Search Toolkit Book for CAlnUserOptions

Options for different alignment manager operations. More...

#include <objtools/alnmgr/aln_user_options.hpp>

Inheritance diagram for CAlnUserOptions:

Collaboration diagram for CAlnUserOptions:

Public Types
enum	EDirection { eBothDirections = 0 , eDirect = 1 , eReverse = 2 , eDefaultDirection = eBothDirections }
	Row direction flags. More...

enum	EMergeAlgo { eMergeAllSeqs = 0 , eQuerySeqMergeOnly = 1 , ePreserveRows = 2 , eDefaultMergeAlgo = eMergeAllSeqs }
	Alignment merging algorithm. More...

enum	EMergeFlags { fTruncateOverlaps = 1 << 0 , fAllowMixedStrand = 1 << 1 , fAllowTranslocation = 1 << 2 , fSkipSortByScore = 1 << 3 , fUseAnchorAsAlnSeq = 1 << 4 , fAnchorRowFirst = 1 << 5 , fIgnoreInsertions = 1 << 6 }
	Additional merge flags. More...

enum	EShowUnalignedOption { eHideUnaligned , eShowFlankingN , eShowAllUnaligned }

typedef CPairwiseAln::TPos	TPos

typedef int	TMergeFlags

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CAlnUserOptions (void)

void	SetAnchorId (const TAlnSeqIdIRef &anchor_id)
	Set anchor id. More...

const TAlnSeqIdIRef &	GetAnchorId (void) const
	Get anchor id. More...

void	SetMergeFlags (TMergeFlags flags, bool set)
	Set/clear merge flags. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Public Attributes
EDirection	m_Direction

EMergeAlgo	m_MergeAlgo

TMergeFlags	m_MergeFlags

bool	m_ClipAlignment

objects::CBioseq_Handle	m_ClipSeq

TPos	m_ClipStart

TPos	m_ClipEnd

bool	m_ExtendAlignment

TPos	m_Extension

EShowUnalignedOption	m_UnalignedOption

TPos	m_ShowUnalignedN

objects::CBioseq_Handle	m_Anchor
	Anchor bioseq - if null then a multiple alignment shall be built. More...

Private Attributes
TAlnSeqIdIRef	m_AnchorId

Additional Inherited Members
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Options for different alignment manager operations.

Definition at line 48 of file aln_user_options.hpp.

Member Typedef Documentation

◆ TMergeFlags

typedef int CAlnUserOptions::TMergeFlags

Definition at line 118 of file aln_user_options.hpp.

◆ TPos

typedef CPairwiseAln::TPos CAlnUserOptions::TPos

Definition at line 51 of file aln_user_options.hpp.

Member Enumeration Documentation

◆ EDirection

enum CAlnUserOptions::EDirection

Row direction flags.

NOTE: in most cases directions are relative to the anchor row.

Enumerator
eBothDirections	No filtering: use both direct and reverse sequences.
eDirect	Use only sequences whose strand is the same as that of the anchor.
eReverse	Use only sequences whose strand is opposite to that of the anchor.
eDefaultDirection	By default don't filter by direction.

Definition at line 55 of file aln_user_options.hpp.

◆ EMergeAlgo

enum CAlnUserOptions::EMergeAlgo

Alignment merging algorithm.

Enumerator
eMergeAllSeqs	Merge all sequences (greedy algo).
eQuerySeqMergeOnly	Only put the query seq on same row (input order is not significant).
ePreserveRows	Preserve all rows as they were in the input (e.g. self-align a sequence). Greedy algo.
eDefaultMergeAlgo

Definition at line 71 of file aln_user_options.hpp.

◆ EMergeFlags

enum CAlnUserOptions::EMergeFlags

Additional merge flags.

Enumerator
fTruncateOverlaps	Truncate overlapping ranges. If not set, the overlaps are put on separate rows.
fAllowMixedStrand	Allow mixed strands on the same row. Experimental feature, not supported for all alignment types.
fAllowTranslocation	Allow translocations on the same row.
fSkipSortByScore	In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.
fUseAnchorAsAlnSeq	Use the anchor sequence as the alignment sequence. Otherwise (by default) a pseudo sequence is created whose coordinates are the alignment coordinates. NOTE: Setting this flag is not recommended. Using it will make all CSparseAln::AlnPos methods inconsistent with CAlnVec::AlnPos methods.
fAnchorRowFirst	Store anchor row in the first pairwise alignment (by default it's stored in the last one).
fIgnoreInsertions	Do not collect and store insertions (gaps on the anchor).

Definition at line 87 of file aln_user_options.hpp.

◆ EShowUnalignedOption

enum CAlnUserOptions::EShowUnalignedOption

Enumerator
eHideUnaligned
eShowFlankingN
eShowAllUnaligned

Definition at line 129 of file aln_user_options.hpp.

Constructor & Destructor Documentation

◆ CAlnUserOptions()

CAlnUserOptions::CAlnUserOptions ( void )

inline

Definition at line 138 of file aln_user_options.hpp.

Member Function Documentation

◆ GetAnchorId()

const TAlnSeqIdIRef& CAlnUserOptions::GetAnchorId ( void ) const

inline

Get anchor id.

