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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fix__for__trans__splicing_8cpp_source.html below:

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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

SetSize(wxSize(280, 550));

sel_srv->GetActiveObjects(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString choices;

=

wxListBox(itemDialog1,

, wxDefaultPosition, wxDefaultSize, choices, wxLB_SINGLE);

itemBoxSizer2->Add(

, 1, wxGROW|wxALL, 5);

=

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 15);

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 15);

itemBoxSizer2->Add(OkCancel, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

->SetStringSelection(

(

));

(cds->IsSetProduct())

(!(*name_it).empty())

[*name_it][bsh].push_back(cds->GetSeq_feat_Handle());

name =

->GetStringSelection().ToStdString();

items2 = items->second.find(bsh);

(items2 == items->second.end())

modified =

;

name =

->GetStringSelection().ToStdString();

vector<CSeq_feat_Handle> feats, genes;

problem(

);

(cds->GetOriginalFeature().IsSetExcept_text() &&

(cds->GetOriginalFeature().GetExcept_text(),

) != string::npos)

(cds->IsSetProduct())

(*name_it == name)

(unique_feats.

(fh) != unique_feats.

() || unique_genes.

(gene) != unique_genes.

())

genes.push_back(gene);

unique_feats.

(fh);

unique_genes.

(gene);

(feats.size() != 3 && feats.size() != 5)

+=

.str() +

;

(feats.size() == 3)

vector<CSeq_feat_Handle> feats1, genes1, feats2, genes2;

feats1.push_back(feats[0]);

feats1.push_back(feats[1]);

feats2.push_back(feats[0]);

feats2.push_back(feats[2]);

genes1.push_back(genes[0]);

genes1.push_back(genes[1]);

genes2.push_back(genes[0]);

genes2.push_back(genes[2]);

(feats.size() == 5)

vector<CSeq_feat_Handle> feats1, genes1, feats2, genes2;

feats1.push_back(feats[0]);

feats1.push_back(feats[1]);

feats1.push_back(feats[2]);

feats2.push_back(feats[0]);

feats2.push_back(feats[3]);

feats2.push_back(feats[4]);

genes1.push_back(genes[0]);

genes1.push_back(genes[1]);

genes1.push_back(genes[2]);

genes2.push_back(genes[0]);

genes2.push_back(genes[3]);

genes2.push_back(genes[4]);

report->SetTitle(

(

));

report->Show(

);

second_pass,

create_general_only)

partial_start(

);

partial_stop(

);

(

= 0;

< feats.size();

++)

(

!= 0 || second_pass)

new_feat->

(partial_start || partial_stop);

new_feat->

().SetWhole().Assign(*new_product_id);

->AddCommand(*retranslate_cmd);

index =

.GetSelection();

name =

->GetStringSelection().ToStdString();

index =

.GetSelection();

name =

->GetStringSelection().ToStdString();

wxWindow* editorWindow = editor->CreateWindow(&edit_dlg);

editorWindow->TransferDataToWindow();

(edit_dlg.ShowModal() == wxID_OK)

@ eExtreme_Positional

numerical value

CIRef< IEditObject > CreateEditorForObject(CConstRef< CObject > obj, objects::CSeq_entry_Handle seh, bool create)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

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()

ICommandProccessor * m_CmdProccessor

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

void CombineFeatures(const vector< CSeq_feat_Handle > &feats, CRef< CCmdComposite > cmd, CScope &scope, int &offset, CSeq_loc::TOpFlags merge_flag, bool second_pass, bool create_general_only)

virtual CRef< CCmdComposite > GetCommand()

CIRef< IFlatFileCtrl > m_FlatFileCtrl

void OnPageLeft(wxCommandEvent &event)

void CollectProteinNames()

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

CFixForTransSplicing()

Constructors.

~CFixForTransSplicing()

Destructor.

CRef< CSelectionClient > m_SelectionClient

wxStaticText * m_BioseqLabel

bool m_SelectionClientAttached

void OnListItemSelected(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Fix For Trans-splicing"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void OnProteinNameSelected(wxCommandEvent &event)

virtual void ExecuteCmd(CRef< CCmdComposite > cmd)

map< string, map< CBioseq_Handle, vector< CSeq_feat_Handle > > > m_name_to_obj

void OnListItemActivated(wxCommandEvent &event)

void Init()

Initialises member variables.

static bool ShowToolTips()

Should we show tooltips?

void OnPageRight(wxCommandEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxArrayString m_ProteinNames

void CreateControls()

Creates the controls and sizers.

vector< CBioseq_Handle > m_bioseqs

map< string, map< CBioseq_Handle, wxArrayString > > m_name_to_cds

void SetText(const wxString &text)

CProjectService - a service providing API for operations with Workspaces and Projects.

void SetSelectedObjects(TConstScopedObjects &objs)

namespace ncbi::objects::

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

IWorkbench is the central interface in the application framework.

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

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

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.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

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

Override Assign() to incorporate cache invalidation.

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

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

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

Add two seq-locs.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

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.

void SetExcept(TExcept value)

Assign a value to Except data member.

const TData & GetData(void) const

Get the Data member data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TProt & GetProt(void) const

Get the variant data.

bool IsSetProduct(void) const

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

@ eMol_na

just a nucleic acid

void GetViewObjects(IWorkbench *workbench, TConstScopedObjects &objects)

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

#define FOR_EACH_NAME_ON_PROTREF(Itr, Var)

FOR_EACH_NAME_ON_PROTREF EDIT_EACH_NAME_ON_PROTREF.

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

string GetTextObjectDescription(const CSeq_feat &sf, CScope &scope)

CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)

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