NCBI C++ ToolKit
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blast_test_util.hpp File Reference

Utilities to develop and debug unit tests for BLAST. More...

#include <string>
#include <exception>
#include <ctime>
#include <corelib/ncbistd.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <serial/serial.hpp>
#include <serial/objostr.hpp>
#include <util/random_gen.hpp>
#include <util/format_guess.hpp>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/api/blast_exception.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include "ensure_enough_corelib.hpp"
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Namespaces

 ncbi
 Magic spell ;-) needed for some weird compilers... very empiric.
 
 ncbi::objects
 
 ncbi::blast
 
 TestUtil
 

Functions

vector< EBlastProgramTypeTestUtil::GetAllBlastProgramTypes ()
 
objects::CSeq_id * TestUtil::GenerateRandomSeqid_Gi ()
 
template<class T >
ncbi::CRef< TTestUtil::ReadObject (const std::string &filename)
 
ncbi::CRef< ncbi::objects::CSeq_align_set > TestUtil::FlattenSeqAlignSet (const ncbi::objects::CSeq_align_set &sset)
 Converts bl2seq and blast style seq-align-sets to the seq-align-set format that the new formatter understands (same flat format as C toolkit seq-aligns) More...
 
void TestUtil::PrintSequence (const Uint1 *seq, TSeqPos len, ostream &out, bool show_markers, TSeqPos chars_per_line)
 
void TestUtil::PrintSequence (const ncbi::objects::CSeqVector &svector, std::ostream &out, bool show_markers=true, ncbi::TSeqPos chars_per_line=80)
 
char TestUtil::GetResidue (unsigned int res)
 Returns character representation of a residue from ncbistdaa. More...
 
BlastQueryInfoTestUtil::CreateProtQueryInfo (unsigned int query_size)
 Creates and initializes a BlastQueryInfo structure for a single protein sequence. More...
 
Uint4 TestUtil::EndianIndependentBufferHash (const char *buffer, Uint4 byte_length, Uint4 swap_size=1, Uint4 hash_seed=1)
 Endianness independent hash function. More...
 

Variables

template<class T >
void CheckForBlastSeqSrcErrors(const BlastSeqSrc *seqsrc) THROWS((ncbi voi TestUtil::PrintTextAsn1Object )(std::string filename, T *obj)
 Convenience template function to print ASN.1 objects to a new file. More...
 

Detailed Description

Utilities to develop and debug unit tests for BLAST.

Definition in file blast_test_util.hpp.

Modified on Thu Feb 22 17:12:56 2024 by modify_doxy.py rev. 669887