Search Toolkit Book for CMultiAlignerOptions

Options and parameters for multiple alignement. More...

#include <algo/cobalt/options.hpp>

Inheritance diagram for CMultiAlignerOptions:

Collaboration diagram for CMultiAlignerOptions:

Classes
class	CPattern
	Representation of CDD pattern. More...

struct	SConstraint
	Structure for representing single user constraint for pair-wise alignment. More...

Public Types
enum	EMode { fNoQueryClusters = 1 , fNoRpsBlast = 1<<2 , fNoPatterns = 1<<3 , fNoIterate = 1<<4 , fNoRealign = 1<<5 , fFastAlign = 1<<6 , fFast = fNoRpsBlast \| fNoIterate \| fNoRealign \| fFastAlign , fNonStandard = 1<<7 }
	Mode of multi aligner setings. Values can be combined. More...

enum	ETreeMethod { eNJ = 0 , eFastME , eClusters }
	Method for construction of guide tree for progressive alignment. More...

enum	EInClustAlnMethod { eNone = 0 , eToPrototype , eMulti }

typedef CNWAligner::TScore	TScore

typedef TKmerMethods< CSparseKmerCounts >	TKMethods

typedef vector< SConstraint >	TConstraints

typedef int	TMode

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
	CMultiAlignerOptions (void)
	Create options with default mode. More...

	CMultiAlignerOptions (TMode mode)
	Create options with desired mode. More...

	CMultiAlignerOptions (const string &rps_db_name, TMode mode=kDefaultMode)
	Create options with RPS database and desired mode. More...

void	SetUseQueryClusters (bool use)
	Set use of query clustering option. More...

bool	GetUseQueryClusters (void) const
	Check if query clustering option is on. More...

void	SetIterate (bool use)
	Set use of iterative alignment option. More...

void	SetRealign (bool r)
	Set realigning MSA with different root nodes in the progressive alignment tree. More...

bool	GetIterate (void) const
	Check if iterative alignmnet option is used. More...

bool	GetRealign (void) const
	Check if MSA is to be realigned for different rooting of progressive alignment tree. More...

void	SetRpsDb (const string &dbname)
	Use RPS Blast with given database. More...

string	GetRpsDb (void) const
	Get RPS Blast data base name. More...

bool	GetUseRpsBlast (void) const
	Determine if RPS Blast is to be used. More...

vector< CPattern > &	SetCddPatterns (void)
	Set regular expression patterns for identification of conserved domains. More...

void	SetDefaultCddPatterns (void)
	Set default patterns for identification of conserved domains. More...

const vector< CPattern > &	GetCddPatterns (void) const
	Get regular expression patterns for identification of conserved domains. More...

TConstraints &	SetUserConstraints (void)
	Set user constraints. More...

const TConstraints &	GetUserConstraints (void) const
	Get user constraints. More...

void	SetUserConstraintsScore (int score)
	Set score for user alignment constraints. More...

int	GetUserConstraintsScore (void) const
	Get score for user alignment constraints. More...

void	SetKmerLength (int len)
	Set word size for creating word count vectors in query clustering. More...

int	GetKmerLength (void) const
	Get word size for creating word count vectors. More...

void	SetKmerAlphabet (TKMethods::ECompressedAlphabet alph)
	Set alphabet for creating word count vectors. More...

TKMethods::ECompressedAlphabet	GetKmerAlphabet (void) const
	Get alphabet used for creating word count vectors. More...

void	SetKmerDistMeasure (TKMethods::EDistMeasures method)
	Set measure for computing distance between word count vectors. More...

TKMethods::EDistMeasures	GetKmerDistMeasure (void) const
	Get method for computing distance between word count vectors. More...

void	SetMaxInClusterDist (double dist)
	Set maximum allowed distance between sequences in a cluster. More...

double	GetMaxInClusterDist (void) const
	Get maximum allowed distance between sequences in a cluster. More...

void	SetRpsEvalue (double evalue)
	Set e-value threshold for accepting RPS Blast hits. More...

double	GetRpsEvalue (void) const
	Get e-value threshold for accepting RPS Blast hits. More...

void	SetDomainHitlistSize (int size)
	Set hitlist size (per sequence) for domain search. More...

int	GetDomainHitlistSize (void) const
	Get hitlist size (per sequence) for domain searches. More...

void	SetDomainResFreqBoost (double boost)
	Set boost for residue frequencies in conserved domains from RPS data base. More...

double	GetDomainResFreqBoost (void) const
	Get boost for residue frequencies in conserved domains from RPS data base. More...

void	SetUsePreRpsHits (bool use)
	Set use of precomputed RPS Blast hits. More...

bool	GetUsePreRpsHits (void) const
	Get use of precomputed RPS Blast hits. More...

void	SetBlastpEvalue (double evalue)
	Set e-value for accepting Blastp hits. More...

double	GetBlastpEvalue (void) const
	Get e-value for accepting Blastp hits. More...

void	SetConservedCutoffScore (double score)
	Set cutoff score for conserved aligned columns. More...

double	GetConservedCutoffScore (void) const
	Get cutoff score for conserved aligned columns. More...

void	SetPseudocount (double pseudocount)
	Set pseudocount for calculating column entropy. More...

double	GetPseudocount (void) const
	Get pseudocount for calculating column entropy. More...

void	SetTreeMethod (ETreeMethod method)
	Set method for creating tree that guides progressive alignment. More...

