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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cds__to__mat__peptide_8cpp_source.html below:

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

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdDlg1->SetSizer(itemBoxSizer2);

=

wxRadioButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, wxRB_GROUP );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->SetValue(

);

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, wxRB_GROUP );

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_LEFT, 0);

=

wxRadioButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

(

->GetValue())

(

->GetValue())

vector<CConstRef<CObject> > objs;

leave_original =

;

->AddCommand(*subcmd);

vector<CConstRef<CObject> > objs;

vector<string> products;

products.push_back(product);

new_loc->

(

->GetLocation());

new_product = product;

add_loc->

(

->GetLocation());

new_cds->

().SetWhole().Assign(*prot_id);

annot->

().SetFtable().push_back(new_cds);

protein->SetId().push_back(prot_id);

pdesc->SetMolinfo().SetBiomol(objects::CMolInfo::eBiomol_peptide);

pdesc->SetMolinfo().SetCompleteness(objects::CMolInfo::eCompleteness_complete);

pdesc->SetMolinfo().SetCompleteness(objects::CMolInfo::eCompleteness_no_left);

(pdesc->GetMolinfo().GetCompleteness() == objects::CMolInfo::eCompleteness_complete) {

pdesc->SetMolinfo().SetCompleteness(objects::CMolInfo::eCompleteness_no_right);

pdesc->SetMolinfo().SetCompleteness(objects::CMolInfo::eCompleteness_no_ends);

protein->SetDescr().Set().push_back(pdesc);

prot_feat->SetData().SetProt();

prot_feat->SetData().SetProt().SetName().push_back(new_product);

prot_feat->SetLocation().SetInt().SetId(*prot_id);

prot_feat->SetLocation().SetInt().SetFrom(0);

prot_feat->SetLocation().SetInt().SetTo(protein->GetLength() - 1);

prot_annot->

().SetFtable().push_back(prot_feat);

protein->SetAnnot().push_back(prot_annot);

prot_entry->

(*protein);

loc->

(*prot_id);

(

< products.size())

mat_peptide->

().SetProt().SetName().push_back(products[

++]);

prot_annot->

().SetFtable().push_back(mat_peptide);

vector<CConstRef<CObject> > objs;

leave_original =

;

(

= 0;

< feats.size();

++)

(!inner->

(*

) && already_converted.

(inner_fh) == already_converted.

())

already_converted.

(inner_fh);

mat_peptide->

(*inner);

mat_peptide->

().SetProt().SetName().push_back(product);

(prot_bsh2 && prot_bsh2.

())

CSeq_entry::TAnnot::iterator annot_it = entry->

().begin();

( annot_it != entry->

().end() )

((*annot_it)->IsSetData() && (*annot_it)->GetData().IsFtable())

((*feat_it)->IsSetData() && (*feat_it)->GetData().GetSubtype() == feat->

().

() && feat->

(**feat_it))

((*annot_it)->GetData().GetFtable().empty())

annot_it = entry->

().erase(annot_it);

(entry->

())

(entry->

())

(entry->

())

((*entry_it)->IsSeq() && (*entry_it)->GetSeq().IsAa() && (*entry_it)->GetSeq().GetFirstId()->Match(*feat->

().

()))

CSeq_entry::TAnnot::iterator annot_it = entry->

().begin();

( annot_it != entry->

().end() )

((*annot_it)->IsSetData() && (*annot_it)->GetData().IsFtable())

((*feat_it)->IsSetData() && (*feat_it)->GetData().GetSubtype() == feat->

().

() && feat->

(**feat_it) == 0)

(!annot && entry->

())

wxSizerItemList& slist = sizer->GetChildren();

(wxSizerItemList::iterator iter = slist.begin(); iter != slist.end(); ++iter, ++

) {

((*iter)->IsSizer()) {

}

((*iter)->IsWindow()) {

wxWindow* child = (*iter)->GetWindow();

wxSizer* subsizer = child->GetSizer();

->GetMatchingIds(matches);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

USING_SCOPE(ncbi::objects)

objects::CSeq_entry_Handle m_TopSeqEntry

bool Create(wxWindow *parent, wxWindowID id, const wxString &title, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxDEFAULT_FRAME_STYLE, const wxString &name=wxFrameNameStr)

bool GetTopLevelSeqEntryAndProcessor()

void UpdateChildrenFeaturePanels(wxSizer *sizer)

void FindAnnot(CRef< CSeq_entry > entry, const CSeq_feat *feat, CRef< CSeq_annot > &annot)

wxCheckBox * m_EntireRange

~CCdsToMatPeptide()

Destructor.

void ConvertEach(CRef< CCmdComposite > cmd)

virtual CRef< CCmdComposite > GetCommand()

void RemoveFeature(CRef< CSeq_entry > entry, const CSeq_feat *feat)

void MergeConvert(CRef< CCmdComposite > cmd)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CStringConstraintPanel * m_StringConstraintPanel

CRef< CMiscSeqTableColumn > m_col

CFeatureFieldNamePanel * m_FeatureConstraint

virtual string GetErrorMessage()

void RemoveProteins(CRef< CSeq_entry > entry, const CSeq_feat *feat, CSeq_entry_Handle seh)

CRef< CConvertFeatureBase > m_converter

static bool ShowToolTips()

Should we show tooltips?

