

116

CGC_Assembly::GetTypeInfo(),

124

table_data->

m_Object

=

object

.object;

125

table_data->

m_Scope

=

object

.scope;

126

table_data->

Init

();

146  if

(unique_seqs.

insert

(*it).second) {

158  if

(unique_seqs.

insert

(*it).second) {

205  if

(replicon && replicon->CanGetName()) {

206  value

= replicon->GetName();

218  value

=

"unlocalized"

;

240

role =

"chromosome"

;

252

role =

"pseudo scaffold"

;

255

role =

"submitter pseudo scaffold"

;

261  if

( !role.empty() ) {

262  if

(!

value

.empty() ) {

307  for

(

size_t i

= 0;

i

< 30 &&

i

<

m_Seqs

.size(); ++

i

) {

310  if

(curr_synonym->

Match

(*p_synonym)) {

330  value

= unit->GetAccession();

337  value

= gc_seq.GetTypeInfo_enum_EPatch_type()->FindName(gc_seq.

GetPatch_type

(),

true

);

392

seq_id.

Reset

(&parent->GetSeq_id());

398  for

(

size_t i

= 0;

i

< 30 &&

i

<

m_Seqs

.size(); ++

i

) {

401  if

(curr_synonym->

Match

(*p_synonym)) {

415  value

.object = seq_id;

User-defined methods of the data storage class.

void CreateHierarchy(CGC_Assembly *target_set=NULL)

Generate the internal up-pointers.

list< CConstRef< CGC_Sequence > > TSequenceList

void GetMolecules(TSequenceList &molecules, ESubset subset) const

Retrieve a subset of molecules.

CConstRef< CGC_Replicon > GetReplicon() const

Access the replicon the sequence belongs to.

CConstRef< CGC_AssemblyUnit > GetAssemblyUnit() const

Access the assembly unit the sequence belongs to.

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

CGC_TaggedSequences::TState GetParentRelation() const

Access the relationship to the parent.

CConstRef< CGC_Sequence > GetParent() const

Access the parent sequence of this sequence.

static void RegisterFactory(const string &interface_name, IInterfaceFactory *factory)

virtual void GetStringValue(size_t row, size_t col, string &value) const

virtual SConstScopedObject GetObjectValue(size_t row, size_t col) const

CConstRef< CObject > m_Object

virtual double GetRealValue(size_t row, size_t col) const

virtual ColumnType GetColumnType(size_t col) const

vector< CConstRef< CGC_Sequence > > m_Seqs

virtual string GetColumnLabel(size_t col) const

virtual size_t GetColsCount() const

virtual SConstScopedObject GetRowObject(size_t row) const

virtual long GetIntValue(size_t row, size_t col) const

virtual size_t GetRowsCount() const

CRef< objects::CScope > m_Scope

static CTableDataGCAssembly * CreateObject(SConstScopedObject &object, ICreateParams *params)

iterator_bool insert(const value_type &val)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TRoles & GetRoles(void) const

Get the Roles member data.

bool IsSetPatch_type(void) const

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

bool CanGetRoles(void) const

Check if it is safe to call GetRoles method.

TPatch_type GetPatch_type(void) const

Get the Patch_type member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

@ eGC_SequenceRole_component

@ eGC_SequenceRole_scaffold

@ eGC_SequenceRole_pseudo_scaffold

@ eGC_SequenceRole_chromosome

@ eGC_SequenceRole_submitter_pseudo_scaffold

@ eState_aligned

exist only on alt-loci/patch units. List all aligned (eg cross-placed) sequences. (unaligned are list...

@ eState_placed

exist only within a replicon. placed sequences on higher sequence

@ eState_bits

exist only on primary/diploid unit. if need to report low-level contigs

@ eState_unlocalized

exist only within a replicon. "random" on a given chromosome

@ eState_unplaced

exist only on primary/diploid assembly-unit. unknown chromosome

bool IsLocal(void) const

Check if variant Local is selected.

const GenericPointer< typename T::ValueType > T2 value

#define row(bind, expected)

static ITableData::ColumnType s_ColTypes[CTableDataGCAssembly::eMaxColNum]

void initCTableDataGCAssembly()

static const string s_ColNames[CTableDataGCAssembly::eMaxColNum]

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