ETreeMethod	GetTreeMethod (void) const
	Get method for creating tree that guides progressive alignment. More...

void	SetLocalResFreqBoost (double boost)
	Set frequency boost for a letter that appears in query sequence in given position. More...

double	GetLocalResFreqBoost (void) const
	Get frequency boost for a letter that appears in query sequence in given position. More...

void	SetScoreMatrixName (const string &matrix)
	Set alignment socre matrix name. More...

string	GetScoreMatrixName (void) const
	Get alignment score matrix name. More...

void	SetGapOpenPenalty (TScore penalty)
	Set gap opening penalty for middle gaps in pairwise global alignment of profiles. More...

TScore	GetGapOpenPenalty (void) const
	Get gap opening penalty for middle gaps in pairwise global alignment of profiles. More...

void	SetGapExtendPenalty (TScore penalty)
	Set gap extension penalty for middle gaps in pairwise global alignment of profiles. More...

TScore	GetGapExtendPenalty (void) const
	Get gap extension penlaty for middle gaps in pairwise global alignment of profiles. More...

void	SetEndGapOpenPenalty (TScore penalty)
	Set gap opening penalty for end gaps in pairwise global alignment of profiles. More...

TScore	GetEndGapOpenPenalty (void) const
	Get gap opening penalty for end gaps in pairwise global alignment of profiles. More...

void	SetEndGapExtendPenalty (TScore penalty)
	Set gap extension penalty for end gaps in pairwise global alignment of profiles. More...

TScore	GetEndGapExtendPenalty (void) const
	Get gap extension penalty for end gaps in pairwise global alignment of profiles. More...

TMode	GetMode (void) const
	Get options mode. More...

bool	IsStandardMode (void) const
	Check whether parameter values belong to any of the standard modes. More...

void	SetVerbose (bool verbose)
	Set verbose mode. More...

bool	GetVerbose (void) const
	Get verbose mode. More...

void	SetInClustAlnMethod (EInClustAlnMethod method)

EInClustAlnMethod	GetInClustAlnMethod (void) const

void	SetDomainHits (CConstRef< objects::CBlast4_archive > archive)
	Set pre-computed domain hits. More...

CConstRef< objects::CBlast4_archive >	GetDomainHits (void) const
	Get pre-computed domain hits. More...

bool	CanGetDomainHits (void) const
	Are pre-computed domain hits set. More...

bool	GetFastAlign (void) const
	Check if fast alignment is to be used. More...

void	SetFastAlign (bool f)
	Turn fast alignment method on/off. More...

int	GetCentralSeq (void) const
	Get central sequence. More...

void	SetCentralSeq (int c)
	Set central sequence. More...

bool	Validate (void)
	Validate parameter values. More...

const vector< string > &	GetMessages (void)
	Get warning messages. 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

Static Public Attributes
static const TMode	kDefaultMode = 0
	Default options mode. More...

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...

Private Member Functions
	CMultiAlignerOptions (const CMultiAlignerOptions &)
	Forbidding copy constructor. More...

CMultiAlignerOptions &	operator= (const CMultiAlignerOptions &)
	Forbidding assignment operator. More...

void	x_InitParams (TMode mode)
	Initiate parameter values based on the specified mode. More...

Private Attributes
TMode	m_Mode

bool	m_UseQueryClusters

TKMethods::ECompressedAlphabet	m_KmerAlphabet

unsigned int	m_KmerLength

double	m_MaxInClusterDist

TKMethods::EDistMeasures	m_ClustDistMeasure

EInClustAlnMethod	m_InClustAlnMethod

int	m_CentralSeq

string	m_RpsDb

double	m_RpsEvalue

int	m_DomainHitlistSize

double	m_DomainResFreqBoost

bool	m_UsePreRpsHits

double	m_BlastpEvalue

vector< CPattern >	m_Patterns

bool	m_Iterate

double	m_ConservedCutoff

double	m_Pseudocount

bool	m_Realign

bool	m_FastAlign

TConstraints	m_UserHits

int	m_UserHitsScore

ETreeMethod	m_TreeMethod

double	m_LocalResFreqBoost

string	m_MatrixName

TScore	m_GapOpen

TScore	m_GapExtend

TScore	m_EndGapOpen

TScore	m_EndGapExtend

CConstRef< objects::CBlast4_archive >	m_DomainHits

bool	m_Verbose

vector< string >	m_Messages

Static Private Attributes
static const int	kDefaultUserConstraintsScore = 1000000

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)

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

Detailed Description

Options and parameters for multiple alignement.

