72 unique_ptr<const CBlastOptionsMemento> opts_memento (opts.
CreateSnapshot());
88 unique_ptr<SSeqLoc> ssloc(
92 tslv.push_back(*ssloc.get());
101 unique_ptr<const CBlastOptionsMemento> opts_memento (opts.
CreateSnapshot());
109 BOOST_REQUIRE(blast_seq_loc !=
NULL);
110 BOOST_REQUIRE(sbp !=
NULL);
113 BOOST_REQUIRE(sbp ==
NULL);
115 BOOST_REQUIRE(blast_seq_loc ==
NULL);
122 unique_ptr<SSeqLoc> ssloc(
126 tslv.push_back(*ssloc.get());
135 unique_ptr<const CBlastOptionsMemento> opts_memento (opts.
CreateSnapshot());
142 BOOST_REQUIRE(search_messages.
HasMessages() ==
false);
143 BOOST_REQUIRE(blast_seq_loc !=
NULL);
144 BOOST_REQUIRE(sbp !=
NULL);
147 BOOST_REQUIRE(sbp ==
NULL);
149 BOOST_REQUIRE(blast_seq_loc ==
NULL);
BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)
Deallocate all BlastSeqLoc objects in a chain.
Classes that capture the state of the BLAST options (or subsets of options) and restore them later (u...
const char * kBlastErrMsg_CantCalculateUngappedKAParams
Declares the CBlastNucleotideOptionsHandle class.
Declares the CBlastProteinOptionsHandle class.
BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)
Deallocates BlastScoreBlk as well as all associated structures.
Defines BLAST error codes (user errors included)
Handle to the nucleotide-nucleotide options to the BLAST algorithm.
Encapsulates ALL the BLAST algorithm's options.
Handle to the protein-protein options to the BLAST algorithm.
NCBI C++ Object Manager dependant implementation of IQueryFactory.
CRef< blast::CBlastSearchQuery > CreateBlastSearchQuery(objects::CSeq_id &id, objects::ENa_strand s=objects::eNa_strand_unknown)
static CTestObjMgr & Instance()
typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...
const CBlastOptionsMemento * CreateSnapshot() const
Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs...
void SetMatchReward(int r)
Sets MatchReward.
CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)
Creates and caches an ILocalQueryData.
CBlastOptions & SetOptions()
Returns a reference to the internal options class which this object is a handle for.
void SetMismatchPenalty(int p)
Sets MismatchPenalty.
static BlastScoreBlk * CreateScoreBlock(const CBlastOptionsMemento *opts_memento, CRef< ILocalQueryData > query_data, BlastSeqLoc **lookup_segments, TSearchMessages &search_messages, TSeqLocInfoVector *masked_query_regions=NULL, const CBlastRPSInfo *rps_info=NULL)
Initializes the BlastScoreBlk.
string ToString() const
Converts messages to a string, which is returned.
range(_Ty, _Ty) -> range< _Ty >
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
BOOST_AUTO_TEST_SUITE(psiblast_iteration)
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
BOOST_AUTO_TEST_CASE(CreateScoreBlockBadReward)
Definition of SSeqLoc structure.
vector< SSeqLoc > TSeqLocVector
Vector of sequence locations.
Structure used for scoring calculations.
Used to hold a set of positions, mostly used for filtering.
Utility stuff for more convenient using of Boost.Test library.