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< EBlastProgramType > | TestUtil::GetAllBlastProgramTypes () |
| objects::CSeq_id * | TestUtil::GenerateRandomSeqid_Gi () |
| template<class T > | |
| ncbi::CRef< T > | TestUtil::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... | |
| BlastQueryInfo * | TestUtil::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.