Definition at line 94 of file options.hpp.

Member Typedef Documentation

◆ TConstraints

typedef vector<SConstraint> CMultiAlignerOptions::TConstraints

Definition at line 222 of file options.hpp.

◆ TKMethods

typedef TKmerMethods<CSparseKmerCounts> CMultiAlignerOptions::TKMethods

Definition at line 99 of file options.hpp.

◆ TMode

typedef int CMultiAlignerOptions::TMode

Definition at line 252 of file options.hpp.

◆ TScore

typedef CNWAligner::TScore CMultiAlignerOptions::TScore

Definition at line 98 of file options.hpp.

Member Enumeration Documentation

◆ EInClustAlnMethod

enum CMultiAlignerOptions::EInClustAlnMethod

Enumerator
eNone	No clustering.
eToPrototype	All cluster elements are aligner to cluster prototype.
eMulti	Alignment guide tree for each cluster is attached to the main alignment guide tree.

Definition at line 264 of file options.hpp.

◆ EMode

enum CMultiAlignerOptions::EMode

Mode of multi aligner setings. Values can be combined.

Enumerator
fNoQueryClusters	No query clustering.
fNoRpsBlast	Do not use RPS Blast.
fNoPatterns	Do not use conserved domain patterns.
fNoIterate	Do not use Iterative alignment.
fNoRealign	Do not realign with different tree root.
fFastAlign	Do Fast and rough profile-profile alignment.
fFast	Set options for very fast alignment (speed over accuracy)
fNonStandard	Not used as input, indicates that. non-standard settings were selected after

Definition at line 225 of file options.hpp.

◆ ETreeMethod

enum CMultiAlignerOptions::ETreeMethod

Method for construction of guide tree for progressive alignment.

Enumerator
eNJ	Neighbot Joining.
eFastME	Fast Minimum Evolution.
eClusters	Clustering dendrogram.

Definition at line 258 of file options.hpp.

Constructor & Destructor Documentation

◆ CMultiAlignerOptions() [1/4]

CMultiAlignerOptions::CMultiAlignerOptions ( void )

Create options with default mode.

Definition at line 48 of file options.cpp.

References fNoQueryClusters, and fNoRpsBlast.

◆ CMultiAlignerOptions() [2/4]

CMultiAlignerOptions::CMultiAlignerOptions ( TMode mode )

explicit

Create options with desired mode.

Parameters

mode	Desired mode of operation

Definition at line 54 of file options.cpp.

References x_InitParams().

◆ CMultiAlignerOptions() [3/4]

CMultiAlignerOptions::CMultiAlignerOptions	(	const string &	rps_db_name,
		TMode	mode = `kDefaultMode`
	)

Create options with RPS database and desired mode.

Parameters

rps_db_name	Name of RPS database
mode	Mode of operation

Definition at line 59 of file options.cpp.

References m_RpsDb, and x_InitParams().

◆ CMultiAlignerOptions() [4/4]

CMultiAlignerOptions::CMultiAlignerOptions ( const CMultiAlignerOptions & )

private

Forbidding copy constructor.

Member Function Documentation

◆ CanGetDomainHits()

bool CMultiAlignerOptions::CanGetDomainHits ( void ) const

inline

Are pre-computed domain hits set.

Returns: true if pre-computed domain hits are set, false otherwise

Definition at line 714 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), Validate(), and CMultiAligner::x_FindDomainHits().

◆ GetBlastpEvalue()

double CMultiAlignerOptions::GetBlastpEvalue ( void ) const

inline

Get e-value for accepting Blastp hits.

Returns: E-value for accepting Blastp hits

Definition at line 540 of file options.hpp.

Referenced by CMultiAligner::x_AlignClusterQueries(), and CMultiAligner::x_AlignFillerBlocks().

◆ GetCddPatterns()

const vector<CPattern>& CMultiAlignerOptions::GetCddPatterns ( void ) const

inline

Get regular expression patterns for identification of conserved domains.

Returns: List of conserved domain patterns

Definition at line 395 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiAligner::x_FindPatternHits().

◆ GetCentralSeq()

int CMultiAlignerOptions::GetCentralSeq ( void ) const

inline

Get central sequence.

This is used for fast alignment of BLAST results. One sequence (typically BLAST query) is made artificially similar to all other sequences to make fast alignment more agreeable with BLAST alignments.

Parameters

Zero-based index of the central sequence [in]

Definition at line 740 of file options.hpp.

Referenced by CMultiAligner::x_FindQueryClusters().

◆ GetConservedCutoffScore()

double CMultiAlignerOptions::GetConservedCutoffScore ( void ) const

inline

Get cutoff score for conserved aligned columns.

