Utilities to develop and debug unit tests that deal with PSSM computation. More...
#include <string>#include <corelib/ncbistd.hpp>#include <blast_objmgr_priv.hpp>#include <algo/blast/api/pssm_input.hpp>#include <algo/blast/api/psi_pssm_input.hpp>#include <algo/blast/api/pssm_engine.hpp>#include <algo/blast/core/blast_stat.h>#include <algo/blast/core/blast_setup.h>#include <objmgr/scope.hpp>#include "blast_psi_priv.h"
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Classes | |
| class | CPssmCreateTestFixture |
| This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine. More... | |
| struct | Deleter< _PSIAlignedBlock > |
| template specializations to automate deallocation of internal BLAST structures with ncbi::AutoPtr More... | |
| struct | Deleter< _PSISequenceWeights > |
| struct | Deleter< _PSIInternalPssmData > |
| struct | Deleter< _PSIMsa > |
| struct | Deleter< _PSIPackedMsa > |
Functions | |
| BlastScoreBlk * | InitializeBlastScoreBlk (const unsigned char *query, Uint4 query_size) |
Detailed Description
Utilities to develop and debug unit tests that deal with PSSM computation.
Definition in file pssm_test_util.hpp.
Function Documentation
◆ InitializeBlastScoreBlk()
| BlastScoreBlk* InitializeBlastScoreBlk | ( | const unsigned char * | query, |
| Uint4 | query_size | ||
| ) |
- Parameters
-
query protein sequence in ncbistdaa with sentinel bytes query_size length of the query sequence (w/o including sentinel
Definition at line 51 of file pssm_test_util.cpp.
References BlastFindMatrixPath(), BlastScoringOptionsNew(), BlastSeqBlkNew(), BlastSeqBlkSetSequence(), BlastSetup_ScoreBlkInit(), TestUtil::CreateProtQueryInfo(), eBlastEncodingProtein, eBlastTypeBlastp, FALSE, CBLAST_SequenceBlk::Get(), GetSentinelByte(), BlastScoreBlk::kbp_ideal, kScaleFactor, BLAST_SequenceBlk::length, Blast_Message::message, NULL, query, BLAST_SequenceBlk::sequence, BLAST_SequenceBlk::sequence_allocated, BLAST_SequenceBlk::sequence_start, and BLAST_SequenceBlk::sequence_start_allocated.
Referenced by BOOST_AUTO_TEST_CASE().
