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NCBI C++ ToolKit: include/algo/blast/api/search_strategy.hpp Source File

1 #ifndef ALGO_BLAST_API___SEARCH_STRATEGY__HPP 2 #define ALGO_BLAST_API___SEARCH_STRATEGY__HPP 88

m_OptionsHandle.

Reset

(0);

91

m_PsiNumOfIterations = 0;

105 bool

ignore_unsupported_options =

false

);

114 string

GetService()

const

;

117 string

GetProgram()

const

;

120 string

GetCreatedBy()

const

;

126 int

GetDBFilteringID() ;

129 string

GetDBFilteringKey() ;

144

objects::CBlast4_parameters* GetAlgoOptions();

148

objects::CBlast4_parameters* GetProgramOptions();

152

objects::CBlast4_parameters* GetWebFormatOptions();

155 unsigned int

GetPsiNumOfIterations();

160 if

(m_OptionsBuilder.get() ==

NULL

) {

164 return

*m_OptionsBuilder.get();

177 void

x_GetProgramOptionIntegerList(

EBlastOptIdx

idx, list<int> & list);

210 unsigned int

psi_num_iterations = 0);

231 unsigned int

psi_num_iterations = 0);

250 void

x_AddParameterToProgramOptions(objects::CBlast4Field & field,

251 const int

int_value);

252 void

x_AddParameterToProgramOptions(objects::CBlast4Field & field,

253 const

vector<int> & int_list);

254 void

x_AddParameterToProgramOptions(objects::CBlast4Field & field,

255 const

vector<Int8> & int_list);

256 void

x_AddParameterToProgramOptions(objects::CBlast4Field & field,

257 const string

str

);

259 void

x_AddPsiNumOfIterationsToFormatOptions(

unsigned int

num_iters);

ESubjectMaskingType

Define the possible subject masking types.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares the CBlastOptionsBuilder class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Class to build CBlastOptionsHandle from blast4 ASN objects.

Class to return parts of the CBlast4_request, or data associated with a CBlast4_request,...

std::ofstream out("events_result.xml")

main entry point for tests

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

unique_ptr< CBlastOptionsBuilder > m_OptionsBuilder

string m_FilteringKey

Filtering key.

ESubjectMaskingType m_SubjectMaskingType

Subject Masking Type.

unique_ptr< CImportStrategyData > m_Data

string m_Task

Task, such as megablast, blastn, blastp, etc.

CBlastOptionsBuilder & GetOptionsBuilder()

Return the BlastOptions builder used in this class.

CRef< blast::CBlastOptionsHandle > m_OptionsHandle

BLAST options.

CImportStrategyData()

Constructor.

unsigned int m_PsiNumOfIterations

CImportStrategy(const CImportStrategy &rhs)

Prohibit copy constructor.

CImportStrategy & operator=(const CImportStrategy &rhs)

Prohibit assignment operator.

bool m_IgnoreUnsupportedOptions

ignore unsupported options when creating blast options builder object

int m_FilteringID

Filtering ID.

CExportStrategy & operator=(const CExportStrategy &)

bool valid

Has the struct been properly filled in?

CRef< CBlast4_queue_search_request > m_QueueSearchRequest

TSeqRange m_QueryRange

Range of query.

CExportStrategy(const CExportStrategy &)

CRef< objects::CBlast4_request > m_Request

void Reset(void)

Reset reference object.

static TThisType GetEmpty(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

EBlastOptIdx

Index of remote BLAST options.

Declares the CRemoteBlast class.

This is the "mutable" data for CImportStrategy.

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