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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/molinfo__edit__dlg_8cpp_source.html below:

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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

( wxWindow* parent, wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer1);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer2, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 3);

wxStaticText* itemStaticText1 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer2->Add(itemStaticText1, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxTOP, 5);

wxStaticText* itemStaticText2 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE|wxST_NO_AUTORESIZE );

itemBoxSizer2->Add(itemStaticText2, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxTOP, 5);

wxStaticText* itemStaticText3 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer2->Add(itemStaticText3, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxTOP, 5);

wxStaticText* itemStaticText4 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE|wxST_NO_AUTORESIZE );

itemBoxSizer2->Add(itemStaticText4, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxTOP, 5);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText5 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer3->Add(itemStaticText5, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString molecule1,molecule2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), molecule1,0,wxDefaultValidator);

wxStaticText* itemStaticText6 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer3->Add(itemStaticText6, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), molecule2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText7 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer4->Add(itemStaticText7, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString technique1,technique2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), technique1,0,wxDefaultValidator);

wxStaticText* itemStaticText8 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer4->Add(itemStaticText8, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), technique2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer5 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText9 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer5->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString complete1,complete2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), complete1,0,wxDefaultValidator);

wxStaticText* itemStaticText10 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer5->Add(itemStaticText10, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), complete2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer6, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText11 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer6->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString class1,class2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), class1,0,wxDefaultValidator);

wxStaticText* itemStaticText12 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer6->Add(itemStaticText12, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), class2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer7 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText13 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer7->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString topology1,topology2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), topology1,0,wxDefaultValidator);

wxStaticText* itemStaticText14 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer7->Add(itemStaticText14, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), topology2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer8 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer8, 0, wxALIGN_CENTER_HORIZONTAL|wxRIGHT, 3);

wxStaticText* itemStaticText15 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer8->Add(itemStaticText15, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString strand1,strand2;

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), strand1,0,wxDefaultValidator);

wxStaticText* itemStaticText16 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

itemBoxSizer8->Add(itemStaticText16, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

=

wxChoice(itemDialog1,

, wxDefaultPosition, wxSize(100, -1), strand2,0,wxDefaultValidator);

wxBoxSizer* itemBoxSizer9 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer9, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 3);

=

wxCheckBox( itemDialog1,

,

(

));

itemBoxSizer9->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

wxBoxSizer* itemBoxSizer10 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer10, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, wxRB_GROUP );

itemBoxSizer10->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

itemBoxSizer10->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

itemBoxSizer10->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

itemBoxSizer10->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

itemBoxSizer10->Add(

, 0, wxALIGN_LEFT|wxALL, 4);

wxBoxSizer* itemBoxSizer11 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer1->Add(itemBoxSizer11, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

wxButton* itemButton1 =

wxButton( itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer11->Add(itemButton1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton2 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer11->Add(itemButton2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(item_mol1 != wxNOT_FOUND && item_mol2 != wxNOT_FOUND &&

item_tech1 != wxNOT_FOUND && item_tech2 != wxNOT_FOUND &&

item_complete1 != wxNOT_FOUND && item_complete2 != wxNOT_FOUND)

sel_mol1,sel_mol2;

(item_mol1 == 0) sel_mol1 = -1;

sel_mol1 =

[choice_mol1];

(item_mol2 == 0) sel_mol2 = -1;

sel_mol2 =

[choice_mol2];

sel_tech1,sel_tech2;

(item_tech1 == 0) sel_tech1 = -1;

sel_tech1 =

[choice_tech1];

(item_tech2 == 0) sel_tech2 = -1;

sel_tech2 =

[choice_tech2];

sel_complete1,sel_complete2;

(item_complete1 == 0) sel_complete1 = -1;

sel_complete1 =

[choice_complete1];

(item_complete2 == 0) sel_complete2 = -1;

sel_complete2 =

[choice_complete2];

