;
76 const char* fname =
"data/archive.asn";
86 const CBioseq& bs = bss_ref->GetSeq_set().front()->GetSeq();
109 false, streamBuffer, 10, 10, *scope);
116BOOST_REQUIRE(myReport.length() > 0);
117BOOST_REQUIRE(myReport.find(
"Query=") != std::string::npos);
124 const char* fname =
"data/archive.asn";
134 const CBioseq& bs = bss_ref->GetSeq_set().front()->GetSeq();
159 false, streamBuffer, 10, 10, *scope));
161vector<SFormatResultValues> results_v;
168BOOST_REQUIRE(myReport.length() > 0);
169BOOST_REQUIRE(myReport.find(
"Query=") != std::string::npos);
181vector<SFormatResultValues> results_v;
193vector<SFormatResultValues> results_v;
Produce formatted blast output for command line applications.
BOOST_AUTO_TEST_CASE(BlastFormatTest)
Declares the CBlastNucleotideOptionsHandle class.
Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...
BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)
build_archive declarations
const CSeq_id * GetFirstId() const
Run as separate thread and format results.
void Finalize()
Close queue for printing. No calls to QueueResults allowed after this.
void Join()
Calls Finalize (if not already called) then CThread::Join(); Should only be called if QueueResults wi...
void QueueResults(int batchNumber, vector< SFormatResultValues > results)
Queue results for printing.
This class formats the BLAST results for command line applications.
void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)
Print all alignment information for a single query sequence along with any errors or warnings (errors...
Int8 GetDbTotalLength()
Get total length of the database.
Handle to the nucleotide-nucleotide options to the BLAST algorithm.
void push_back(const value_type &element)
Add a value to the back of this container.
Class whose purpose is to create CScope objects which have data loaders added with different prioriti...
Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...
CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:
NCBI C++ Object Manager free implementation of IQueryFactory.
API for Remote Blast Requests.
bool LoadFromArchive()
Loads next chunk of archive from file.
CRef< objects::CBlast4_queries > GetQueries()
Get the queries used for this search.
const CBlastOptions & GetOptions() const
Return the object which this object is a handle for.
CRef< CSearchResultSet > GetResultSet()
Submit the search (if necessary) and return the results.
@ eBlastDbIsNucleotide
nucleotide
CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
Add bioseq, return bioseq handle.
bool Run(TRunMode flags=fRunDefault)
Run the thread.
Declares class which provides internal BLAST database representations to the internal BLAST APIs.
Magic spell ;-) needed for some weird compilers... very empiric.
Defines NCBI C++ exception handling.
NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.
Useful/utility classes and methods.
std::istream & in(std::istream &in_, double &x_)
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)
Configuration structure for the CBlastScopeSource.
Contains query, results and CBlastFormat for one batch.
Utility stuff for more convenient using of Boost.Test library.
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