rpsblast_local.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbiapp.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <corelib/ncbithr.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/ncbimtx.hpp>
#include <corelib/ncbiexpt.hpp>
#include <algo/blast/api/rpsblast_local.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/api/blast_rps_options.hpp>

Include dependency graph for rpsblast_local.cpp:

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Classes
class	CRPSThread

Functions
static void	s_ConvertConcatStringToVectorOfString (const string &s, vector< string > &v)
static void	s_MergeAlignSet (CSeq_align_set &final_set, const CSeq_align_set &input_set)
static CRef< CSearchResultSet >	s_CombineSearchSets (vector< CRef< CSearchResultSet > > &t, unsigned int num_of_threads)
static void	s_ModifyVolumePaths (vector< string > &rps_database)
static bool	s_SortDbSize (const pair< string, Int8 > &a, const pair< string, Int8 > &b)
static void	s_MapDbToThread (vector< string > &db, unsigned int num_of_threads)
CRef< CSearchResultSet >	s_RunLocalRpsSearch (const string &db, CBlastQueryVector &query_vector, CRef< CBlastOptionsHandle > opt_handle)

Variables
static const char	delimiter [] = "#rps#"
static const size_t	delimiter_len = sizeof(delimiter) - 1

Function Documentation

s_CombineSearchSets()

static CRef<CSearchResultSet> s_CombineSearchSets ( vector< CRef< CSearchResultSet > > &  t, unsigned int  num_of_threads  )

static

Definition at line 139 of file rpsblast_local.cpp.

s_ConvertConcatStringToVectorOfString()

static void s_ConvertConcatStringToVectorOfString ( const string &  s, vector< string > &  v  )

static

Definition at line 53 of file rpsblast_local.cpp.

s_MapDbToThread()

static void s_MapDbToThread ( vector< string > &  db, unsigned int  num_of_threads  )

static

Definition at line 207 of file rpsblast_local.cpp.

s_MergeAlignSet()

static void s_MergeAlignSet ( CSeq_align_set &  final_set, const CSeq_align_set &  input_set  )

static

Definition at line 69 of file rpsblast_local.cpp.

s_ModifyVolumePaths()

static void s_ModifyVolumePaths ( vector< string > &  rps_database )

static

Definition at line 192 of file rpsblast_local.cpp.

s_RunLocalRpsSearch()

CRef<CSearchResultSet> s_RunLocalRpsSearch	(	const string &	db,
		CBlastQueryVector &	query_vector,
		CRef< CBlastOptionsHandle >	opt_handle
	)

Definition at line 250 of file rpsblast_local.cpp.

s_SortDbSize()

static bool s_SortDbSize ( const pair< string, Int8 > &  a, const pair< string, Int8 > &  b  )

static

Definition at line 202 of file rpsblast_local.cpp.

Variable Documentation

delimiter

const char delimiter[] = "#rps#"

static

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.

Definition at line 49 of file rpsblast_local.cpp.

Referenced by NMacroUtil::ActionTypeToExistingTextOption(), callout_callback(), callout_function(), compile_branch(), CStringUtil::ConcatenateStrings(), NMacroUtil::ConvertMultiSpaces(), ct_cursor(), CwxGridTableExport::CwxGridTableExport(), CStringUtil::FormatStringsOccurrences(), get_auth(), get_next_tok(), CMacroApplySrcTablePanel::GetDelimiter(), CPluginManager_DllResolver::GetDllName(), CPluginManager_DllResolver::GetDllNameMask(), operator<<(), parse_regex(), process_pattern(), CTableImportDataSource::ReplaceSpaces(), s_DelimitedOutput(), CApplyTableItemData::s_GetMatchFieldConstraint(), LbsmLookup::s_Resolve(), s_TokenizeString(), CSrcWriter::SetDelimiter(), CRegexpUtil::SetRange(), IMacroBioDataIter::SetTableToApply(), CTableImportDataSource::SplitColumn(), CMacroFunction_SetStringQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_AddDBLink::TheFunction(), CMacroFunction_ConvertStringQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ConvertRNARelQual::TheFunction(), CMacroFunction_ParseStringQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_ParseRNARelQual::TheFunction(), CMacroFunction_AddParsedText::TheFunction(), CMacroFunction_AddParsedToFeatQual::TheFunction(), CMacroFunction_ParseToStructComm::TheFunction(), CMacroFunction_CopyStringQual::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_CopyRNARelQual::TheFunction(), CMacroFunction_AddorSetContElement::TheFunction(), CMacroFunction_SetStructCommDb::TheFunction(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), CMacroFunction_SetPubTitle::TheFunction(), CMacroFunction_SetPubAffil::TheFunction(), CMacroFunction_SetPubAuthor::TheFunction(), CMacroFunction_SetPubJournal::TheFunction(), CMacroFunction_SetPubVolIssuePages::TheFunction(), TokenString(), CRegexpUtil::x_Divide(), CTableReaderMacro::x_GetMatchFieldConstraint(), IEditMacroFunction::x_GetOptionalArgs(), variation_ref::CHgvsParser::x_list(), and CMacroApplySrcTablePanel::x_ProcessFirstLine().

delimiter_len

const size_t delimiter_len = sizeof(delimiter) - 1

static

Definition at line 50 of file rpsblast_local.cpp.