Returns: Cutoff score

Definition at line 554 of file options.hpp.

Referenced by CMultiAligner::x_FindConservedColumns().

◆ GetDomainHitlistSize()

int CMultiAlignerOptions::GetDomainHitlistSize ( void ) const

inline

Get hitlist size (per sequence) for domain searches.

Returns: Hitlist size for domain searches

Definition at line 501 of file options.hpp.

Referenced by CMultiAligner::x_FindRPSHits().

◆ GetDomainHits()

CConstRef<objects::CBlast4_archive> CMultiAlignerOptions::GetDomainHits ( void ) const

inline

Get pre-computed domain hits.

Returns: Blast4 archive with pre-computed domain hits

Definition at line 708 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiAligner::x_FindDomainHits().

◆ GetDomainResFreqBoost()

double CMultiAlignerOptions::GetDomainResFreqBoost ( void ) const

inline

Get boost for residue frequencies in conserved domains from RPS data base.

Returns: Boost for RPS residue frequencies

Definition at line 514 of file options.hpp.

Referenced by CMultiAligner::x_AddRpsFreqsToCluster(), and CMultiAligner::x_AssignRPSResFreqs().

◆ GetEndGapExtendPenalty()

TScore CMultiAlignerOptions::GetEndGapExtendPenalty ( void ) const

inline

Get gap extension penalty for end gaps in pairwise global alignment of profiles.

Returns: Gap extension penalty

Definition at line 658 of file options.hpp.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

◆ GetEndGapOpenPenalty()

TScore CMultiAlignerOptions::GetEndGapOpenPenalty ( void ) const

inline

Get gap opening penalty for end gaps in pairwise global alignment of profiles.

Returns: Gap open penalty

Definition at line 645 of file options.hpp.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

◆ GetFastAlign()

bool CMultiAlignerOptions::GetFastAlign ( void ) const

inline

Check if fast alignment is to be used.

Fast alignment means that constraints will be used instead of profile- profile alignment

Returns: If true, fast alignment will be used, regural otherwise

Definition at line 723 of file options.hpp.

Referenced by CMultiAligner::x_AlignProfileProfileUsingHit().

◆ GetGapExtendPenalty()

TScore CMultiAlignerOptions::GetGapExtendPenalty ( void ) const

inline

Get gap extension penlaty for middle gaps in pairwise global alignment of profiles.

Returns: Gap extension penalty

Definition at line 632 of file options.hpp.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

◆ GetGapOpenPenalty()

TScore CMultiAlignerOptions::GetGapOpenPenalty ( void ) const

inline

Get gap opening penalty for middle gaps in pairwise global alignment of profiles.

Returns: Gap open penalty

Definition at line 619 of file options.hpp.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

◆ GetInClustAlnMethod()

EInClustAlnMethod CMultiAlignerOptions::GetInClustAlnMethod ( void ) const

inline

Definition at line 696 of file options.hpp.

Referenced by CMultiAligner::x_InitParams().

◆ GetIterate()

bool CMultiAlignerOptions::GetIterate ( void ) const

inline

Check if iterative alignmnet option is used.

Returns

True if iterative alignment option is on,
False otherwise

Definition at line 337 of file options.hpp.

Referenced by CMultiAligner::x_BuildAlignmentIterative().

◆ GetKmerAlphabet()

TKMethods::ECompressedAlphabet CMultiAlignerOptions::GetKmerAlphabet ( void ) const

inline

Get alphabet used for creating word count vectors.

Returns: Alphabet

Definition at line 450 of file options.hpp.

Referenced by CMultiAligner::x_FindQueryClusters().

◆ GetKmerDistMeasure()

TKMethods::EDistMeasures CMultiAlignerOptions::GetKmerDistMeasure ( void ) const

inline

Get method for computing distance between word count vectors.

Returns: Distance method

Definition at line 463 of file options.hpp.

Referenced by CMultiAligner::x_FindQueryClusters().

◆ GetKmerLength()

int CMultiAlignerOptions::GetKmerLength ( void ) const

inline

Get word size for creating word count vectors.

Returns: Number of letters in a word

Definition at line 439 of file options.hpp.

Referenced by CMultiAligner::x_FindQueryClusters().

◆ GetLocalResFreqBoost()

double CMultiAlignerOptions::GetLocalResFreqBoost ( void ) const

inline

Get frequency boost for a letter that appears in query sequence in given position.

Returns: Frequency boost

Definition at line 592 of file options.hpp.

Referenced by CMultiAligner::x_AssignDefaultResFreqs().

◆ GetMaxInClusterDist()

double CMultiAlignerOptions::GetMaxInClusterDist ( void ) const

inline

Get maximum allowed distance between sequences in a cluster.

Returns: Maxium allowed distance in cluster

Definition at line 476 of file options.hpp.

Referenced by CMultiAligner::x_FindQueryClusters().