Definition at line 158 of file aln_user_options.hpp.

References m_AnchorId.

Referenced by CreateAnchoredAlnFromAln(), and CAlnBuildApp::Run().

◆ SetAnchorId()

void CAlnUserOptions::SetAnchorId ( const TAlnSeqIdIRef & anchor_id )

inline

Set anchor id.

Definition at line 152 of file aln_user_options.hpp.

References m_AnchorId.

Referenced by BOOST_AUTO_TEST_CASE(), CAlnBuildApp::Run(), and CAlnTestApp::Run().

◆ SetMergeFlags()

void CAlnUserOptions::SetMergeFlags	(	TMergeFlags	flags,
		bool	set
	)

inline

Set/clear merge flags.

Definition at line 164 of file aln_user_options.hpp.

References flags, and m_MergeFlags.

Referenced by CAlignCleanup::CreatePairwiseFromMultiple(), CMultiAlignView::OnProjectChanged(), CAlnTestApp::Run(), CAlignCleanup::x_Cleanup_AnchoredAln(), and CMergeAlignmentsJob::x_CreateProjectItems().

Member Data Documentation

◆ m_Anchor

objects::CBioseq_Handle CAlnUserOptions::m_Anchor

Anchor bioseq - if null then a multiple alignment shall be built.

Definition at line 175 of file aln_user_options.hpp.

◆ m_AnchorId

TAlnSeqIdIRef CAlnUserOptions::m_AnchorId

private

Definition at line 178 of file aln_user_options.hpp.

Referenced by GetAnchorId(), and SetAnchorId().

◆ m_ClipAlignment

bool CAlnUserOptions::m_ClipAlignment

Definition at line 121 of file aln_user_options.hpp.

Referenced by CBuildOptionsDlg::SetParams().

◆ m_ClipEnd

TPos CAlnUserOptions::m_ClipEnd

Definition at line 124 of file aln_user_options.hpp.

◆ m_ClipSeq

objects::CBioseq_Handle CAlnUserOptions::m_ClipSeq

Definition at line 122 of file aln_user_options.hpp.

◆ m_ClipStart

TPos CAlnUserOptions::m_ClipStart

Definition at line 123 of file aln_user_options.hpp.

◆ m_Direction

EDirection CAlnUserOptions::m_Direction

Definition at line 68 of file aln_user_options.hpp.

Referenced by BuildAlignDataSource(), CreateAnchoredAlnFromAln(), CAlignCleanup::CreatePairwiseFromMultiple(), CAlnBuildApp::Run(), CAlnTestApp::Run(), CAlignCleanup::x_Cleanup_AnchoredAln(), and CMergeAlignmentsJob::x_CreateProjectItems().

◆ m_ExtendAlignment

bool CAlnUserOptions::m_ExtendAlignment

Definition at line 126 of file aln_user_options.hpp.

Referenced by CBuildOptionsDlg::SetParams().

◆ m_Extension

TPos CAlnUserOptions::m_Extension

Definition at line 127 of file aln_user_options.hpp.

◆ m_MergeAlgo

EMergeAlgo CAlnUserOptions::m_MergeAlgo

Definition at line 84 of file aln_user_options.hpp.

Referenced by BuildAlignDataSource(), BuildAln(), CAlnSpanVertModel::CAlnSpanVertModel(), CAlignCleanup::CreatePairwiseFromMultiple(), CAlnBuildApp::Run(), CBuildOptionsDlg::SetParams(), CAlignCleanup::x_Cleanup_AnchoredAln(), CMergeAlignmentsJob::x_CreateProjectItems(), and CTreeBuilderJob::x_CreateProjectItems().

◆ m_MergeFlags

TMergeFlags CAlnUserOptions::m_MergeFlags

Definition at line 119 of file aln_user_options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), BuildAln(), CreateAnchoredAlnFromAln(), CAlnBuildApp::Run(), SetMergeFlags(), and CBuildOptionsDlg::SetParams().

◆ m_ShowUnalignedN

TPos CAlnUserOptions::m_ShowUnalignedN

Definition at line 136 of file aln_user_options.hpp.

◆ m_UnalignedOption

EShowUnalignedOption CAlnUserOptions::m_UnalignedOption

Definition at line 135 of file aln_user_options.hpp.

The documentation for this class was generated from the following file:

include/objtools/alnmgr/aln_user_options.hpp

Public Types

Public Member Functions

Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TMergeFlags

◆ TPos

Member Enumeration Documentation

◆ EDirection

◆ EMergeAlgo

◆ EMergeFlags

◆ EShowUnalignedOption

Constructor & Destructor Documentation

◆ CAlnUserOptions()

Member Function Documentation

◆ GetAnchorId()

◆ SetAnchorId()

◆ SetMergeFlags()

Member Data Documentation

◆ m_Anchor

◆ m_AnchorId

◆ m_ClipAlignment

◆ m_ClipEnd

◆ m_ClipSeq

◆ m_ClipStart

◆ m_Direction

◆ m_ExtendAlignment

◆ m_Extension

◆ m_MergeAlgo

◆ m_MergeFlags

◆ m_ShowUnalignedN

◆ m_UnalignedOption