#include <ncbi_pch.hpp>#include <corelib/test_boost.hpp>#include <algo/blast/api/blast_aux.hpp>#include <algo/blast/core/lookup_wrap.h>#include <algo/blast/core/blast_setup.h>#include <algo/blast/core/blast_encoding.h>#include <algo/blast/core/phi_lookup.h>#include <algo/blast/core/phi_gapalign.h>#include <blast_setup.hpp>#include "ensure_enough_corelib.hpp"
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Classes | |
| class | CPhiblastTestFixture |
Functions | |
| USING_SCOPE (blast) | |
| BOOST_AUTO_TEST_CASE (testPHILookupTableLong) | |
| Tests the values in the PHI BLAST lookup table. More... | |
| BOOST_AUTO_TEST_CASE (testPHILookupTableShort) | |
| Tests the values in the PHI BLAST lookup table. More... | |
| BOOST_AUTO_TEST_CASE (testFindQueryOccurrencesLong) | |
| Tests the finding of pattern occurrences in query. More... | |
| BOOST_AUTO_TEST_CASE (testFindQueryOccurrencesShort) | |
| Tests the finding of pattern occurrences in query. More... | |
| BOOST_AUTO_TEST_CASE (testPHICalcEvalues) | |
| Tests PHI BLAST calculation of e-values. More... | |
| BOOST_AUTO_TEST_CASE (testPHIScanSubject) | |
| Tests finding of pattern occurrences in subject. More... | |
| BOOST_AUTO_TEST_CASE (testPHIGappedAlignmentWithTraceback) | |
| BOOST_AUTO_TEST_CASE (testPHIBlastHSPResultsSplit) | |
| BOOST_AUTO_TEST_CASE (testPHIBlastHSPResultsSplitNoHits) | |
| BOOST_AUTO_TEST_CASE (testPHIBlastHitSavingParameters) | |
Variables | |
| USING_NCBI_SCOPE | |
Function Documentation
◆ BOOST_AUTO_TEST_CASE() [1/10]
| BOOST_AUTO_TEST_CASE | ( | testFindQueryOccurrencesLong | ) |
Tests the finding of pattern occurrences in query.
Definition at line 265 of file phiblast_unit_test.cpp.
References NULL, and pattern_info().
◆ BOOST_AUTO_TEST_CASE() [2/10]
| BOOST_AUTO_TEST_CASE | ( | testFindQueryOccurrencesShort | ) |
Tests the finding of pattern occurrences in query.
Definition at line 278 of file phiblast_unit_test.cpp.
References NULL, and pattern_info().
◆ BOOST_AUTO_TEST_CASE() [3/10]
| BOOST_AUTO_TEST_CASE | ( | testPHIBlastHitSavingParameters | ) |
Definition at line 425 of file phiblast_unit_test.cpp.
References BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastGappedCutoffs::cutoff_score, BlastHitSavingParameters::cutoff_score_min, BlastHitSavingParameters::cutoffs, eBlastTypePhiBlastp, and NULL.
◆ BOOST_AUTO_TEST_CASE() [4/10]
| BOOST_AUTO_TEST_CASE | ( | testPHIBlastHSPResultsSplit | ) |
Definition at line 390 of file phiblast_unit_test.cpp.
References Blast_HSPResultsFree(), NULL, pattern_info(), PHIBlast_HSPResultsSplit(), results, and SPHIQueryInfoFree().
◆ BOOST_AUTO_TEST_CASE() [5/10]
| BOOST_AUTO_TEST_CASE | ( | testPHIBlastHSPResultsSplitNoHits | ) |
Definition at line 405 of file phiblast_unit_test.cpp.
References Blast_HSPResultsFree(), NULL, pattern_info(), PHIBlast_HSPResultsSplit(), results, sfree, and SPHIQueryInfoFree().
◆ BOOST_AUTO_TEST_CASE() [6/10]
| BOOST_AUTO_TEST_CASE | ( | testPHICalcEvalues | ) |
Tests PHI BLAST calculation of e-values.
Definition at line 291 of file phiblast_unit_test.cpp.
References Blast_HSPListFree(), Blast_HSPListNew(), Blast_HSPListPHIGetEvalues(), Blast_HSPNew(), BlastHSP::evalue, BlastHSPList::hsp_array, BlastHSPList::hspcnt, NULL, SPHIPatternSearchBlk::num_patterns_db, and BlastHSP::score.
◆ BOOST_AUTO_TEST_CASE() [7/10]
| BOOST_AUTO_TEST_CASE | ( | testPHIGappedAlignmentWithTraceback | ) |
Definition at line 344 of file phiblast_unit_test.cpp.
References BLAST_GapAlignStructNew(), BlastExtensionOptionsNew(), BlastExtensionParametersNew(), BlastScoringOptionsNew(), BlastScoringParametersNew(), BlastScoringOptions::gapped_calculation, BLAST_SequenceBlk::length, PHIGappedAlignmentWithTraceback(), and BLAST_SequenceBlk::sequence.
◆ BOOST_AUTO_TEST_CASE() [8/10]
| BOOST_AUTO_TEST_CASE | ( | testPHILookupTableLong | ) |
Tests the values in the PHI BLAST lookup table.
Definition at line 219 of file phiblast_unit_test.cpp.
References eVeryLong, SLongPatternItems::extra_long_items, SPHIPatternSearchBlk::flagPatternLength, SPHIPatternSearchBlk::minPatternMatchLength, SPHIPatternSearchBlk::multi_word_items, NULL, SLongPatternItems::numWords, and SPHIPatternSearchBlk::patternProbability.
◆ BOOST_AUTO_TEST_CASE() [9/10]
| BOOST_AUTO_TEST_CASE | ( | testPHILookupTableShort | ) |
Tests the values in the PHI BLAST lookup table.
Definition at line 241 of file phiblast_unit_test.cpp.
References eOneWord, SLongPatternItems::extra_long_items, SPHIPatternSearchBlk::flagPatternLength, SShortPatternItems::match_mask, SPHIPatternSearchBlk::minPatternMatchLength, SPHIPatternSearchBlk::multi_word_items, NULL, SLongPatternItems::numWords, SPHIPatternSearchBlk::one_word_items, SPHIPatternSearchBlk::patternProbability, and SShortPatternItems::whichPositionPtr.
◆ BOOST_AUTO_TEST_CASE() [10/10]
| BOOST_AUTO_TEST_CASE | ( | testPHIScanSubject | ) |
Tests finding of pattern occurrences in subject.
Definition at line 314 of file phiblast_unit_test.cpp.
References calloc(), GetOffsetArraySize(), NULL, PHIBlastScanSubject(), BlastOffsetPair::s_end, BlastOffsetPair::s_start, and sfree.
◆ USING_SCOPE()
| USING_SCOPE | ( | blast | ) |
Variable Documentation
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 47 of file phiblast_unit_test.cpp.
