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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/split_query_unit_test.cpp File Reference

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◆ TGiLengthVector ◆ TGiLenPair ◆ TSplitQueryChunkMap ◆ BOOST_AUTO_TEST_CASE() [1/23] BOOST_AUTO_TEST_CASE ( CalculateNumberChunks  ) ◆ BOOST_AUTO_TEST_CASE() [2/23] BOOST_AUTO_TEST_CASE ( InvalidChunkSizeBlastx  ) ◆ BOOST_AUTO_TEST_CASE() [3/23] BOOST_AUTO_TEST_CASE ( InvalidChunkSizeTblastx  ) ◆ BOOST_AUTO_TEST_CASE() [4/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnMultiQueryMultiChunk_BothStrands  ) ◆ BOOST_AUTO_TEST_CASE() [5/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnMultiQueryMultiChunk_MinusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [6/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnMultiQueryMultiChunk_MixedStrands  ) ◆ BOOST_AUTO_TEST_CASE() [7/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnMultiQueryMultiChunk_PlusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [8/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnSingleQueryMultiChunk_BothStrands  ) ◆ BOOST_AUTO_TEST_CASE() [9/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnSingleQueryMultiChunk_MinusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [10/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastnSingleQueryMultiChunk_PlusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [11/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastpMultiQueryMultiChunk  )

Tests blastp of multiple queries into multiple chunks.

Definition at line 1496 of file split_query_unit_test.cpp.

References BlastQueryInfoFree(), CBlastOptionsFactory::Create(), eBlastp, CQuerySplitter::GetChunkSize(), CQuerySplitter::GetNumberOfChunks(), CSplitQueryBlk::GetNumChunks(), CBlastOptions::GetProgramType(), ILocalQueryData::GetSumOfSequenceLengths(), NMacroArgs::kTestName, IQueryFactory::MakeLocalQueryData(), NON_CONST_ITERATE, s_ConvertToBlastQueries(), CBlastOptionsHandle::SetOptions(), and CQuerySplitter::Split().

◆ BOOST_AUTO_TEST_CASE() [12/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_BlastpSingleQueryMultiChunk  )

Tests blastp of a single query into multiple chunks.

Definition at line 1438 of file split_query_unit_test.cpp.

References BlastQueryInfoFree(), CBlastOptionsFactory::Create(), CSeq_id_Base::e_Gi, eBlastp, CQuerySplitter::GetChunkSize(), CQuerySplitter::GetNumberOfChunks(), CSplitQueryBlk::GetNumChunks(), CBlastOptions::GetProgramType(), ILocalQueryData::GetSumOfSequenceLengths(), CTestObjMgr::Instance(), NMacroArgs::kTestName, IQueryFactory::MakeLocalQueryData(), NON_CONST_ITERATE, query, CBlastOptionsHandle::SetOptions(), and CQuerySplitter::Split().

◆ BOOST_AUTO_TEST_CASE() [13/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_NoSplit  )

Tests the CQuerySplitter class when no splitting should occur.

Definition at line 1828 of file split_query_unit_test.cpp.

References CBlastOptionsFactory::Create(), CSeq_id_Base::e_Gi, eBlastn, CQuerySplitter::GetChunkSize(), CQuerySplitter::GetNumberOfChunks(), CSplitQueryBlk::GetNumChunks(), CSplitQueryBlk::GetNumQueriesForChunk(), CQuerySplitter::GetQueryFactoryForChunk(), CTestObjMgr::Instance(), CQuerySplitter::IsQuerySplit(), NMacroArgs::kTestName, query, CBlastOptionsHandle::SetOptions(), and CQuerySplitter::Split().

◆ BOOST_AUTO_TEST_CASE() [14/23] BOOST_AUTO_TEST_CASE ( QuerySplitter_ValidateQueryFactoriesBlastn  ) ◆ BOOST_AUTO_TEST_CASE() [15/23] BOOST_AUTO_TEST_CASE ( Split4QueriesIn3Chunks  ) ◆ BOOST_AUTO_TEST_CASE() [16/23] BOOST_AUTO_TEST_CASE ( SplitQueriesIn1Chunk  )

Definition at line 1147 of file split_query_unit_test.cpp.

References CSplitQueryBlk::GetCStruct(), i, ITERATE, kBadParameter, NULL, sfree, SplitQueryBlk_AddContextToChunk(), SplitQueryBlk_AddQueryToChunk(), SplitQueryBlk_GetNumQueriesForChunk(), SplitQueryBlk_GetQueryContextsForChunk(), SplitQueryBlk_GetQueryIndicesForChunk(), and UINT4_MAX.

◆ BOOST_AUTO_TEST_CASE() [17/23] BOOST_AUTO_TEST_CASE ( SplitQueriesRandomly  ) ◆ BOOST_AUTO_TEST_CASE() [18/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastnMultiQuery_BothStrands  ) ◆ BOOST_AUTO_TEST_CASE() [19/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastnMultiQuery_MinusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [20/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastnMultiQuery_PlusStrand  ) ◆ BOOST_AUTO_TEST_CASE() [21/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastxSingleQuery_BothStrands_0  ) ◆ BOOST_AUTO_TEST_CASE() [22/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastxSingleQuery_BothStrands_1  ) ◆ BOOST_AUTO_TEST_CASE() [23/23] BOOST_AUTO_TEST_CASE ( TestCContextTranslator_BlastxSingleQuery_BothStrands_2  ) ◆ s_CalculateMaxLength() ◆ s_ConvertToBlastQueries()

Convert a vector of GIs with its lengths into a TSeqLocVector.

Parameters
gi_length vector of TGiLenPair containing GIs and their length [in] retval the return value of this function [out] tot_length total length of sequence data contained in gi_length (optional) [in] strands vector of strands to use (optional), if provided it must match the size of the gi_length vector [in] masks vector of masks (optional), if provided it must match the size of the gi_length vector [in]

Definition at line 92 of file split_query_unit_test.cpp.

References CSeq_id_Base::e_Gi, first(), GI_FROM, i, CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPacked_int(), ITERATE, mask, CSimpleOM::NewScope(), NULL, CSeq_loc::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetPacked_int(), CSeq_loc::SetStrand(), and CSeq_loc::SetWhole().

Referenced by BOOST_AUTO_TEST_CASE(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), and CSplitQueryTestFixture::x_TestCContextTranslator().

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