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NCBI C++ ToolKit: src/objects/seqset/Seq_entry.cpp Source File

(*si)->SetParentEntry(

);

(*si)->SetParentEntry(

);

(

() ) {

(

() ) {

(

() ) {

(

() ) {

(

() ) {

(

() ) {

(

() ) {

( desc.

() == choice ) {

(level !=

) {

(level !=

) {

(

() ) {

pair<CSeq_id_Handle, CConstRef<CBioseq> >

;

( new_id->

() ) {

( obj_id->

() ) {

base = obj_id->

();

(

k = suffix_id.

(); ; ++k ) {

(

(id_map, new_idh).second ) {

( level2 > level1 ) {

( level1 > level2 ) {

( entry1 != entry2 ) {

( level2 > level1 ) {

( level1 > level2 ) {

( parent == parent2 ) {

( *it == entry1 ) {

( *it == entry2 ) {

it != id_map.

() && it->first.first ==

; ++it ) {

( !it->first.second ) {

& seq = *it->first.second;

seq_level = 0;

( entry == &annot_entry ) {

( seq_level < closest_level ) {

closest_level = seq_level;

closest_entry = seq_entry;

( seq_level == closest_level &&

closest_entry, closest_level) ) {

closest_entry = seq_entry;

annot_level =

(&annot_entry);

closest_seq_level =

;

it != id_map.

() && it->first.first ==

; ++it ) {

( !it->first.second ) {

& seq = *it->first.second;

seq_level =

(seq_entry);

seq_entry, seq_level);

level = annot_level - parent_level;

( level < closest_level ) {

closest_level = level;

closest_seq_level = seq_level;

closest_entry = seq_entry;

( level == closest_level &&

seq_level < closest_seq_level ) {

closest_seq_level = seq_level;

closest_entry = seq_entry;

( level == closest_level &&

seq_level == closest_seq_level &&

closest_entry, closest_seq_level) ) {

closest_entry = seq_entry;

id_it = id_map.

(

(idh,

));

( id_it == id_map.

() || !id_it->second ) {

( !new_id.

() ) {

has_conflict =

;

<<

(*idit)->AsFastaString());

(id_map,

, &*it).first->second = gi1;

has_conflict =

;

( !ins.first->second ) {

ins.first->second = gi1;

( !has_conflict ) {

( map_it != id_map.

() && !map_it->second ) {

( it->IsSetAnnot() ) {

static CBioseq_set::ELabelType s_GetBioseqSetLabelType(CSeq_entry::ELabelType lt)

size_t sx_Level(const CSeq_entry *entry)

TIdInsert sx_AddId(TIdMap &id_map, const CSeq_id_Handle &id, const CBioseq *seq=0)

const CSeq_id_Handle & sx_FindBestId(const TIdMap &id_map, TIdMapCache &cache, const CSeq_entry &annot_entry, const CSeq_id_Handle &id)

map< TIdKey, CSeq_id_Handle > TIdMap

map< CSeq_id_Handle, CSeq_id_Handle > TIdMapCache

bool sx_ComesBefore(const CSeq_entry *entry1, size_t level1, const CSeq_entry *entry2, size_t level2)

static CBioseq::ELabelType s_GetBioseqLabelType(CSeq_entry::ELabelType lt)

CSeq_id_Handle sx_MakeUniqueId(const CSeq_id_Handle &idh, TIdMap &id_map)

size_t sx_GetParentLevel(const CSeq_entry *entry1, size_t level1, const CSeq_entry *entry2, size_t level2)

bool sx_CanReassign(CSeq_id::E_Choice type)

pair< TIdMap::iterator, bool > TIdInsert

pair< CSeq_id_Handle, CConstRef< CBioseq > > TIdKey

void sx_ProcessId(const TIdMap &id_map, TIdMapCache &cache, const CSeq_entry &entry, CSeq_id &id)

void SetParentEntry(CSeq_entry *entry)

void GetLabel(string *label, ELabelType type) const

CSeq_entry * GetParentEntry(void) const

void SetParentEntry(CSeq_entry *entry)

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

void GetLabel(string *label, ELabelType type, bool worst=false) const

@Seq_descr.hpp User-defined methods of the data storage class.

CSeq_entry * m_ParentEntry

const TAnnot & GetAnnot(void) const

const CSeq_descr & GetDescr(void) const

bool IsSetAnnot(void) const

void ResetParentEntry(void)

CSeq_descr & SetDescr(void)

virtual bool UserOp_Equals(const CSerialUserOp &object) const

Will be called after comparing the datatool-generated members.

void ReassignConflictingIds(void)

void GetLabel(string *label, ELabelType type) const

virtual void UserOp_Assign(const CSerialUserOp &source)

Will be called after copying the datatool-generated members.

void ParentizeOneLevel(void)

bool IsSetDescr(void) const

void SetParentEntry(CSeq_entry *entry)

list< CRef< CSeq_annot > > TAnnot

CSeq_entry * GetParentEntry(void) const

Root class for all serialization exceptions.

Base class for user-defined serializable classes to allow for objects assignment and comparison.

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

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

static const char si[8][64]

#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.

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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.

static const char label[]

bool IsStr(void) const

Check if variant Str is selected.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

TId GetId(void) const

Get the variant data.

TGeneral & SetGeneral(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

TLocal & SetLocal(void)

Select the variant.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_General

for other databases

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

E_Choice Which(void) const

Which variant is currently selected.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

@ e_not_set

No variant selected.

list< CRef< CSeqdesc > > Tdata

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_id > > TId

E_Choice

Choice variants.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

E_Choice Which(void) const

Which variant is currently selected.

const GenericPointer< typename T::ValueType > T2 value

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