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NCBI C++ ToolKit: CMultiAlignerOptions Class Reference

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Options and parameters for multiple alignement. More...

#include <algo/cobalt/options.hpp>

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 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...
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...
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...
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

Options and parameters for multiple alignement.

Definition at line 94 of file options.hpp.

◆ TConstraints ◆ TKMethods ◆ TMode ◆ TScore ◆ 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

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

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.

◆ CMultiAlignerOptions() [1/4] CMultiAlignerOptions::CMultiAlignerOptions ( void ) ◆ 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]

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]

Forbidding copy constructor.

◆ CanGetDomainHits() bool CMultiAlignerOptions::CanGetDomainHits ( void ) const inline ◆ GetBlastpEvalue() double CMultiAlignerOptions::GetBlastpEvalue ( void ) const inline ◆ GetCddPatterns() const vector<CPattern>& CMultiAlignerOptions::GetCddPatterns ( void ) const inline ◆ 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 ◆ GetDomainHitlistSize() int CMultiAlignerOptions::GetDomainHitlistSize ( void ) const inline ◆ GetDomainHits() CConstRef<objects::CBlast4_archive> CMultiAlignerOptions::GetDomainHits ( void ) const inline ◆ GetDomainResFreqBoost() double CMultiAlignerOptions::GetDomainResFreqBoost ( void ) const inline ◆ GetEndGapExtendPenalty() TScore CMultiAlignerOptions::GetEndGapExtendPenalty ( void ) const inline ◆ GetEndGapOpenPenalty() TScore CMultiAlignerOptions::GetEndGapOpenPenalty ( void ) const inline ◆ GetFastAlign() bool CMultiAlignerOptions::GetFastAlign ( void ) const inline ◆ GetGapExtendPenalty() TScore CMultiAlignerOptions::GetGapExtendPenalty ( void ) const inline ◆ GetGapOpenPenalty() TScore CMultiAlignerOptions::GetGapOpenPenalty ( void ) const inline ◆ GetInClustAlnMethod() ◆ GetIterate() bool CMultiAlignerOptions::GetIterate ( void ) const inline ◆ GetKmerAlphabet() ◆ GetKmerDistMeasure() ◆ GetKmerLength() int CMultiAlignerOptions::GetKmerLength ( void ) const inline ◆ GetLocalResFreqBoost() double CMultiAlignerOptions::GetLocalResFreqBoost ( void ) const inline ◆ GetMaxInClusterDist() double CMultiAlignerOptions::GetMaxInClusterDist ( void ) const inline ◆ GetMessages() const vector<string>& CMultiAlignerOptions::GetMessages ( void ) inline ◆ GetMode() TMode CMultiAlignerOptions::GetMode ( void ) const inline ◆ GetPseudocount() double CMultiAlignerOptions::GetPseudocount ( void ) const inline ◆ GetRealign() bool CMultiAlignerOptions::GetRealign ( void ) const inline ◆ GetRpsDb() string CMultiAlignerOptions::GetRpsDb ( void ) const inline ◆ GetRpsEvalue() double CMultiAlignerOptions::GetRpsEvalue ( void ) const inline ◆ GetScoreMatrixName() string CMultiAlignerOptions::GetScoreMatrixName ( void ) const inline ◆ GetTreeMethod() ETreeMethod CMultiAlignerOptions::GetTreeMethod ( void ) const inline ◆ 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 ◆ GetUserConstraints() ◆ GetUserConstraintsScore() int CMultiAlignerOptions::GetUserConstraintsScore ( void ) const inline ◆ 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=()

Forbidding assignment operator.

◆ SetBlastpEvalue() void CMultiAlignerOptions::SetBlastpEvalue ( double evalue ) inline ◆ 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 ◆ SetDefaultCddPatterns() void CMultiAlignerOptions::SetDefaultCddPatterns ( void )

Set default patterns for identification of conserved domains.

Definition at line 67 of file options.cpp.

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

◆ SetDomainHitlistSize() void CMultiAlignerOptions::SetDomainHitlistSize ( int size ) inline ◆ SetDomainHits() void CMultiAlignerOptions::SetDomainHits ( CConstRef< objects::CBlast4_archive > archive ) inline ◆ 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() ◆ 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() ◆ SetKmerDistMeasure()

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 ◆ 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 ◆ 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 ◆ SetRpsEvalue() void CMultiAlignerOptions::SetRpsEvalue ( double evalue ) inline ◆ SetScoreMatrixName() void CMultiAlignerOptions::SetScoreMatrixName ( const string & matrix ) inline ◆ 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

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 ◆ SetUserConstraintsScore() void CMultiAlignerOptions::SetUserConstraintsScore ( int score ) inline

Set score for user alignment constraints.

Parameters

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

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().

◆ kDefaultMode const TMode CMultiAlignerOptions::kDefaultMode = 0 static ◆ kDefaultUserConstraintsScore const int CMultiAlignerOptions::kDefaultUserConstraintsScore = 1000000 staticprivate ◆ m_BlastpEvalue double CMultiAlignerOptions::m_BlastpEvalue private ◆ m_CentralSeq int CMultiAlignerOptions::m_CentralSeq private ◆ m_ClustDistMeasure ◆ m_ConservedCutoff double CMultiAlignerOptions::m_ConservedCutoff private ◆ m_DomainHitlistSize int CMultiAlignerOptions::m_DomainHitlistSize private ◆ m_DomainHits CConstRef<objects::CBlast4_archive> CMultiAlignerOptions::m_DomainHits private

Definition at line 831 of file options.hpp.

◆ m_DomainResFreqBoost double CMultiAlignerOptions::m_DomainResFreqBoost private ◆ m_EndGapExtend TScore CMultiAlignerOptions::m_EndGapExtend private ◆ m_EndGapOpen TScore CMultiAlignerOptions::m_EndGapOpen private ◆ m_FastAlign bool CMultiAlignerOptions::m_FastAlign private ◆ m_GapExtend TScore CMultiAlignerOptions::m_GapExtend private ◆ m_GapOpen TScore CMultiAlignerOptions::m_GapOpen private ◆ m_InClustAlnMethod ◆ m_Iterate bool CMultiAlignerOptions::m_Iterate private ◆ m_KmerAlphabet ◆ m_KmerLength unsigned int CMultiAlignerOptions::m_KmerLength private ◆ m_LocalResFreqBoost double CMultiAlignerOptions::m_LocalResFreqBoost private ◆ m_MatrixName string CMultiAlignerOptions::m_MatrixName private ◆ m_MaxInClusterDist double CMultiAlignerOptions::m_MaxInClusterDist private ◆ m_Messages vector<string> CMultiAlignerOptions::m_Messages private ◆ m_Mode TMode CMultiAlignerOptions::m_Mode private ◆ m_Patterns vector<CPattern> CMultiAlignerOptions::m_Patterns private ◆ m_Pseudocount double CMultiAlignerOptions::m_Pseudocount private ◆ m_Realign bool CMultiAlignerOptions::m_Realign private ◆ m_RpsDb string CMultiAlignerOptions::m_RpsDb private ◆ m_RpsEvalue double CMultiAlignerOptions::m_RpsEvalue private ◆ m_TreeMethod ◆ m_UsePreRpsHits bool CMultiAlignerOptions::m_UsePreRpsHits private ◆ m_UseQueryClusters bool CMultiAlignerOptions::m_UseQueryClusters private ◆ m_UserHits ◆ m_UserHitsScore int CMultiAlignerOptions::m_UserHitsScore private ◆ m_Verbose bool CMultiAlignerOptions::m_Verbose private

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

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

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