src/algo/blast/unit_tests/api/scoreblk_unit_test.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <corelib/metareg.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <blast_objmgr_priv.hpp>
#include <algo/blast/core/ncbi_math.h>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_encoding.h>
#include "test_objmgr.hpp"
#include <string>
#include <vector>

Include dependency graph for scoreblk_unit_test.cpp:

Go to the source code of this file.

Functions
	BOOST_AUTO_TEST_CASE (GetScoreBlockNucl)
	BOOST_AUTO_TEST_CASE (GetScoreBlockProtein)
	BOOST_AUTO_TEST_CASE (GetScoreBlockPHI)
	BOOST_AUTO_TEST_CASE (GetScoreBlockForFullyMaskedProtein)
	BOOST_AUTO_TEST_CASE (BlastResFreqStdCompProteinTest)
	BOOST_AUTO_TEST_CASE (BlastResFreqStdCompNucleotideTest)
	BOOST_AUTO_TEST_CASE (EqualRewardPenaltyLHtoK)
	BOOST_AUTO_TEST_CASE (NuclGappedCalc)

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Function Documentation

BOOST_AUTO_TEST_CASE (  NuclGappedCalc   )

Definition at line 354 of file scoreblk_unit_test.cpp. References Blast_GetNuclAlphaBeta(), Blast_KarlinBlkFree(), Blast_KarlinBlkNew(), Blast_KarlinBlkNuclGappedCalc(), Blast_ScoreBlkKbpIdealCalc(), Blast_ScoreBlkMatrixInit(), BLASTNA_SEQ_CODE, BlastScoreBlkNew(), BlastScoringOptionsNew(), eBlastTypeBlastn, FALSE, CBlast_Message::Get(), Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, Blast_KarlinBlk::logK, CBlast_Message::Reset(), util::strcmp(), util::strncmp(), and TRUE.

BOOST_AUTO_TEST_CASE (  EqualRewardPenaltyLHtoK   )

Definition at line 337 of file scoreblk_unit_test.cpp. References Blast_ScoreBlkKbpIdealCalc(), Blast_ScoreBlkMatrixInit(), BLASTNA_SEQ_CODE, BlastScoreBlkFree(), BlastScoreBlkNew(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), eBlastTypeBlastn, Blast_KarlinBlk::K, BlastScoreBlk::kbp_ideal, BlastScoringOptions::penalty, and BlastScoringOptions::reward.

BOOST_AUTO_TEST_CASE (  BlastResFreqStdCompNucleotideTest   )

Definition at line 314 of file scoreblk_unit_test.cpp. References Blast_ResFreq::alphabet_code, BlastScoreBlk::alphabet_code, BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, Blast_ResFreqFree(), Blast_ResFreqNew(), Blast_ResFreqStdComp(), FALSE, Blast_ResFreq::prob, and BlastScoreBlk::protein_alphabet.

BOOST_AUTO_TEST_CASE (  BlastResFreqStdCompProteinTest   )

Definition at line 289 of file scoreblk_unit_test.cpp. References Blast_ResFreq::alphabet_code, BlastScoreBlk::alphabet_code, BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, BLAST_Nint(), Blast_ResFreqFree(), Blast_ResFreqNew(), Blast_ResFreqStdComp(), Blast_ResFreq::prob, BlastScoreBlk::protein_alphabet, and TRUE.

BOOST_AUTO_TEST_CASE (  GetScoreBlockForFullyMaskedProtein   )

Definition at line 230 of file scoreblk_unit_test.cpp. References BlastScoreBlk::alphabet_code, BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, Blast_MessageFree(), BLASTAA_SIZE, BlastFindMatrixPath(), BlastMaskLocFree(), BlastMaskLocNew(), BlastScoreBlkFree(), BlastScoringOptionsNew(), BlastSeqLocNew(), BlastSetUp_MaskQuery(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), eBlastp, eBlastTypeBlastp, CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), BlastScoreBlk::hiscore, id, CTestObjMgr::Instance(), ITERATE, BlastScoreBlk::loscore, prog, BlastScoreBlk::protein_alphabet, BlastMaskLoc::seqloc_array, SetupQueries(), and SetupQueryInfo().

BOOST_AUTO_TEST_CASE (  GetScoreBlockPHI   )

Definition at line 149 of file scoreblk_unit_test.cpp. References Blast_MessageFree(), BlastFindMatrixPath(), BlastScoreBlkFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), eBlastp, eBlastTypePhiBlastp, CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), Blast_KarlinBlk::H, id, CTestObjMgr::Instance(), ITERATE, Blast_KarlinBlk::K, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastScoreBlk::kbp_gap_std, BlastScoreBlk::kbp_std, Blast_KarlinBlk::Lambda, Blast_Message::message, prog, SetupQueries(), SetupQueryInfo(), sfree, strdup, and util::strncmp().

BOOST_AUTO_TEST_CASE (  GetScoreBlockProtein   )

Definition at line 108 of file scoreblk_unit_test.cpp. References BlastScoreBlk::alphabet_code, BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, BLASTAA_SIZE, BlastFindMatrixPath(), BlastScoreBlkFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), eBlastp, eBlastTypeBlastp, CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), BlastScoreBlk::hiscore, id, CTestObjMgr::Instance(), ITERATE, BlastScoreBlk::loscore, prog, BlastScoreBlk::protein_alphabet, SetupQueries(), and SetupQueryInfo().

BOOST_AUTO_TEST_CASE (  GetScoreBlockNucl   )

Definition at line 64 of file scoreblk_unit_test.cpp. References BlastScoreBlk::alphabet_code, BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, BlastFindMatrixPath(), BlastScoreBlkFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), eBlastn, eBlastTypeBlastn, eNa_strand_both, CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), BlastScoreBlk::hiscore, id, CTestObjMgr::Instance(), ITERATE, BlastScoreBlk::loscore, BlastScoreBlk::penalty, prog, BlastScoreBlk::protein_alphabet, BlastScoreBlk::reward, SetupQueries(), and SetupQueryInfo().

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