aln_test_app.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <connect/ncbi_core_cxx.hpp>
#include <serial/objistr.hpp>
#include <objtools/alnmgr/aln_user_options.hpp>
#include <objtools/alnmgr/aln_asn_reader.hpp>
#include <objtools/alnmgr/aln_container.hpp>
#include <objtools/alnmgr/aln_tests.hpp>
#include <objtools/alnmgr/aln_stats.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_serial.hpp>
#include <objtools/alnmgr/sparse_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <objtools/alnmgr/aln_builders.hpp>
#include <objtools/alnmgr/sparse_ci.hpp>
#include <objtools/alnmgr/aln_generators.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>

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Classes
class	CAlnTestApp

Typedefs
typedef CSeq_align::TDim	TDim
	Types we use here: More...
typedef vector< const CSeq_align * >	TAlnVector
typedef const CSeq_id *	TSeqIdPtr
typedef vector< TSeqIdPtr >	TSeqIdVector

Functions
void	DumpPairwiseAln (const CPairwiseAln &pw, const string ind)
void	DumpAnchoredAln (const CAnchoredAln &aaln, const string &ind)
void	DumpSparseAln (const CSparseAln &sparse_aln)
void	TestSparseIt (const CSparseAln &aln, int row, const CSparse_CI::TSignedRange &rg, CSparse_CI::EFlags flags)
void	TestIterators (const CSparseAln &aln, const CSparse_CI::TSignedRange &rg)
void	TestSparseIterator (const CSparseAln &aln)
TAlnSeqIdIRef	ArgToSeq_id (const CArgValue &arg)
int	main (int argc, const char *argv[])

Variables
static bool	s_PrintSeq = false

Typedef Documentation

TAlnVector

typedef vector<const CSeq_align*> TAlnVector

Definition at line 68 of file aln_test_app.cpp.

TDim

typedef CSeq_align::TDim TDim

Types we use here:

Definition at line 67 of file aln_test_app.cpp.

TSeqIdPtr

typedef const CSeq_id* TSeqIdPtr

Definition at line 69 of file aln_test_app.cpp.

TSeqIdVector

typedef vector<TSeqIdPtr> TSeqIdVector

Definition at line 70 of file aln_test_app.cpp.

Function Documentation

ArgToSeq_id()

TAlnSeqIdIRef ArgToSeq_id

(

const CArgValue &

arg

)

Definition at line 409 of file aln_test_app.cpp.

References CArgValue::AsString(), CSeq_id_Base::e_not_set, in(), MSerial_AsnText, Ref(), CRef< C, Locker >::Reset(), str(), and CSeq_id_Base::Which().

Referenced by CAlnTestApp::Run().

DumpAnchoredAln()

void DumpAnchoredAln	(	const CAnchoredAln &	aaln,
		const string &	ind
	)

Definition at line 215 of file aln_test_app.cpp.

References DumpPairwiseAln(), CAnchoredAln::GetPairwiseAlns(), and ITERATE.

Referenced by CAlnTestApp::Run().

DumpPairwiseAln()

void DumpPairwiseAln	(	const CPairwiseAln &	pw,
		const string	ind
	)

Definition at line 175 of file aln_test_app.cpp.

References CPairwise_CI::eGap, CAlignRangeCollectionList< TAlnRange >::GetFirstFrom(), CAlignRange< Position >::GetFirstFrom(), CPairwiseAln::GetFirstId(), CAlignRangeCollectionList< TAlnRange >::GetFirstRange(), CAlignRangeCollectionList< TAlnRange >::GetFlags(), COpenRange< Position >::GetFrom(), CAlignRangeCollectionList< TAlnRange >::GetInsertions(), CPairwiseAln::GetSecondId(), CAlignRangeCollectionList< TAlnRange >::GetSecondPosByFirstPos(), COpenRange< Position >::GetToOpen(), CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsFirstDirect(), ITERATE, and COpenRange< Position >::SetToOpen().

Referenced by DumpAnchoredAln(), and CAlnTestApp::Run().

DumpSparseAln()

void DumpSparseAln

(

const CSparseAln &

sparse_aln

)

Definition at line 227 of file aln_test_app.cpp.

References CSparseAln::AlnRangeToNativeFrames(), CSparseAln::AlnRangeToNativeSeqRange(), IAlnSegmentIterator::eAllSegments, COpenRange< Position >::Empty(), IAlnSegment::fGap, IAlnSegment::fIndel, IAlnSegment::fUnaligned, CSparseAln::GetAlnRange(), IAlnSegment::GetAlnRange(), CSparseAln::GetAlnSeqString(), CSparseAln::GetAnchor(), CSparseAln::GetBaseWidth(), CSparseAln::GetDim(), CRange_Base::GetFrom(), CSparseAln::GetNumRows(), IAlnSegment::GetRange(), CSparseAln::GetSeqAlnRange(), CSparseAln::GetSeqAlnStart(), CSparseAln::GetSeqAlnStop(), CSparseAln::GetSeqId(), CSparseAln::GetSeqRange(), CSparseAln::GetSeqString(), CRange_Base::GetTo(), IAlnSegment::GetType(), row, s_PrintSeq, and string.

Referenced by CAlnTestApp::Run().

main()

int main	(	int	argc,
		const char *	argv[]
	)

Definition at line 577 of file aln_test_app.cpp.

References CNcbiApplicationAPI::AppMain().

TestIterators()

void TestIterators	(	const CSparseAln &	aln,
		const CSparse_CI::TSignedRange &	rg
	)

Definition at line 375 of file aln_test_app.cpp.

References IAlnSegmentIterator::eAllSegments, IAlnSegmentIterator::eInsertsOnly, IAlnSegmentIterator::eSkipGaps, IAlnSegmentIterator::eSkipInserts, CSparseAln::GetAnchor(), CSparseAln::GetNumRows(), CSparseAln::GetSeqId(), row, and TestSparseIt().

Referenced by TestSparseIterator().

TestSparseIt()

void TestSparseIt	(	const CSparseAln &	aln,
		int	row,
		const CSparse_CI::TSignedRange &	rg,
		CSparse_CI::EFlags	flags
	)

Definition at line 333 of file aln_test_app.cpp.

References IAlnExplorer::eForward, IAlnSegment::fAligned, IAlnSegment::fGap, IAlnSegment::fIndel, flags, IAlnSegment::fSegTypeMask, IAlnSegment::fUnaligned, CSparseAln::GetAnchor(), CSparseAln::GetSeqPosFromAlnPos(), and row.

Referenced by TestIterators().

TestSparseIterator()

void TestSparseIterator

(

const CSparseAln &

aln

)

Definition at line 402 of file aln_test_app.cpp.

References COpenRange< TSignedSeqPos >::GetWhole(), and TestIterators().

Referenced by CAlnTestApp::Run().

Variable Documentation

s_PrintSeq

bool s_PrintSeq = false

static

Definition at line 224 of file aln_test_app.cpp.

Referenced by DumpSparseAln(), and CAlnTestApp::Run().