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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/remove__sequences_8cpp_source.html below:

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

49 #include <wx/listctrl.h> 50 #include <wx/hyperlink.h> 69

objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_na);

70  for

( ; b_iter ; ++b_iter ) {

71

m_Seqs.push_back(*b_iter);

75

Create(parent,

id

, caption, pos,

size

, style);

82

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

83

itemPanel1->SetSizer(itemBoxSizer2);

85

wxBoxSizer* itemBoxSizer3 =

new

wxBoxSizer(wxHORIZONTAL);

86

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

88  m_ListCtrl1

=

new

wxListCtrl( itemPanel1,

wxID_ANY

, wxDefaultPosition, wxSize(400, 320), wxLC_REPORT|wxLC_NO_HEADER );

89

itemBoxSizer3->Add(

m_ListCtrl1

, 1, wxGROW|wxALL, 5);

92  m_ListCtrl2

=

new

wxListCtrl( itemPanel1,

wxID_ANY

, wxDefaultPosition, wxSize(400, 320), wxLC_REPORT|wxLC_NO_HEADER );

93

itemBoxSizer3->Add(

m_ListCtrl2

, 1, wxGROW|wxALL, 5);

95

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxHORIZONTAL);

96

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

98

wxButton* itemButton1 =

new

wxButton( itemPanel1,

ID_REMOVE_SEQ_LEFT

,

_

(

"<<<"

), wxDefaultPosition, wxDefaultSize, 0 );

99

itemBoxSizer4->Add(itemButton1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 15);

101

wxButton* itemButton2 =

new

wxButton( itemPanel1,

ID_REMOVE_SEQ_RIGHT

,

_

(

">>>"

), wxDefaultPosition, wxDefaultSize, 0 );

102

itemBoxSizer4->Add(itemButton2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 15);

104

wxBoxSizer* itemBoxSizer17 =

new

wxBoxSizer(wxHORIZONTAL);

105

itemBoxSizer2->Add(itemBoxSizer17, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

107

wxStaticText* itemStaticText4 =

new

wxStaticText( itemPanel1, wxID_STATIC,

_

(

"Seq-id"

), wxDefaultPosition, wxDefaultSize, 0 );

108

itemBoxSizer17->Add(itemStaticText4, 0, wxALIGN_TOP|wxALL, 5);

114

wxFlexGridSizer* itemFlexGridSizer5 =

new

wxFlexGridSizer(0, 2, 0, 0);

115

itemBoxSizer2->Add(itemFlexGridSizer5, 0, wxALIGN_CENTER_HORIZONTAL | wxALL, 0);

117

wxStaticText* itemStaticText5 =

new

wxStaticText( itemPanel1, wxID_STATIC,

_

(

"Select sequences longer than"

), wxDefaultPosition, wxDefaultSize, 0 );

118

itemFlexGridSizer5->Add(itemStaticText5, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

120  m_Min

=

new

wxTextCtrl(itemPanel1,

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxSize(250, -1), 0);

121

itemFlexGridSizer5->Add(

m_Min

, 0, wxALIGN_LEFT | wxALIGN_CENTER_VERTICAL | wxTOP|wxBOTTOM, 5);

123

wxStaticText* itemStaticText6 =

new

wxStaticText( itemPanel1, wxID_STATIC,

_

(

"Select sequences less than"

), wxDefaultPosition, wxDefaultSize, 0 );

124

itemFlexGridSizer5->Add(itemStaticText6, 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL |wxALL, 5);

126  m_Max

=

new

wxTextCtrl( itemPanel1,

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxSize(250, -1), 0 );

127

itemFlexGridSizer5->Add(

m_Max

, 0, wxALIGN_LEFT | wxALIGN_CENTER_VERTICAL | wxTOP | wxBOTTOM, 5);

129

wxBoxSizer* itemBoxSizer12 =

new

wxBoxSizer(wxHORIZONTAL);

130

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 3);

132

wxButton* itemButton13 =

new

wxButton(itemPanel1,

ID_REMOVE_SEQ_SELECT

,

_

(

"Select"

), wxDefaultPosition, wxDefaultSize, 0);

