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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/group_explode.cpp Source File

sel_srv->GetCurrentSelection(

);

* ptr = it->object.GetPointer();

objects::CSeq_feat* seqfeat =

objects::CSeq_feat*

(ptr);

.push_back(seqfeat);

vector<const objects::CSeq_feat*> orig_vec;

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

create_general_only =

;

(vector<const objects::CSeq_feat*>, orig_it, orig_vec)

objects::CSeq_feat*

= *orig_it;

is_exon =

;

(

->IsSetData() &&

->GetData().IsImp() &&

->GetData().GetImp().IsSetKey() &&

->GetData().GetImp().GetKey() ==

)

((*qual)->IsSetQual() && (*qual)->GetQual() ==

&& (*qual)->IsSetVal())

is_cds =

;

objects::CBioseq_Handle product;

(

->IsSetData() &&

->GetData().IsCdregion())

interval->

().SetFrom(feat_start);

interval->

().SetTo(feat_stop);

->Assign(*feat_loc.

());

interval->

().SetId(*

);

(loc_it.IsSetStrand())

interval->

().SetStrand(loc_it.GetStrand());

(loc_it.GetPos() == 0)

(loc_it.GetPos() + 1 == loc_it.GetSize())

(is_exon && exon_number > 0)

((*qual)->IsSetQual() && (*qual)->GetQual() ==

&& (*qual)->IsSetVal())

objects::CFeat_CI prot_feat_ci(product, objects::SAnnotSelector(objects::CSeqFeatData::eSubtype_prot));

prot_feat.

(

objects::CSeq_feat());

prot_feat->Assign(*(prot_feat_ci->GetSeq_feat()));

new_feat->

().SetCdregion().SetFrame(objects::CSeqTranslator::FindBestFrame(*new_feat,scope));

(is_cds && product)

cmd_processor->

(composite);

,

,

,

,

,

,

(!name.empty())

(

==

||

==

||

==

||

==

)

+=

;

(

j = 0; j < name.size(); j++)

modified =

;

(

feat_ci(tse); feat_ci; ++feat_ci)

(!feat_ci->GetOriginalFeature().IsSetData() || !feat_ci->GetOriginalFeature().GetData().IsRna())

(name.empty() && feat_ci->GetOriginalFeature().IsSetData() && feat_ci->GetOriginalFeature().GetData().IsRna())

name = feat_ci->GetOriginalFeature().GetData().GetRna().GetRnaProductName();

vector<string>

;

interval->

().SetFrom(feat_start);

interval->

().SetTo(feat_stop);

->Assign(*feat_loc.

());

interval->

().SetId(*

);

(loc_it.IsSetStrand())

interval->

().SetStrand(loc_it.GetStrand());

(loc_it.GetPos() == 0)

(loc_it.GetPos() + 1 == loc_it.GetSize())

new_feat->

(feat_ci->GetOriginalFeature());

(num_locs <

.size())

new_feat->

().SetRna().SetRnaProductName(

, reminder);

@ eExtreme_Positional

numerical value

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

void AddCommand(IEditCommand &command)

static CRef< CCmdComposite > apply(objects::CSeq_entry_Handle tse)

static void RNAWordsFromString(string name, vector< string > &names)

static void apply(IWorkbench *wb, ICommandProccessor *cmd_processor, CScope &scope)

static void GetSeqFeats(IWorkbench *wb, vector< const objects::CSeq_feat * > &result)

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

IWorkbench is the central interface in the application framework.

static const struct name_t names[]

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

const CSeq_id * GetId(void) const

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

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

vector< CSeq_entry_Handle > TTSE_Handles

bool IsSetComment(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

virtual const CSeq_loc & GetLocation(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const string & GetComment(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

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.

@ eTrunc_Begin

Truncate leading whitespace only.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void SetData(TData &value)

Assign a value to Data data member.

USING_SCOPE(ncbi::objects)

static const char * RNA_words[]

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define FOR_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

FOR_EACH_GBQUAL_ON_SEQFEAT EDIT_EACH_GBQUAL_ON_SEQFEAT.

#define EDIT_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

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