◆ GetMessages()

const vector<string>& CMultiAlignerOptions::GetMessages ( void )

inline

Get warning messages.

Returns: Warning messages

Definition at line 762 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ GetMode()

TMode CMultiAlignerOptions::GetMode ( void ) const

inline

Get options mode.

Returns: Options mode

Definition at line 666 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetPseudocount()

double CMultiAlignerOptions::GetPseudocount ( void ) const

inline

Get pseudocount for calculating column entropy.

Returns: Pseudocount

Definition at line 565 of file options.hpp.

Referenced by CMultiAligner::x_GetScoreOneCol().

◆ GetRealign()

bool CMultiAlignerOptions::GetRealign ( void ) const

inline

Check if MSA is to be realigned for different rooting of progressive alignment tree.

Returns: True if MSA is to be realigned, false otherwise

Definition at line 343 of file options.hpp.

Referenced by CMultiAligner::x_BuildAlignmentIterative().

◆ GetRpsDb()

string CMultiAlignerOptions::GetRpsDb ( void ) const

inline

Get RPS Blast data base name.

Returns: RPS Blast data base name

Definition at line 362 of file options.hpp.

Referenced by CMultiAligner::x_FindDomainHits(), CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().

◆ GetRpsEvalue()

double CMultiAlignerOptions::GetRpsEvalue ( void ) const

inline

Get e-value threshold for accepting RPS Blast hits.

Returns: E-value for accepting RPS Blast hits

Definition at line 490 of file options.hpp.

Referenced by CMultiAligner::x_FindRPSHits(), and CMultiAligner::x_SetDomainHits().

◆ GetScoreMatrixName()

string CMultiAlignerOptions::GetScoreMatrixName ( void ) const

inline

Get alignment score matrix name.

Returns: Score matrix name

Definition at line 606 of file options.hpp.

Referenced by CMultiAligner::x_ComputeTree(), and CMultiAligner::x_InitAligner().

◆ GetTreeMethod()

ETreeMethod CMultiAlignerOptions::GetTreeMethod ( void ) const

inline

Get method for creating tree that guides progressive alignment.

Returns: Tree method

Definition at line 579 of file options.hpp.

Referenced by CMultiAligner::x_ComputeClusterTrees(), CMultiAligner::x_ComputeTree(), and CMultiAligner::x_FindQueryClusters().

◆ GetUsePreRpsHits()

bool CMultiAlignerOptions::GetUsePreRpsHits ( void ) const

inline

Get use of precomputed RPS Blast hits.

Returns

True if use precomputed RPS hits is on,
False otherwise

Definition at line 526 of file options.hpp.

◆ GetUseQueryClusters()

bool CMultiAlignerOptions::GetUseQueryClusters ( void ) const

inline

Check if query clustering option is on.

Returns

True if query clustering option is on,
False otherwise

Definition at line 311 of file options.hpp.

Referenced by CMultiAligner::x_InitParams().

◆ GetUserConstraints()

const TConstraints& CMultiAlignerOptions::GetUserConstraints ( void ) const

inline

Get user constraints.

Returns: User constraits

Definition at line 410 of file options.hpp.

Referenced by s_TestResults(), and CMultiAligner::x_InitParams().

◆ GetUserConstraintsScore()

int CMultiAlignerOptions::GetUserConstraintsScore ( void ) const

inline

Get score for user alignment constraints.

Returns: Score for user alignmnet constraints

Definition at line 424 of file options.hpp.

Referenced by CMultiAligner::x_InitParams().

◆ GetUseRpsBlast()

bool CMultiAlignerOptions::GetUseRpsBlast ( void ) const

inline

Determine if RPS Blast is to be used.

Returns: True if RPS Blast will be used, false otherwise

Definition at line 368 of file options.hpp.

◆ GetVerbose()

bool CMultiAlignerOptions::GetVerbose ( void ) const

inline

Get verbose mode.

If set, intermidiate results will be provided in stdout

Returns

true if verbose mode set
false otherwise

Definition at line 691 of file options.hpp.

◆ IsStandardMode()

bool CMultiAlignerOptions::IsStandardMode ( void ) const

inline

Check whether parameter values belong to any of the standard modes.

The mode is standard when parameters are not changed after the options object is created, with exception of RPS database name.

Returns: True if parameter values belong to a stanard mode, False otherwise

Definition at line 676 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ operator=()

CMultiAlignerOptions& CMultiAlignerOptions::operator= ( const CMultiAlignerOptions & )

private

Forbidding assignment operator.

◆ SetBlastpEvalue()

void CMultiAlignerOptions::SetBlastpEvalue ( double evalue )

inline

Set e-value for accepting Blastp hits.

Parameters

evalue E-value for accepting Blastp hits [in]

Definition at line 534 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetCddPatterns()

vector<CPattern>& CMultiAlignerOptions::SetCddPatterns ( void )

inline

Set regular expression patterns for identification of conserved domains.

