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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/link__mrna__cds_8cpp_source.html below:

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

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

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

mrna.

(seqfeat);

modified =

;

(!cds_hasid || !mrna_hasid) {

new_feat->

(*orig_feat);

new_feat->

().SetLocal().SetId(top_id);

(orig_feat == mrna ) {

}

(orig_feat == cds) {

->AddCommand(*chg_feat);

->AddCommand(*chg_mrna);

->AddCommand(*chg_cds);

}

(cds_hasid && mrna_hasid) {

modified =

;

->AddCommand(*chg_mrna);

->AddCommand(*chg_cds);

->AddCommand(*chg_mrna);

->AddCommand(*chg_cds);

(xref->IsSetId() && xref->GetId().IsLocal()) {

xref->SetId().SetLocal().Assign(to_feat.

().

());

assigned =

;

new_feat->

(*feat_it->GetOriginalSeq_feat());

new_feat->

().SetLocal().SetId(top_id);

->AddCommand(*chg_feat);

(cds_it->GetLocation(),

(linked_mRNAs.

(mrna) != linked_mRNAs.

()) {

linked_mRNAs.

(mrna);

(!linked_mRNAs.

()) {

(assigned || !linked_mRNAs.

()) {

cmdProcessor->

(link_cmd);

(mrna_it->IsSetProduct()) {

mrna_products.emplace(idh, mrna_it->GetOriginalSeq_feat());

(cds_it->IsSetProduct()) {

cds_products.emplace(idh, cds_it->GetOriginalSeq_feat());

(mrna_products.

() || cds_products.

()) {

(

& mrna_it : mrna_products) {

(linked_feats.

(mrna_it.second) != linked_feats.

()) {

(!cdna)

;

vector<CSeq_id_Handle> prot_ids = prot_it->

();

(

&& id_it : prot_ids) {

found_cds_it = cds_products.

(id_it);

(found_cds_it != cds_products.

()) {

(linked_feats.

(found_cds_it->second) != linked_feats.

()) {

linked_feats.

(mrna_it.second);

linked_feats.

(found_cds_it->second);

(!linked_feats.

()) {

(assigned || !linked_feats.

()) {

cmdProcessor->

(link_cmd);

(linked_mRNAs.

(mrna) != linked_mRNAs.

()) {

linked_mRNAs.

(mrna);

(!linked_mRNAs.

()) {

(assigned || !linked_mRNAs.

()) {

cmdProcessor->

(link_cmd);

((*xref_it)->IsSetId() && (*xref_it)->GetId().IsLocal()) {

(; pair_it; ++pair_it) {

(best_fit.

()) {

best_fit = feat_pair;

best_diff = (best_fit_length > feat_length) ? (best_fit_length - feat_length) : (feat_length - best_fit_length);

current_diff = (candidate_length > feat_length) ? (candidate_length - feat_length) : (feat_length - candidate_length);

(current_diff < best_diff) {

best_fit = feat_pair;

best_diff = current_diff;

linked_feats.

(feat);

linked_feats.

(best_fit);

(!linked_feats.

()) {

(assigned || !linked_feats.

()) {

cmdProcessor->

(link_cmd);

linked =

;

((*xref_it)->IsSetId() && (*xref_it)->GetId().IsLocal() && (*xref_it)->GetId().GetLocal().IsId()) {

has_xref =

;

((*it)->IsSetId() && (*it)->GetId().IsLocal() && (*it)->GetId().GetLocal().IsId()) {

& pair_feat_id = (*it)->GetId();

cmdProcessor->

(link_cmd);

.assign(

);

}

(cds && !mrna) {

.assign(

);

}

(!cds && mrna) {

.assign(

);

xref->SetId().Assign(to_feat.

());

from_feat.

().push_back(xref);

&& (*it)->GetId().IsLocal()

&& feat_id.

((*it)->GetId()))

vector<CConstRef<CObject> > objs;

wxOK | wxICON_INFORMATION);

count_feat = 0;

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

(count_feat > 1) {

wxOK | wxICON_INFORMATION);

wxOK | wxICON_INFORMATION);

(!is_cds && !is_mrna) {

wxOK | wxICON_INFORMATION);

((*it)->IsSetId() && (*it)->GetId().IsLocal() && (*it)->GetId().GetLocal().IsId()) {

wxOK | wxICON_INFORMATION);

objs.push_back(

[0].

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void AddCommand(IEditCommand &command)

static const string & s_GetProteinName(const objects::CSeq_feat_Handle &fh)

static TId s_FindHighestFeatureId(const objects::CSeq_entry_Handle &entry)

implements special composite command, which does not call to its internal commands when run the very ...

string GetRnaProductName(void) const

ESubtype GetSubtype(void) const

namespace ncbi::objects::

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

bool AssignFeatureIds(CRef< CMacroCmdComposite > cmd)

bool x_ReplaceExistingFeatIdXrefs(objects::CSeq_feat &from_feat, const objects::CSeq_feat &to_feat)

void LinkByOverlap(ICommandProccessor *cmdProcessor)

void CompleteHalfFormedXrefPairs(ICommandProccessor *cmdProcessor)

static void s_CreateXRefLink(objects::CSeq_feat &from_feat, const objects::CSeq_feat &to_feat)

static bool s_IsDirectXrefBetween(const objects::CSeq_feat &from_feat, const objects::CSeq_feat &to_feat)

bool ReplaceExistingXrefs(const objects::CSeq_feat &mrna, const objects::CSeq_feat &cds, CRef< CCmdComposite > cmd)

void LinkSelectedFeatures(TConstScopedObjects &objects, ICommandProccessor *cmdProcessor)

void LinkByLabelAndLocation(ICommandProccessor *cmdProcessor)

objects::CSeq_entry_Handle m_TopSeqEntry

bool SetReciprocalXrefs(const objects::CSeq_feat &mrna, const objects::CSeq_feat &cds, CRef< CCmdComposite > cmd)

void LinkByLabel(ICommandProccessor *cmdProcessor)

void LinkByProduct(ICommandProccessor *cmdProcessor)

vector< CConstRef< CObject > > GetReferencedmRNA_CDS(TConstScopedObjects &objects)

returns the pair of cross-referenced mRNA and CDS features, when one of them is selected

bool x_OkForLinking(CConstRef< objects::CSeq_feat > mrna, CConstRef< objects::CSeq_feat > cds)

Undo/Redo interface for editing operations.

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

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

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.

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

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

Check if both objects contain the same values.

TRange GetTotalRange(void) const

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_CheckIntRev

1st is a subset of 2nd with matching boundaries

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

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

const CFeat_id & GetId(void) const

const CSeq_feat::TXref & GetXref(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

bool IsSetXref(void) const

bool IsSetClass(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

const TId & GetId(void) const

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static const char label[]

TXref & SetXref(void)

Assign a value to Xref data member.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsLocal(void) const

Check if variant Local is selected.

const TData & GetData(void) const

Get the Data member data.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetId(void) const

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

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

const TRna & GetRna(void) const

Get the variant data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

@ eClass_nuc_prot

nuc acid and coded proteins

static string s_GetFeatureLabel(const CSeq_feat_Handle &fh)

static bool s_DoesFeatureHasXRef(const CSeq_feat &feat)

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

#define EDIT_EACH_XREF_ON_SEQFEAT(Itr, Var)

#define FOR_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

FOR_EACH_SEQFEATXREF_ON_SEQFEAT EDIT_EACH_SEQFEATXREF_ON_SEQFEAT.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

wxString ToWxString(const string &s)

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