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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__search__task_8cpp_source.html below:

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

37 #include <wx/msgdlg.h> 48  const string

& tool_name)

49

: m_SrvLocator(srv_locator),

51

m_ToolName(tool_name),

71  m_Descr

+= (

n

==1) ?

" sequence"

:

" sequences"

;

91  size_t n

=descriptors.size();

93  m_Descr

+= (

n

==1) ?

" sequence"

:

" sequences"

;

104  size_t n

= RIDs.size();

106  m_Descr

+= (

n

== 1) ?

" RID"

:

" RIDs"

;

139  for

(

i

= 0;

i

< descriptors.size(); ++

i

) {

142  m_Descr

+= descriptors[

i

]->GetRID();

147  if

(

i

< descriptors.size())

178  return "Submitting results to NCBI Net BLAST server"

;

181  return "Executing BLAST jobs remotely on NCBI Net BLAST server"

;

184  return "Retrieving results from NCBI Net BLAST server"

;

212  if

( ! descriptors.empty()) {

249

vector<string> errors;

251  if

( ! errors.empty()) {

257

vector<string> errors;

259  if

( ! errors.empty()) {

277  size_t n

= errors.size();

279  msg

+=

" cannot be retrieved for the following reasons:"

;

280  for

(

size_t i

= 0;

i

<

n

;

i

++) {

281  msg

+=

"\n "

+ errors[

i

];

284  string

title = (

n

== 1) ?

"Error in"

:

"Errors in"

;

CAppJobTask CAppJobTask is an adapter that allows for running IAppJobs as Tasks in App Task Service.

string m_Descr

task description

CBLASTParams - save user-specified parameters and preferences.

virtual ETaskState x_RunCurrentSubTask()

runs the current subtask; one may override this function in order to perform special pre-execution or...

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

void SetOptions(const CSelectProjectOptions &options)

virtual CScope * GetScope() const

CNetBlastLoadingJob - an application job for loading RIDs from NCBI Net BLAST server.

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

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

TProjectId GetTargetProjectId()

IServiceLocator - an abstract mechanism for locating services.

CIRef< T > GetServiceByType()

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

void SetReportErrors(bool report)

enabled / disbale error reporting for failed Jobs

ETaskState

List of task states defining the task management FSM.

@ eCompleted

successfully finished

void GetErrors(vector< string > &errors) const

virtual CIRef< IAppTask > x_NextSubTask()

prepares the next subtask (makes it current), this function is used for iterating subtasks.

ECommand m_Command

the command associated with the task

void x_ReportErrors(vector< string > &errors)

TConstScopedObjects & GetSeqLocs()

vector< CRef< CNetBlastJobDescriptor > > TDescriptors

virtual string GetStatusText() const

overriding CAppTask::GetStatusText()

virtual ETaskState x_RunCurrentSubTask()

runs the current subtask; one may override this function in order to perform special pre-execution or...

virtual void Init_Monitoring(TDescriptors &descriptors)

setup the task for monitoring BLAST jobs and for retrieving results

virtual CIRef< IAppTask > x_GetCurrentSubTask()

returns a references to the current subtask

CIRef< IAppTask > m_CurrTask

virtual void Init_RetrieveRID(const vector< string > &RIDs)

setup the task for retrieving results

virtual void SetLoadingOptions(CSelectProjectOptions &options)

define how the task results shall be handled

virtual void SetLoadingOptions(CSelectProjectOptions &options)

CSelectProjectOptions m_LoadingOptions

string m_ToolName

name of the tool that launched the task; used in UI

virtual void Init_SubmitSearch(const CBLASTParams &params)

setup the task for submitting and monitoring BLAST jobs, and for retrieving results

void GetDescriptors(TDescriptors &descriptors)

void x_InitMonitoringStage(TDescriptors &descriptors)

preapres App Job for monitoring stage of the task

ECommand m_Stage

defines the current stage of the task

IServiceLocator * m_SrvLocator

CRef< CNetBlastLoadingJob > m_LoadingJob

void GetErrors(vector< string > &errors) const

virtual ~CBlastSearchTask()

CRef< CNetBlastSubmittingJob > m_SubmittingJob

CRef< CNetBLASTUIDataSource > m_NetBlastDS

CRef< CNetBlastMonitoringJob > m_MonitoringJob

CBlastSearchTask(IServiceLocator *srv_locator, CNetBLASTUIDataSource &ds, const string &tool_name)

CBlastSearchTask.

@ eFinished

only retrieve resutlts

@ eMonitor

submit request, monitor and retrieve results

@ eRetrieve

monitor and retrieve resutlts

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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

wxString ToWxString(const string &s)

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