(item_class1 != wxNOT_FOUND && item_class2 != wxNOT_FOUND &&

item_topology1 != wxNOT_FOUND && item_topology2 != wxNOT_FOUND &&

item_strand1 != wxNOT_FOUND && item_strand2 != wxNOT_FOUND)

sel_class1,sel_class2;

(item_class1 == 0) sel_class1 = -1;

sel_class1 =

(

[choice_class1]);

(item_class2 == 0) sel_class2 = -1;

sel_class2 =

(

[choice_class2]);

sel_topology1,sel_topology2;

(item_topology1 == 0) sel_topology1 = -1;

sel_topology1 =

(

[choice_topology1]);

(item_topology2 == 0) sel_topology2 = -1;

sel_topology2 =

(

[choice_topology2]);

sel_strand1,sel_strand2;

(item_strand1 == 0) sel_strand1 = -1;

sel_strand1 =

(

[choice_strand1]);

(item_strand2 == 0) sel_strand2 = -1;

sel_strand2 =

(

[choice_strand2]);

(*(

.GetCompleteSeq_entry()),

, sel_class1, sel_class2, sel_topology1, sel_topology2, sel_strand1, sel_strand2);

(!

)

res;

(

->IsSetData() &&

->GetData().IsProt() &&

->GetData().GetProt().IsSetProcessed())

CSeq_loc& prot_loc =

->GetLocation();

(!partial3 && !partial5)

(partial3 && !partial5)

(!partial3 && partial5)

(partial3 && partial5)

(choice_mol2 == -1 && choice_tech2 == -1 && choice_complete2 == -1)

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

(choice_mol2 != -1)

molinfo->SetBiomol(choice_mol2);

(choice_complete2 != -1)

molinfo->SetCompleteness(choice_complete2);

(choice_tech2 != -1)

molinfo->SetTech(choice_tech2);

((*it)->IsMolinfo())

& molinfo = (*it)->GetMolinfo();

edited_desc->

(**it);

modified =

;

((molinfo.

() == choice_mol1 || choice_mol1 == -1) && choice_mol2 != -1 && choice_mol1 != choice_mol2)

(choice_mol2 != -1)

((molinfo.

() == choice_tech1 || choice_tech1 == -1) && choice_tech2 != -1 && choice_tech1 != choice_tech2)

edited_molinfo.

(choice_tech2);

(choice_tech2 != -1)

edited_molinfo.

(choice_tech2);

((molinfo.

() == choice_complete1 || choice_complete1 == -1) && choice_complete2 != -1 && choice_complete1 != choice_complete2)

(choice_complete2 != -1)

(**it, composite, choice_mol1, choice_mol2, choice_tech1, choice_tech2, choice_complete1, choice_complete2);

edited_object->

(inst);

modified =

;

((choice_class1 == -1 || (inst.

() && inst.

() ==

(choice_class1))) && choice_class2 != -1 && choice_class1 != choice_class2)

((choice_strand1 == -1 || (inst.

() && inst.

() ==

(choice_strand1))) && choice_strand2 != -1 && choice_strand1 != choice_strand2)

(**it, composite, choice_class1, choice_class2, choice_topology1, choice_topology2, choice_strand1, choice_strand2);

@ eExtreme_Biological

5' and 3'

void AddCommand(IEditCommand &command)

map< string, int > m_tech

CMolInfo::ECompleteness compute_peptide_completeness(CSeq_entry_Handle seh)

wxChoice * m_ChoiceTopology2

map< string, CSeq_inst::EMol > m_class

wxChoice * m_ChoiceTopology1

bool Create(wxWindow *parent, wxWindowID id=11000, const wxString &caption=_("Edit MolInfo"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

wxChoice * m_ChoiceClass2

wxChoice * m_ChoiceTechnique2

static bool ShowToolTips()

Should we show tooltips?

wxChoice * m_ChoiceStrand2

CMolInfoEditDlg()

Constructors.