Patterns are not freed when object is deleted.

Regular expresion patterns will be used to find conserved domains. Pairwise alignmnents will be constained to so that matching conserved domains are aligned. Parameter ownership is transfered to options.

Returns: Reference to the list of conserved domain patterns

Definition at line 379 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetCentralSeq()

void CMultiAlignerOptions::SetCentralSeq ( int c )

inline

Set central sequence.

This is used for fast alignment of BLAST results. One sequence (typically BLAST query) is made artificially similar to all other sequences to make fast alignment more agreeable with BLAST alignments.

Returns: Zero-based index of the central sequence

Definition at line 749 of file options.hpp.

◆ SetConservedCutoffScore()

void CMultiAlignerOptions::SetConservedCutoffScore ( double score )

inline

Set cutoff score for conserved aligned columns.

Parameters

score Cutoff score [in]

Definition at line 548 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetDefaultCddPatterns()

void CMultiAlignerOptions::SetDefaultCddPatterns ( void )

Set default patterns for identification of conserved domains.

Regular expresion patterns will be used to find conserved domains. Pairwise alignmnents will be constained to so that matching conserved domains are aligned. Parameter ownership is transfered to options.

Definition at line 67 of file options.cpp.

References AssignDefaultPatterns(), fNonStandard, m_Mode, and m_Patterns.

◆ SetDomainHitlistSize()

void CMultiAlignerOptions::SetDomainHitlistSize ( int size )

inline

Set hitlist size (per sequence) for domain search.

Parameters

size	Hitlist size [in]

Definition at line 495 of file options.hpp.

References ncbi::grid::netcache::search::fields::size.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetDomainHits()

void CMultiAlignerOptions::SetDomainHits ( CConstRef< objects::CBlast4_archive > archive )

inline

Set pre-computed domain hits.

Parameters

archive Blast4 archive with precomputed domain hits [in]

Definition at line 702 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetDomainResFreqBoost()

void CMultiAlignerOptions::SetDomainResFreqBoost ( double boost )

inline

Set boost for residue frequencies in conserved domains from RPS data base.

Parameters

boost Boost for RPS residue frequencies [in]

Definition at line 507 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetEndGapExtendPenalty()

void CMultiAlignerOptions::SetEndGapExtendPenalty ( TScore penalty )

inline

Set gap extension penalty for end gaps in pairwise global alignment of profiles.

Parameters

penalty Gap extension penalty [in]

Definition at line 651 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetEndGapOpenPenalty()

void CMultiAlignerOptions::SetEndGapOpenPenalty ( TScore penalty )

inline

Set gap opening penalty for end gaps in pairwise global alignment of profiles.

Parameters

penalty Gap open penalty [in]

Definition at line 638 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetFastAlign()

void CMultiAlignerOptions::SetFastAlign ( bool f )

inline

Turn fast alignment method on/off.

Fast alignment means that constraints will be used instead of profile- profile alignment

Parameters

Fast	alignment will be used if true [in]

Definition at line 731 of file options.hpp.

References f.

◆ SetGapExtendPenalty()

void CMultiAlignerOptions::SetGapExtendPenalty ( TScore penalty )

inline

Set gap extension penalty for middle gaps in pairwise global alignment of profiles.

Parameters

penalty Gap extension penalty [in]

Definition at line 625 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetGapOpenPenalty()

void CMultiAlignerOptions::SetGapOpenPenalty ( TScore penalty )

inline

Set gap opening penalty for middle gaps in pairwise global alignment of profiles.

Parameters

penalty Gap open penalty [in]

Definition at line 612 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetInClustAlnMethod()

void CMultiAlignerOptions::SetInClustAlnMethod ( EInClustAlnMethod method )

inline

Definition at line 693 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetIterate()

void CMultiAlignerOptions::SetIterate ( bool use )

inline

Set use of iterative alignment option.

After initial multiple alignment is done, conserved columns will be found and sequences will be re-aligned using this information. Default parameters will be used. Iterative alignment parameters can be changed with expert functions.

Parameters

use	Option used if true, otherwise not used [in]

Definition at line 322 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetKmerAlphabet()

void CMultiAlignerOptions::SetKmerAlphabet ( TKMethods::ECompressedAlphabet alph )

inline

Set alphabet for creating word count vectors.

Parameters

alph	Alphabet [in]

Definition at line 444 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetKmerDistMeasure()

void CMultiAlignerOptions::SetKmerDistMeasure ( TKMethods::EDistMeasures method )

inline

Set measure for computing distance between word count vectors.

Parameters

method Distance method [in]

Definition at line 456 of file options.hpp.

◆ SetKmerLength()

void CMultiAlignerOptions::SetKmerLength ( int len )

inline

Set word size for creating word count vectors in query clustering.

Parameters

len	Number of letters in a word [in]

Definition at line 434 of file options.hpp.