CCdsToMatPeptide()

Constructors.

COkCancelPanel * m_OkCancel

void ConvertInner(CRef< CCmdComposite > cmd)

void OnRadioButton(wxCommandEvent &event)

wxRadioButton * m_ProductFirst

void Init()

Initialises member variables.

wxTextCtrl * m_ProductName

void CreateControls()

Creates the controls and sizers.

wxRadioButton * m_ProductThis

bool Create(wxWindow *parent, wxWindowID id=10568, const wxString &caption=_("Convert CDS to Mat-peptide"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(900, 500), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void ProcessUpdateFeatEvent(wxCommandEvent &event)

static CRef< CConvertFeatureBase > Create(objects::CSeqFeatData::ESubtype subtype_from, objects::CSeqFeatData::ESubtype subtype_to)

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

string x_GetCDSProduct(const objects::CSeq_feat &orig, objects::CScope &scope)

map< CSeq_id_Handle, TSeqPos > m_SeqLen

map< CSeq_id_Handle, set< CSeq_id_Handle > > m_Synonyms

void AddSeq(const CSeq_id_Handle &idh, TSeqType seq_type, TSeqPos seq_len)

virtual TSeqType GetSequenceType(const CSeq_id_Handle &idh)

Get information about sequence type (nuc or prot).

map< CSeq_id_Handle, TSeqType > m_SeqType

void AddSynonym(const CSeq_id_Handle &idh1, const CSeq_id_Handle &idh2)

virtual void CollectSynonyms(const CSeq_id_Handle &id, TSynonyms &synonyms)

Collect all synonyms for the id including the id itself.

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Get sequence length or kInvalidSeqPos.

void PopulateFeatureListbox(void)

virtual string GetFieldName(const bool subfield=false)

Returns the name of the field as selected in the panel.

void ListPresentFeaturesFirst(const objects::CSeq_entry_Handle &entry, vector< const objects::CFeatListItem * > *featlist=nullptr)

vector< CConstRef< CObject > > GetObjects(objects::CBioseq_Handle bsh)

ESubtype GetSubtype(void) const

@ eSubtype_mat_peptide_aa

const TAnnot & GetAnnot(void) const

namespace ncbi::objects::

int Compare(const CSeq_feat &f2) const

Compare relative order of this feature and feature f2, ordering first by features' coordinates,...

CSeq_loc_Mapper_Base –.

CSeq_loc_Mapper_Options –.

CRef< edit::CStringConstraint > GetStringConstraint()

IWorkbench is the central interface in the application framework.

const_iterator end() const

iterator_bool insert(const value_type &val)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

const string kPartialStart

#define EVT_UPDATE_FEATURE_LIST(id, fn)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

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

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

@ eOverlap_Subset

2nd is a subset of 1st ranges

CConstRef< CSeq_feat > GetOverlappingmRNA(const CSeq_loc &loc, CScope &scope)

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

vector< TFeatScore > TFeatScores

void GetOverlappingFeatures(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)

Find all features overlapping the location.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CRef< CSeq_loc > MapTotalRange(const CSeq_loc &seq_loc)

Take the total range from the location and run it through the mapper.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

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

@ eLocationToProduct

Map from the feature's location to product.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CBioseq_set_Handle GetParentBioseq_set(void) const

Get parent bioseq-set handle.

bool IsProtein(void) const

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

TInst_Length GetInst_Length(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

const TId & GetId(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsSetDesc(void) const

description (instead of name) Check if a value has been assigned to Desc data member.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void ResetComment(void)

Reset Comment data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TProt & GetProt(void) const

Get the variant data.

void ResetProduct(void)

Reset Product data member.

bool IsSetProduct(void) const

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

bool IsInt(void) const

Check if variant Int is selected.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

void ResetAnnot(void)

Reset Annot data member.

bool IsSet(void) const

Check if variant Set is selected.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

void ResetAnnot(void)

Reset Annot data member.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

#define ERASE_SEQFEAT_ON_SEQANNOT(Itr, Var)

ERASE_SEQFEAT_ON_SEQANNOT.

#define EDIT_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var)

#define FOR_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var)

FOR_EACH_SEQFEAT_ON_SEQANNOT EDIT_EACH_SEQFEAT_ON_SEQANNOT.

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

#define FOR_EACH_SEQENTRY_ON_SEQSET(Itr, Var)

FOR_EACH_SEQENTRY_ON_SEQSET EDIT_EACH_SEQENTRY_ON_SEQSET.

#define EDIT_EACH_SEQENTRY_ON_SEQSET(Itr, Var)

#define ERASE_SEQENTRY_ON_SEQSET(Itr, Var)

ERASE_SEQENTRY_ON_SEQSET.

void GetProductToCDSMap(objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

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