133

itemBoxSizer12->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

135

wxButton* itemButton14 =

new

wxButton(itemPanel1,

ID_REMOVE_SEQ_SELECT_ALL

,

_

(

"Select All"

), wxDefaultPosition, wxDefaultSize, 0);

136

itemBoxSizer12->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

138

wxButton* itemButton15 =

new

wxButton(itemPanel1,

ID_REMOVE_SEQ_UNSELECT_ALL

,

_

(

"Unselect All"

), wxDefaultPosition, wxDefaultSize, 0);

139

itemBoxSizer12->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

141

wxBoxSizer* itemBoxSizer16 =

new

wxBoxSizer(wxHORIZONTAL);

142

itemBoxSizer2->Add(itemBoxSizer16, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

144

wxButton* itemButton16 =

new

wxButton( itemPanel1, wxID_OK,

_

(

"Accept"

), wxDefaultPosition, wxDefaultSize, 0 );

145

itemBoxSizer16->Add(itemButton16, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

147

wxButton* itemButton17 =

new

wxButton( itemPanel1, wxID_CANCEL,

_

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

148

itemBoxSizer16->Add(itemButton17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

150

wxHyperlinkCtrl* itemHyperlinkCtrl =

new

wxHyperlinkCtrl( itemPanel1, wxID_HELP,

_

(

"Help"

),

wxT

(

"https://www.ncbi.nlm.nih.gov/tools/gbench/manual9/#remove-sequences"

), wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

151

itemHyperlinkCtrl->SetForegroundColour(wxColour(192, 192, 192));

152

itemBoxSizer16->Add(itemHyperlinkCtrl, 0, wxALIGN_CENTER_VERTICAL, 5);

159  if

(

id

.IsGenbank() &&

id

.GetGenbank().IsSetAccession())

160

labels[0] =

id

.GetGenbank().GetAccession();

161  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsStr())

162

labels[1] =

id

.GetGeneral().GetTag().GetStr();

163  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsId())

165  if

(

id

.IsLocal() &&

id

.GetLocal().IsStr())

166

labels[3] =

id

.GetLocal().GetStr();

170

labels.push_back(

label

);

175

vector<string> labels(5);

179  for

(CBioseq_Handle::TId::const_iterator it = seh.

GetSeq

().

GetId

().begin(); it != seh.

GetSeq

().

GetId

().end(); ++it)

190  for

(

int i

=0;

i

<labels.size();

i

++)

191  if

(!labels[

i

].

empty

())

192

strs.push_back(labels[

i

]);

207  if

(

id

.IsGenbank() &&

id

.GetGenbank().IsSetAccession())

209  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetDb() &&

id

.GetGeneral().GetDb() ==

"BankIt"

&&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsStr())

211

labels.

insert

(

id

.GetGeneral().GetTag().GetStr());

212

labels.

insert

(

"BankIt"

+

id

.GetGeneral().GetTag().GetStr());

213  string first

, second;

218  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetDb() &&

id

.GetGeneral().GetDb() ==

"NCBIFILE"

&&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsStr())

220

labels.

insert

(

id

.GetGeneral().GetTag().GetStr());

221

labels.

insert

(

"NCBIFILE"

+

id

.GetGeneral().GetTag().GetStr());

223  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsStr())

224

labels.

insert

(

id

.GetGeneral().GetTag().GetStr());

225  if

(

id

.IsGeneral() &&

id

.GetGeneral().IsSetTag() &&

id

.GetGeneral().GetTag().IsId())

227  if

(

id

.IsLocal() &&

id

.GetLocal().IsStr())

228

labels.

insert

(

id

.GetLocal().GetStr());

239  for

(CBioseq_Handle::TId::const_iterator it = seh.

GetSeq

().

GetId

().begin(); it != seh.

GetSeq

().

