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CMultiAlignerOptions Class Reference

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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< CSparseKmerCountsTKMethods
 
typedef vector< SConstraintTConstraints
 
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< Uint8TCounter
 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...
 
TConstraintsSetUserConstraints (void)
 Set user constraints. More...
 
const TConstraintsGetUserConstraints (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...
 
CObjectoperator= (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...
 
CMultiAlignerOptionsoperator= (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< CPatternm_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< stringm_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

Definition at line 222 of file options.hpp.

◆ TKMethods

Definition at line 99 of file options.hpp.

◆ TMode

Definition at line 252 of file options.hpp.

◆ TScore

Definition at line 98 of file options.hpp.

Member Enumeration Documentation

◆ 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.

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
modeDesired 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_nameName of RPS database
modeMode 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-basedindex 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

◆ 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
evalueE-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
scoreCutoff 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
sizeHitlist 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
archiveBlast4 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
boostBoost 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
penaltyGap 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
penaltyGap 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
Fastalignment 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
penaltyGap 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
penaltyGap 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
useOption 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
alphAlphabet [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
methodDistance 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
lenNumber 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
boostFrequency 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
distMaximum 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
pseudocountPseudocount [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
rDo 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
dbnamePath 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
evalueE-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
matrixScore 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
methodTree 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
useOption 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
scoreScore

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
verboseVerbose 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  )

◆ x_InitParams()

void CMultiAlignerOptions::x_InitParams ( TMode  mode)
private

Member Data Documentation

◆ kDefaultMode

const TMode CMultiAlignerOptions::kDefaultMode = 0
static

Default options mode.

Definition at line 255 of file options.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ kDefaultUserConstraintsScore

const int CMultiAlignerOptions::kDefaultUserConstraintsScore = 1000000
staticprivate

Definition at line 837 of file options.hpp.

Referenced by x_InitParams().

◆ m_BlastpEvalue

double CMultiAlignerOptions::m_BlastpEvalue
private

Definition at line 798 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_CentralSeq

int CMultiAlignerOptions::m_CentralSeq
private

Definition at line 788 of file options.hpp.

Referenced by x_InitParams().

◆ m_ClustDistMeasure

TKMethods::EDistMeasures CMultiAlignerOptions::m_ClustDistMeasure
private

Definition at line 786 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_ConservedCutoff

double CMultiAlignerOptions::m_ConservedCutoff
private

Definition at line 805 of file options.hpp.

Referenced by x_InitParams().

◆ m_DomainHitlistSize

int CMultiAlignerOptions::m_DomainHitlistSize
private

Definition at line 793 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ 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

Definition at line 794 of file options.hpp.

Referenced by x_InitParams().

◆ m_EndGapExtend

TScore CMultiAlignerOptions::m_EndGapExtend
private

Definition at line 828 of file options.hpp.

Referenced by x_InitParams().

◆ m_EndGapOpen

TScore CMultiAlignerOptions::m_EndGapOpen
private

Definition at line 827 of file options.hpp.

Referenced by x_InitParams().

◆ m_FastAlign

bool CMultiAlignerOptions::m_FastAlign
private

Definition at line 813 of file options.hpp.

Referenced by x_InitParams().

◆ m_GapExtend

TScore CMultiAlignerOptions::m_GapExtend
private

Definition at line 826 of file options.hpp.

Referenced by x_InitParams().

◆ m_GapOpen

TScore CMultiAlignerOptions::m_GapOpen
private

Definition at line 825 of file options.hpp.

Referenced by x_InitParams().

◆ m_InClustAlnMethod

EInClustAlnMethod CMultiAlignerOptions::m_InClustAlnMethod
private

Definition at line 787 of file options.hpp.

Referenced by SetUseQueryClusters(), Validate(), and x_InitParams().

◆ m_Iterate

bool CMultiAlignerOptions::m_Iterate
private

Definition at line 804 of file options.hpp.

Referenced by x_InitParams().

◆ m_KmerAlphabet

TKMethods::ECompressedAlphabet CMultiAlignerOptions::m_KmerAlphabet
private

Definition at line 783 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_KmerLength

unsigned int CMultiAlignerOptions::m_KmerLength
private

Definition at line 784 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_LocalResFreqBoost

double CMultiAlignerOptions::m_LocalResFreqBoost
private

Definition at line 821 of file options.hpp.

Referenced by x_InitParams().

◆ m_MatrixName

string CMultiAlignerOptions::m_MatrixName
private

Definition at line 824 of file options.hpp.

Referenced by x_InitParams().

◆ m_MaxInClusterDist

double CMultiAlignerOptions::m_MaxInClusterDist
private

Definition at line 785 of file options.hpp.

Referenced by x_InitParams().

◆ m_Messages

vector<string> CMultiAlignerOptions::m_Messages
private

Definition at line 835 of file options.hpp.

Referenced by Validate().

◆ m_Mode

TMode CMultiAlignerOptions::m_Mode
private

Definition at line 779 of file options.hpp.

Referenced by SetDefaultCddPatterns(), SetUseQueryClusters(), Validate(), and x_InitParams().

◆ m_Patterns

vector<CPattern> CMultiAlignerOptions::m_Patterns
private

Definition at line 801 of file options.hpp.

Referenced by SetDefaultCddPatterns(), Validate(), and x_InitParams().

◆ m_Pseudocount

double CMultiAlignerOptions::m_Pseudocount
private

Definition at line 806 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_Realign

bool CMultiAlignerOptions::m_Realign
private

Definition at line 809 of file options.hpp.

Referenced by x_InitParams().

◆ m_RpsDb

string CMultiAlignerOptions::m_RpsDb
private

Definition at line 791 of file options.hpp.

Referenced by CMultiAlignerOptions(), and Validate().

◆ m_RpsEvalue

double CMultiAlignerOptions::m_RpsEvalue
private

Definition at line 792 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_TreeMethod

ETreeMethod CMultiAlignerOptions::m_TreeMethod
private

Definition at line 820 of file options.hpp.

Referenced by Validate(), and x_InitParams().

◆ m_UsePreRpsHits

bool CMultiAlignerOptions::m_UsePreRpsHits
private

Definition at line 795 of file options.hpp.

Referenced by x_InitParams().

◆ m_UseQueryClusters

bool CMultiAlignerOptions::m_UseQueryClusters
private

Definition at line 782 of file options.hpp.

Referenced by SetUseQueryClusters(), Validate(), and x_InitParams().

◆ m_UserHits

TConstraints CMultiAlignerOptions::m_UserHits
private

Definition at line 816 of file options.hpp.

Referenced by Validate().

◆ m_UserHitsScore

int CMultiAlignerOptions::m_UserHitsScore
private

Definition at line 817 of file options.hpp.

Referenced by x_InitParams().

◆ m_Verbose

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:
Modified on Sat Jun 22 10:44:11 2024 by modify_doxy.py rev. 669887