#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <corelib/ncbitime.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <serial/objostr.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/seqsrc_multiseq.hpp>
#include <blast_objmgr_priv.hpp>
#include <blast_psi_priv.h>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_kappa.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/core/hspfilter_collector.h>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_prot_options.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/composition_adjustment/composition_constants.h>
#include <algo/blast/composition_adjustment/matrix_frequency_data.h>
#include "test_objmgr.hpp"
#include "blast_test_util.hpp"

Include dependency graph for redoalignment_unit_test.cpp:

Go to the SVN repository for this file.

Classes
struct	CRedoAlignmentTestFixture

Functions
	BOOST_AUTO_TEST_CASE (testRedoAlignmentWithCompBasedStats)

	BOOST_AUTO_TEST_CASE (testRedoAlignmentWithConditionalAdjust)

	BOOST_AUTO_TEST_CASE (testPSIRedoAlignmentWithCompBasedStats)

	BOOST_AUTO_TEST_CASE (testRedoAlignmentWithCompBasedStatsBadlyBiasedSequence)

	BOOST_AUTO_TEST_CASE (testRedoAlignmentWithSW)

	BOOST_AUTO_TEST_CASE (testRedoAlignmentWithCompBasedStatsAndSW)

	BOOST_AUTO_TEST_CASE (testPSIRedoAlignmentWithCompBasedStatsAndSW)

	BOOST_AUTO_TEST_CASE (testRedoAlignmentUseXdropEvalue)

	BOOST_AUTO_TEST_CASE (CheckLowerCaseMatrix)