References len.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetLocalResFreqBoost()

void CMultiAlignerOptions::SetLocalResFreqBoost ( double boost )

inline

Set frequency boost for a letter that appears in query sequence in given position.

Parameters

boost Frequency boost [in]

Definition at line 585 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetMaxInClusterDist()

void CMultiAlignerOptions::SetMaxInClusterDist ( double dist )

inline

Set maximum allowed distance between sequences in a cluster.

Parameters

dist	Maximum allowed distance in cluster [in]

Definition at line 470 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetPseudocount()

void CMultiAlignerOptions::SetPseudocount ( double pseudocount )

inline

Set pseudocount for calculating column entropy.

Parameters

pseudocount Pseudocount [in]

Definition at line 559 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetRealign()

void CMultiAlignerOptions::SetRealign ( bool r )

inline

Set realigning MSA with different root nodes in the progressive alignment tree.

Parameters

r	Do realignment if true [in]

Definition at line 329 of file options.hpp.

References r().

◆ SetRpsDb()

void CMultiAlignerOptions::SetRpsDb ( const string & dbname )

inline

Use RPS Blast with given database.

RPS Blast will be used to find conserved domains in query sequences. Pairwise alignments are constrainted so that matching conserved domains are aligned. Default RPS Blast parameters will be used. RPS Blast parameters can be changed with expetr functions.

Parameters

dbname Path and name of RPS Blast data base [in]

Definition at line 355 of file options.hpp.

References dbname().

Referenced by BOOST_AUTO_TEST_CASE(), CMultiAlignerFixture::CMultiAlignerFixture(), and CMultiApplication::Run().

◆ SetRpsEvalue()

void CMultiAlignerOptions::SetRpsEvalue ( double evalue )

inline

Set e-value threshold for accepting RPS Blast hits.

Parameters

evalue E-value for acceting RPS Blast hits [in]

Definition at line 484 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetScoreMatrixName()

void CMultiAlignerOptions::SetScoreMatrixName ( const string & matrix )

inline

Set alignment socre matrix name.

Parameters

matrix Score matrix name [in]

Definition at line 600 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetTreeMethod()

void CMultiAlignerOptions::SetTreeMethod ( ETreeMethod method )

inline

Set method for creating tree that guides progressive alignment.

Parameters

method Tree computation method [in]

Definition at line 573 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ SetUsePreRpsHits()

void CMultiAlignerOptions::SetUsePreRpsHits ( bool use )

inline

Set use of precomputed RPS Blast hits.

Parameters

use

Definition at line 518 of file options.hpp.

◆ SetUseQueryClusters()

void CMultiAlignerOptions::SetUseQueryClusters ( bool use )

Set use of query clustering option.

If the option in set on, query sequences will be clustered. Each cluster Will be aligned independently without searching for conserved domains (RPS Blast) and local hist (Blastp). Multiple alignment will be performed on cluster profiles. Parameters of clustering procedure are set based on EMode value and can be chanded with expert functions.

Parameters

use	Option used if true [in]

Definition at line 75 of file options.cpp.

References eMulti, fNonStandard, m_InClustAlnMethod, m_Mode, and m_UseQueryClusters.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetUserConstraints()

TConstraints& CMultiAlignerOptions::SetUserConstraints ( void )

inline

Set user constraints.

The constraits are used in progressive alignment.

Returns: Reference to the list of user constraints

Definition at line 403 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ SetUserConstraintsScore()

void CMultiAlignerOptions::SetUserConstraintsScore ( int score )

inline

Set score for user alignment constraints.

Parameters

score Score

Definition at line 417 of file options.hpp.

◆ SetVerbose()

void CMultiAlignerOptions::SetVerbose ( bool verbose )

inline

Set verbose mode.

If set, intermidiate results will be provided in stdout

Parameters

verbose Verbose mode set if true, not set otherwise [in]

Definition at line 683 of file options.hpp.

Referenced by CMultiApplication::Run().

◆ Validate()

bool CMultiAlignerOptions::Validate ( void )

Validate parameter values.

Returns: True if parameters valid, false otherwise

Definition at line 86 of file options.cpp.

References CanGetDomainHits(), eClusters, eFastME, TKmerMethods< TKmerCounts >::eFractionCommonKmersGlobal, TKmerMethods< TKmerCounts >::eFractionCommonKmersLocal, TKmerMethods< TKmerCounts >::eLastAlphabet, eNJ, eNone, fNoIterate, fNonStandard, fNoPatterns, fNoQueryClusters, fNoRpsBlast, ITERATE, m_BlastpEvalue, m_ClustDistMeasure, m_DomainHitlistSize, m_InClustAlnMethod, m_KmerAlphabet, m_KmerLength, m_Messages, m_Mode, m_Patterns, m_Pseudocount, m_RpsDb, m_RpsEvalue, m_TreeMethod, m_UseQueryClusters, m_UserHits, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), and CMultiApplication::Run().

