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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/updateseqworker_8cpp_source.html below:

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

45 #include <wx/msgdlg.h> 59 for

(

size_t i

= 0;

i

< msg_listener.

(); ++

i

) {

64

message += (

"Hyphens in the update sequence have been ignored.\n"

);

71

message += (

"Invalid character was found (and ignored):"

);

86 bool

input_ok =

false

;

127 unsigned int

count_bioseqs = updseq_in.

();

128 if

(count_bioseqs > 1) {

129 string msg

(

"You selected update single sequence but the update file contains " 130

+

NStr::UIntToString

(count_bioseqs) +

" bioseqs. Do you want to continue and use the first record only?"

);

135 if

(!warn_message.empty()) {

150 if

(!input_ok)

return

;

168 if

(!input_ok)

return

;

182 if

(count_bioseqs > 1) {

183 string msg

(

"You selected update single sequence but the update file contains " 184

+

NStr::UIntToString

(count_bioseqs) +

" bioseqs. Do you want to continue and use the first record only?"

);

189

warn_message.clear();

193

}

while

(res ==

);

195 if

(!warn_message.empty()) {

212 string msg

(

"You are about to update a delta sequence with a raw sequence, which\n will convert the delta sequence to raw. Do you want to continue?"

);

218 string msg

(

"The update sequence is a delta sequence with far pointers. Do you want to continue?"

);

228 if

(dlg.ShowModal() == wxID_OK) {

240 if

(!citsub_msg.empty()) {

249

report.append(

"\n"

);

253 if

(!report.empty()) {

255

reportdlg->SetTitle(

"Update Sequence Log"

);

257

reportdlg->Show(

true

);

275 bool

input_ok =

false

;

315 int

retcode = dlg.ShowModal();

316 if

(retcode == wxOK || retcode == wxCLOSE) {

319

cmdProcessor->

(update_cmd);

322 if

(!

.empty()) {

324

report->SetTitle(

"Update Sequence Log"

);

326

report->Show(

true

);

343 string

invalidRes_msg;

344 string

duplicateids_msg;

346 for

(

size_t i

= 0;

i

< msg_listener.

(); ++

i

) {

355 if

(!hyphens_msg.empty()) {

356

hyphens_msg +=

", "

;

358

hyphens_msg += line_err.

();

366 if

(!invalidRes_msg.empty()) {

367

invalidRes_msg +=

"\n"

;

369

invalidRes_msg += line_err.

();

370

invalidRes_msg +=

.substr(pos + 2,

);

375 if

(

.find(

"Seq-id"

) !=

&&

.find(

"is a duplicate"

) !=

) {

376 if

(duplicateids_msg.find(line_err.

()) ==

) {

377 if

(!duplicateids_msg.empty()) {

378

duplicateids_msg +=

"\n"

;

380

duplicateids_msg += line_err.

();

387 if

(!hyphens_msg.empty()) {

388

message +=

"Hyphens have been ignored in the following update sequences:\n"

;

389

message += hyphens_msg;

392 if

(!invalidRes_msg.empty()) {

393 if

(!message.empty()) {

396

message +=

"Invalid residues were found and ignored in the following update sequences:\n"

;

397

message += invalidRes_msg;

400 if

(!message.empty()) {

404 if

(!duplicateids_msg.empty()) {

405

duplicateids_msg =

"Duplicate sequence ids were found in the update sequence file:\n"

+ duplicateids_msg;

407

reportdlg->SetTitle(

"Duplicate seq-ids"

);

409

reportdlg->Show(

true

);

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

void SetText(const wxString &text)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Sequence update exception class.

void UpdateSingleSequence_Ext(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor) const

void x_LaunchSingleUpdateSequence(CUpdateSeq_Input &updseq_in, SUpdateSeqParams &params, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor) const

void UpdateMultipleSequences(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor)

void UpdateSingleSequence(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse, ICommandProccessor *cmdProcessor) const

void x_GetSeqsWithIgnoredResidues(objects::ILineErrorListener &msg_listener)

Class responsible for executing the sequence update for one old-update sequence pair.

string GetRevCompReport() const

const string & GetCitSubMessage() const

void GetNotImportedFeatsReport(CNcbiOstream &out) const

CRef< CCmdComposite > Update(bool create_general_only)

Main function responsible to update the old sequence with the update sequence.

const string & GetRevCompReport() const

bool ReadUpdSeqs_FromClipboard(objects::ILineErrorListener *msg_listener)

bool SetOldEntryAndScope(const objects::CSeq_entry_Handle &tse)

bool ReadUpdSeqs_FromFile(objects::ILineErrorListener *msg_listener)

void SetData(const SUpdateSeqParams &params)

SUpdateSeqParams GetData() const

Sets up the old and the update sequences, and generates the alignment between them.

bool SetOldBioseqAndScope(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse)

unsigned int CountBioseqs()

bool ReadSingleAccession(void)

Reads single update sequence identified by an accession.

bool ReadSingleUpdateSequence(objects::ILineErrorListener *msg_listener)

Reads (ASN.1 or FASTA) single update sequence from a file.

static bool s_IsDeltaWithFarPointers(const objects::CBioseq &bseq)

const objects::CBioseq_Handle & GetUpdateBioseq(void) const

bool ReadUpdateSequenceFromClipboard(objects::ILineErrorListener *msg_listener)

Reads single update sequence from the clipboard. It supports FASTA and text ASN formats.

void ResetUpdateSequence()

const objects::CBioseq_Handle & GetOldBioseq(void) const

static bool s_IsDeltaWithNoGaps(const objects::CBioseq &bseq)

Undo/Redo interface for editing operations.

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

virtual size_t Count() const =0

virtual const ILineError & GetError(size_t) const =0

0-based error retrieval.

@ eProblem_InvalidResidue

@ eProblem_IgnoredResidue

@ eProblem_GeneralParsingError

virtual EProblem Problem(void) const =0

virtual const string & SeqId(void) const =0

virtual const string & ErrorMessage() const

virtual EDiagSev GetSeverity(void) const

IWorkbench is the central interface in the application framework.

Stores parameters regarding the type of sequence update, on how to handle existing features and on ho...

ESequenceUpdateType m_SeqUpdateOption

bool AreUpdateParamsValid(void)

@ eSeqUpdateReplace

do not change the old sequence

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDiag_Warning

Warning message.

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

EDialogReturnValue NcbiInfoBox(const string &message, const string &title="Info")

specialized Message Box function for reporting general information messages

void NcbiWarningBox(const string &message, const string &title="Warning")

specialized Message Box function for reporting non-critical errors

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

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool IsSetInst_Repr(void) const

TInst_Repr GetInst_Repr(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsOssEmpty(CNcbiOstrstream &oss)

NCBI_NS_STD::string::size_type SIZE_TYPE

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 UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

@ eRepr_raw

continuous sequence

EDialogReturnValue

enumerated return values for dialog boxes, starting from 1 to undermine attempts to cast it "bool"

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

static string s_WarnAboutIgnoredResidues(ILineErrorListener &msg_listener)

wxString ToWxString(const string &s)

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