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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__jobs_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/blast_jobs.cpp Source File

72 m_Descr

= tool_name +

" - submitting sequences to NCBI Net BLAST"

;

88 static const char

* kLogMsg =

"CNetBlastSubmittingJob::Run() - exception in x_Run() "

;

89 static string

kErrorMsg =

"Unhandled exception in CNetBlastSubmittingJob::Run()"

;

90 static const char

* kBlastError =

"BLAST returned error(s) in CNetBlastSubmittingJob::Run() :"

;

103

}

catch

(std::exception& ee) {

104

err_msg = kLogMsg +

GetDescr

() +

". "

+ ee.what();

109 if

( !err_msg.empty() ){

110 string

s = kErrorMsg + err_msg;

115 string

s = kBlastError;

133 static const char

* kFailedToSubmit =

"Failed to submit BLAST search for "

;

161

descr->MarkDeleted(

false

);

163

descr->Submit(*bset);

164 string

rid = descr->GetRID();

170 string

err =

"Failed to create a bioseq for item "

str

;

171

err +=

" The item has not been submitted."

;

179 catch

(std::exception& e) {

180 string

err =

string

(kFailedToSubmit) +

str

". "

+ e.

what

();

265 const string

& tool_name,

268

m_WaitPeriodIndex(0),

269

m_Descriptors(descriptors)

287 static const char

* kLogMsg =

"CNetBlastMonitoringJob::Run() - exception in x_Run() "

;

288 static string

kErrorMsg =

"Unhandled exception in CNetBlastMonitoringJob::Run()"

;

289 static const char

* kBlastError =

"BLAST returned error(s) in CNetBlastMonitoringJob::Run() :"

;

304

}

catch

(std::exception& ee) {

305

err_msg = kLogMsg +

GetDescr

() +

". "

+ ee.what();

311 if

( !err_msg.empty() ){

312 string

s = kErrorMsg + err_msg;

317 string

s = kBlastError;

339

vector<string> retrieve_ids;

353 switch

(descr->GetState()) {

355

retrieve_ids.push_back(descr->GetRID());

361 m_Errors

.push_back(descr->GetErrors());

370 string

s =

"RID "

+ descr->GetRID() +

" is invalid or expired"

;

386 if

( ! retrieve_ids.empty() && !

IsCanceled

() ){

414

task->Init_RetrieveRID(RIDs);

471 static long

periods[] = { 1, 1, 1, 2, 3, 4, 6, 10, 20, 30, 60 };

472 static const int

max_index =

sizeof

(periods) /

sizeof

(

long

) - 1;

483 const

vector<string>* RIDs,

492 m_Descr

"NCBI Net BLAST - retrieving results"

;

498 for

(

size_t i

= 0;

< RIDs.size();

++) {

499 const string

& rid = RIDs[

];

502

descr->MarkDeleted(

false

);

529 string

rid = descr.

GetRID

();

545 string

s =

"BLAST Search for RID "

+ rid +

" produced no results"

;

551 string

s =

"RID "

+ rid +

" is still pending"

;

562 string

s =

"RID "

+ descr.

GetRID

() +

" is invalid or expired"

;

580

scope.

Reset

(

new

objects::CScope(*obj_mgr));

581

scope->AddDefaults();

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message an...

CAppTaskService - Application Task Service.

CBLASTParams - save user-specified parameters and preferences.

CProjectSelectOptions - describes how new Project Items shall be added to a workspace.

IServiceLocator - an abstract mechanism for locating services.

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

void AddTask(IAppTask &task)

Add a task to the queue.

void GetErrors(vector< string > &errors) const

EJobState x_Run()

this functions performs real work every call to this function does pools each job once,...

void DeleteJobDescriptors(TJobDescrVec &descriptors)

virtual CRef< CObject > GetResult()

Returns the Job Result.

CRef< CNetBLASTUIDataSource > m_NetBlastDS

virtual CTimeSpan GetWaitPeriod()

returns a period of time after which the task shall be executed again

vector< CRef< CNetBlastJobDescriptor > > TDescriptors

void x_StartRetrivingTask(const vector< string > &RIDs)

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

TConstScopedObjects & GetSeqLocs()

CRef< CNetBlastJobDescriptor > FindJobDescriptor(const string &rid)

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

void x_SetStatusText(const string &text)

vector< CRef< CNetBlastJobDescriptor > > TDescriptors

vector< string > m_Errors

TConstScopedObjects m_SeqLocs

virtual CRef< CObject > GetResult()

Returns the Job Result.

CRef< blast::CRemoteBlast > GetRemoteBlast()

CNetBlastLoadingJob(CNetBLASTUIDataSource &ds, const vector< string > *RIDs=NULL, CScope *scope=NULL)

CNetBlastLoadingJob.

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

virtual void x_CreateProjectItems()

iterates on the given RIDs and creates Project Items or accumulates error

CNetBlastMonitoringJob(CNetBLASTUIDataSource &ds, IServiceLocator *srv_locator, const string &tool_name, TDescriptors &descriptors)

CNetBlastSubmittingJob.

CNetBlastSubmittingJob(string tool_name, const CBLASTParams &params, CNetBLASTUIDataSource &ds)

CNetBlastSubmittingJob.

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

CRef< objects::CSeq_align_set > Retrieve()

virtual void SetLoadingOptions(CSelectProjectOptions &options)

void x_Run()

this fucntions performs real work

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

string m_Descr

mutex to sync our internals

vector< CRef< CNetBlastJobDescriptor > > m_Descriptors

CSelectProjectOptions m_LoadingOptions

void GetDescriptors(TDescriptors &descriptors)

vector< string > m_Errors

string m_ToolName

mutex to sync our internals

void x_CreateProjectItemsFromBlastResult(objects::CSeq_align_set &results, CRef< blast::CRemoteBlast > RemoteBlast)

TDescriptors m_Descriptors

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

void SetRIDs(CNetBLASTUIDataSource &ds, const vector< string > &RIDs)

CRef< CAppJobError > m_Error

TDescriptors m_Descriptors

CRef< CNetBlastJobDescriptor > CreateJobDescriptor(const CBLASTParams &params)

void GetErrors(vector< string > &errors) const

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

vector< string > m_Errors

CRef< CAppJobError > m_Error

IServiceLocator * m_SrvLocator

void x_SetStatusText(const string &text)

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

void x_AddError(const string &error)

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

string m_Descr

mutex to sync our internals

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

static void AddProjectItemsFromRID(CRef< objects::CScope > scope, CSeq_align_set &results, bool isFindComp, CRef< blast::CRemoteBlast > RemoteBlast, const set< string > &filter, CDataLoadingAppJob &job, SRIDStatInfo &RIDStatInfo)

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

TObjectType * GetPointer(void) 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.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

CRef< objects::CBioseq > SeqLocToBioseq(const objects::CSeq_loc &loc, objects::CScope &scope)

static void text(MDB_val *v)

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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