◆ x_InitParams()

void CMultiAlignerOptions::x_InitParams ( TMode mode )

private

Initiate parameter values based on the specified mode.

Parameters

mode Mode

Definition at line 215 of file options.cpp.

References AssignDefaultPatterns(), COBALT_BLAST_EVALUE, COBALT_CONSERVED_CUTOFF, COBALT_DEFAULT_MATRIX, COBALT_DOMAIN_BOOST, COBALT_DOMAIN_HITLIST_SIZE, COBALT_END_GAP_EXTNT, COBALT_END_GAP_OPEN, COBALT_GAP_EXTNT, COBALT_GAP_OPEN, COBALT_KMER_ALPH, COBALT_KMER_LEN, COBALT_LOCAL_BOOST, COBALT_MAX_CLUSTER_DIAM, COBALT_PSEUDO_COUNT, COBALT_RPS_EVALUE, COBALT_TREE_METHOD, TKmerMethods< TKmerCounts >::eFractionCommonKmersGlobal, eMulti, eNone, fFastAlign, fNoIterate, fNonStandard, fNoPatterns, fNoQueryClusters, fNoRealign, kDefaultUserConstraintsScore, m_BlastpEvalue, m_CentralSeq, m_ClustDistMeasure, m_ConservedCutoff, m_DomainHitlistSize, m_DomainResFreqBoost, m_EndGapExtend, m_EndGapOpen, m_FastAlign, m_GapExtend, m_GapOpen, m_InClustAlnMethod, m_Iterate, m_KmerAlphabet, m_KmerLength, m_LocalResFreqBoost, m_MatrixName, m_MaxInClusterDist, m_Mode, m_Patterns, m_Pseudocount, m_Realign, m_RpsEvalue, m_TreeMethod, m_UsePreRpsHits, m_UseQueryClusters, m_UserHitsScore, m_Verbose, and NCBI_THROW.

Referenced by CMultiAlignerOptions().

Member Data Documentation

◆ kDefaultMode

const TMode CMultiAlignerOptions::kDefaultMode = 0

int CMultiAlignerOptions::m_DomainHitlistSize

private

Definition at line 793 of file options.hpp.

Referenced by Validate(), and x_InitParams().

bool CMultiAlignerOptions::m_Verbose

private

Definition at line 833 of file options.hpp.

Referenced by x_InitParams().

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

include/algo/cobalt/options.hpp
src/algo/cobalt/options.cpp

Classes

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TConstraints

◆ TKMethods

◆ TMode

◆ TScore

Member Enumeration Documentation

◆ EInClustAlnMethod

◆ EMode

◆ ETreeMethod

Constructor & Destructor Documentation

◆ CMultiAlignerOptions() [1/4]

◆ CMultiAlignerOptions() [2/4]

◆ CMultiAlignerOptions() [3/4]

◆ CMultiAlignerOptions() [4/4]

Member Function Documentation

◆ CanGetDomainHits()

◆ GetBlastpEvalue()

◆ GetCddPatterns()

◆ GetCentralSeq()

◆ GetConservedCutoffScore()

◆ GetDomainHitlistSize()

◆ GetDomainHits()

◆ GetDomainResFreqBoost()

◆ GetEndGapExtendPenalty()

◆ GetEndGapOpenPenalty()

◆ GetFastAlign()

◆ GetGapExtendPenalty()

◆ GetGapOpenPenalty()

◆ GetInClustAlnMethod()

◆ GetIterate()

◆ GetKmerAlphabet()

◆ GetKmerDistMeasure()

◆ GetKmerLength()

◆ GetLocalResFreqBoost()

◆ GetMaxInClusterDist()

◆ GetMessages()

◆ GetMode()

◆ GetPseudocount()

◆ GetRealign()

◆ GetRpsDb()

◆ GetRpsEvalue()

◆ GetScoreMatrixName()

◆ GetTreeMethod()

◆ GetUsePreRpsHits()

◆ GetUseQueryClusters()

◆ GetUserConstraints()

◆ GetUserConstraintsScore()

◆ GetUseRpsBlast()

◆ GetVerbose()

◆ IsStandardMode()

◆ operator=()

◆ SetBlastpEvalue()

◆ SetCddPatterns()

◆ SetCentralSeq()

◆ SetConservedCutoffScore()

◆ SetDefaultCddPatterns()

◆ SetDomainHitlistSize()

◆ SetDomainHits()

◆ SetDomainResFreqBoost()

◆ SetEndGapExtendPenalty()

◆ SetEndGapOpenPenalty()

◆ SetFastAlign()

◆ SetGapExtendPenalty()

◆ SetGapOpenPenalty()

◆ SetInClustAlnMethod()

◆ SetIterate()

◆ SetKmerAlphabet()

◆ SetKmerDistMeasure()

◆ SetKmerLength()

◆ SetLocalResFreqBoost()

◆ SetMaxInClusterDist()