GetId

().end(); ++it)

255

vector<string> vec(strs.

begin

(), strs.

end

());

256  return

constraint->DoesListMatch(vec);

275  for

(

unsigned int i

=0;

i

<set_size; ++

i

)

294

item =

m_ListCtrl1

->GetNextItem(item, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

295  if

( item == -1 )

break

;

296  int i

=

static_cast<int>

(

m_ListCtrl1

->GetItemData(item));

307

item =

m_ListCtrl2

->GetNextItem(item, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

308  if

( item == -1 )

break

;

309  int i

=

static_cast<int>

(

m_ListCtrl2

->GetItemData(item));

320  for

(

unsigned int i

=0;

i

<set_size; ++

i

)

335  long

min_length = -1;

336  long

max_length = LONG_MAX;

337  bool

min_num =

m_Min

->GetValue().ToLong(&min_length);

338  bool

max_num =

m_Max

->GetValue().ToLong(&max_length);

341  if

( !min_num && !max_num && !constraint)

365  else if

(min_num || max_num)

367  if

(length > min_length && length < max_length)

384

wxDialog::Create( parent,

id

, caption, pos,

size

, style );

388

GetSizer()->SetSizeHints(

this

);

417

report->SetTitle(

wxT

(

"Bioseqs Removed"

));

419

report->Show(

true

);

428  for

(

int i

= 0;

i

<

m_Seqs

.size();

i

++) {

445

objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_aa);

446  for

( ; b_iter ; ++b_iter ) {

459

objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_aa);

460  for

( ; b_iter ; ++b_iter )

477  if

(!fi->IsSetProduct())

482

proteins.

insert

(prot_bsh);

485

objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_aa);

486  for

( ; b_iter ; ++b_iter )

489  if

(proteins.

find

(bsh) == proteins.

end

())

const CBioseq & GetNucFromNucProtSet(void) const

TSeqPos GetLength(void) const

bool IsSetLength(void) const

void SetText(const wxString &text)

static CRef< CCmdComposite > JustRemoveProteins(objects::CSeq_entry_Handle seh)

static CRef< CCmdComposite > OrphanedProteins(objects::CSeq_entry_Handle seh)

static CRef< CCmdComposite > AndRenormalizeNucProtSets(objects::CSeq_entry_Handle seh)

vector< CBioseq_Handle > m_Seqs

CRef< CCmdComposite > GetCommand()

void OnSelectAll(wxCommandEvent &event)

CSeq_entry_Handle GetSeqEntry(unsigned int i)

void ChooseSequence(CBioseq_Handle bsh)

void OnButtonMoveRight(wxCommandEvent &event)

bool MatchConstraint(CRef< objects::edit::CStringConstraint > constraint, CSeq_entry_Handle seh)

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

void CollectLabelsAll(CSeq_entry_Handle seh, set< string > &strs)

void OnUnselectAll(wxCommandEvent &event)

void OnSelect(wxCommandEvent &event)

void CombineLabels(const CSeq_id &id, vector< string > &labels)

string GetLabel(CSeq_entry_Handle seh)

void OnButtonMoveLeft(wxCommandEvent &event)

vector< int > m_Available

void CollectLabels(CSeq_entry_Handle seh, list< string > &strs)

CStringConstraintPanel * m_StringConstraintPanel

void CombineLabelsAll(const CSeq_id &id, set< string > &labels)

void SetStringSelection(const wxString &str)

CRef< edit::CStringConstraint > GetStringConstraint()

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

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

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

const string & GetMsg(void) const

Get message string.

EDialogReturnValue NcbiMessageBox(const string &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const string &title="Error", EDialogTextMode text_mode=eRaw)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TClass GetClass(void) const

TSeqPos GetBioseqLength(void) const

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

bool IsProtein(void) const

bool IsSetClass(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TId & GetId(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static const char label[]

@ eClass_nuc_prot

nuc acid and coded proteins

const TId & GetId(void) const

Get the Id member data.

bool IsSetId(void) const

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

constexpr bool empty(list< Ts... >) noexcept

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

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

#define ID_REMOVE_SEQ_SELECT_ALL

#define ID_REMOVE_SEQ_RIGHT

#define ID_REMOVE_SEQ_UNSELECT_ALL

#define ID_REMOVE_SEQ_LEFT

#define ID_REMOVE_SEQ_SELECT

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

CRef< CCmdComposite > GetDeleteSequenceCommand(objects::CBioseq_Handle bsh)

wxString ToWxString(const string &s)

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