void CreateNewMolInfo(const CSeq_entry &se, CCmdComposite *composite, int choice_mol2, int choice_tech2, int choice_complete2)

wxChoice * m_ChoiceStrand1

wxChoice * m_ChoiceTechnique1

map< string, int > m_biomol

~CMolInfoEditDlg()

Destructor.

wxChoice * m_ChoiceMolecule1

wxChoice * m_ChoiceClass1

void CreateControls()

Creates the controls and sizers.

map< string, CSeq_inst::ETopology > m_topology

wxChoice * m_ChoiceComplete1

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

map< string, int > m_complete

objects::CSeq_entry_Handle m_TopSeqEntry

void ApplyToInst(const CSeq_entry &se, CCmdComposite *composite, int choice_class1, int choice_class2, int choice_topology1, int choice_topology2, int choice_strand1, int choice_strand2)

void Init()

Initialises member variables.

map< string, CSeq_inst::EStrand > m_strand

void ApplyToMolInfo(const CSeq_entry &se, CCmdComposite *composite, int choice_mol1, int choice_mol2, int choice_tech1, int choice_tech2, int choice_complete1, int choice_complete2)

CRef< CCmdComposite > GetCommand()

wxChoice * m_ChoiceMolecule2

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxChoice * m_ChoiceComplete2

static bool IsAa(EMol mol)

static bool IsNa(EMol mol)

Base class for all serializable objects.

const_iterator begin() const

const_iterator end() const

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

Set object to copy of another one.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

EProcessed

processing status

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

bool IsSetCompleteness(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

const TInst & GetInst(void) const

Get the Inst member data.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetMol(void) const

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

bool IsSetStrand(void) const

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

bool IsSetBiomol(void) const

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

TTech GetTech(void) const

Get the Tech member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TMol GetMol(void) const

Get the Mol member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetTopology(TTopology value)

Assign a value to Topology data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

ETopology

topology of molecule

EMol

molecule class in living organism

bool IsSetTech(void) const

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

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

EStrand

strandedness in living organism

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetTech(TTech value)

Assign a value to Tech data member.

TMolinfo & SetMolinfo(void)

Select the variant.

void SetMol(TMol value)

Assign a value to Mol data member.

bool IsSetTopology(void) const

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

@ eCompleteness_has_left

5' or NH3 end present

@ eCompleteness_complete

complete biological entity

@ eCompleteness_has_right

3' or COOH end present

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_partial

partial but no details given

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_physmap

from physical mapping techniques

@ eTech_other

use Source.techexp

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_seq_pept_homol

sequenced peptide, ordered by homology

@ eTech_composite_wgs_htgs

composite of WGS and HTGS

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_seq_pept_overlap

sequenced peptide, ordered by overlap

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_concept_trans

conceptual translation

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_standard

standard sequencing

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_seq_pept

peptide was sequenced

@ eTech_survey

one-pass genomic sequence

@ eTech_barcode

barcode of life project

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_derived

derived from other data, not a primary entity

@ eTech_fli_cdna

full length insert cDNA

@ eTech_est

Expressed Sequence Tag.

@ eTech_concept_trans_a

conceptual transl. supplied by author

@ eTech_genemap

from genetic mapping techniques

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_genomic_mRNA

reported a mix of genomic and cdna sequence

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ eBiomol_other_genetic

other genetic material

@ eTopology_tandem

some part of tandem repeat

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

@ eStrand_other

default ds for DNA, ss for RNA, pept

@ eStrand_ds

double strand

@ eStrand_ss

single strand

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

#define FOR_EACH_SEQENTRY_ON_SEQSET(Itr, Var)

FOR_EACH_SEQENTRY_ON_SEQSET EDIT_EACH_SEQENTRY_ON_SEQSET.

#define FOR_EACH_SEQDESC_ON_SEQENTRY(Itr, Var)

FOR_EACH_SEQDESC_ON_SEQENTRY EDIT_EACH_SEQDESC_ON_SEQENTRY.

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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