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NCBI C++ ToolKit: include/algo/cobalt/options.hpp Source File

: m_Pattern((char*)

), m_IsPointer(

) {}

: m_Pattern(pattern), m_IsPointer(

) {}

: m_Pattern(pattern), m_IsPointer(

) {}

{

(m_IsPointer ? m_Pattern.pointer

: m_Pattern.str.c_str());}

{

(m_IsPointer ? (

)m_Pattern.pointer : m_Pattern.str);}

{

m_IsPointer ? !m_Pattern.pointer : m_Pattern.str.empty();}

: seq1_index(

), seq1_start(start1), seq1_stop(end1),

seq2_index(

), seq2_start(start2), seq2_stop(end2)

fNoQueryClusters = 1,

fFast = fNoRpsBlast | fNoIterate | fNoRealign | fFastAlign,

kDefaultMode = 0;

SetUseQueryClusters(

use);

{m_Iterate = use; m_Mode = fNonStandard;}

{m_Realign =

; m_Mode = fNonStandard;}

{m_RpsDb =

; m_Mode = m_Mode & ~fNoRpsBlast;}

{m_Mode = fNonStandard;

m_Patterns;}

SetDefaultCddPatterns(

);

{m_Mode = fNonStandard;

m_UserHits;}

{

m_UserHits;}

{m_UserHitsScore = score; m_Mode = fNonStandard;}

{m_KmerAlphabet = alph; m_Mode = fNonStandard;}

{

m_KmerAlphabet;}

{m_ClustDistMeasure = method; m_Mode = fNonStandard;}

{

m_ClustDistMeasure;}

{m_MaxInClusterDist = dist; m_Mode = fNonStandard;}

{m_RpsEvalue = evalue; m_Mode = fNonStandard;}

{m_DomainHitlistSize =

; m_Mode = fNonStandard;}

{m_DomainResFreqBoost =

; m_Mode = fNonStandard;}

{m_UsePreRpsHits = use; m_Mode = fNonStandard;}

{m_BlastpEvalue = evalue; m_Mode = fNonStandard;}

{m_ConservedCutoff = score; m_Mode = fNonStandard;}

{m_Pseudocount = pseudocount; m_Mode = fNonStandard;}

{m_TreeMethod = method; m_Mode = fNonStandard;}

{m_LocalResFreqBoost =

; m_Mode =fNonStandard;}

{m_MatrixName = matrix; m_Mode = fNonStandard;}

{m_GapOpen = penalty; m_Mode = fNonStandard;}

{m_GapExtend = penalty; m_Mode = fNonStandard;}

{m_EndGapOpen = penalty; m_Mode = fNonStandard;}

{m_EndGapExtend = penalty; m_Mode = fNonStandard;}

{m_InClustAlnMethod = method;}

{

m_InClustAlnMethod;}

{m_DomainHits = archive;}

{

m_DomainHits;}

{

!m_DomainHits.Empty();}

Validate(

);

kDefaultUserConstraintsScore = 1000000;

User-defined methods of the data storage class.

Representation of CDD pattern.

CPattern(const string &pattern)

Create pattern as string.

bool IsEmpty(void) const

Check if pattern is empty.

string AsString(void) const

Get a copy of a pattern as string.

bool IsPointer(void) const

Check if pattern is stored as pointer.

CPattern(void)

Create empty pattern.

CPattern(char *pattern)

Create pattern as pointer.

CPattern(const CPattern &pattern)

Create copy of a pattern.

CPattern & operator=(const CPattern &pattern)

Assignment operator.

const char * AsPointer(void) const

Get pattern as pointer.

Options and parameters for multiple alignement.

ETreeMethod

Method for construction of guide tree for progressive alignment.

@ eFastME

Fast Minimum Evolution.

bool GetFastAlign(void) const

Check if fast alignment is to be used.

EInClustAlnMethod m_InClustAlnMethod

TScore GetEndGapExtendPenalty(void) const

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

void SetDomainHitlistSize(int size)

Set hitlist size (per sequence) for domain search.

void SetKmerAlphabet(TKMethods::ECompressedAlphabet alph)

Set alphabet for creating word count vectors.

void SetFastAlign(bool f)

Turn fast alignment method on/off.

void SetKmerLength(int len)

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

void SetKmerDistMeasure(TKMethods::EDistMeasures method)

Set measure for computing distance between word count vectors.

double m_MaxInClusterDist

vector< string > m_Messages

double GetMaxInClusterDist(void) const

Get maximum allowed distance between sequences in a cluster.

string GetScoreMatrixName(void) const

Get alignment score matrix name.

void SetEndGapOpenPenalty(TScore penalty)

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

void SetScoreMatrixName(const string &matrix)

Set alignment socre matrix name.

string GetRpsDb(void) const

Get RPS Blast data base name.

void SetLocalResFreqBoost(double boost)

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

void SetUserConstraintsScore(int score)

Set score for user alignment constraints.

TKMethods::EDistMeasures GetKmerDistMeasure(void) const

Get method for computing distance between word count vectors.

double GetLocalResFreqBoost(void) const

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

bool GetUsePreRpsHits(void) const

Get use of precomputed RPS Blast hits.

void SetVerbose(bool verbose)

Set verbose mode.

void SetMaxInClusterDist(double dist)

Set maximum allowed distance between sequences in a cluster.

bool GetUseRpsBlast(void) const

Determine if RPS Blast is to be used.

int GetCentralSeq(void) const

Get central sequence.

void SetBlastpEvalue(double evalue)

Set e-value for accepting Blastp hits.

EInClustAlnMethod GetInClustAlnMethod(void) const

int GetDomainHitlistSize(void) const

Get hitlist size (per sequence) for domain searches.

bool IsStandardMode(void) const

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

unsigned int m_KmerLength

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

Set pre-computed domain hits.

void SetTreeMethod(ETreeMethod method)

Set method for creating tree that guides progressive alignment.

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

Get pre-computed domain hits.

TKmerMethods< CSparseKmerCounts > TKMethods

TMode GetMode(void) const

Get options mode.

vector< CPattern > m_Patterns

const vector< string > & GetMessages(void)

Get warning messages.

const vector< CPattern > & GetCddPatterns(void) const

Get regular expression patterns for identification of conserved domains.

void SetGapOpenPenalty(TScore penalty)

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

void SetRpsDb(const string &dbname)

Use RPS Blast with given database.

double m_LocalResFreqBoost

double GetConservedCutoffScore(void) const

Get cutoff score for conserved aligned columns.

void SetConservedCutoffScore(double score)

Set cutoff score for conserved aligned columns.

bool GetIterate(void) const

Check if iterative alignmnet option is used.

CConstRef< objects::CBlast4_archive > m_DomainHits

double GetPseudocount(void) const

Get pseudocount for calculating column entropy.

TScore GetGapExtendPenalty(void) const

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

bool CanGetDomainHits(void) const

Are pre-computed domain hits set.

const TConstraints & GetUserConstraints(void) const

Get user constraints.

TConstraints & SetUserConstraints(void)

Set user constraints.

TScore GetGapOpenPenalty(void) const

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

TScore GetEndGapOpenPenalty(void) const

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

bool GetRealign(void) const

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

vector< CPattern > & SetCddPatterns(void)

Set regular expression patterns for identification of conserved domains.

double GetRpsEvalue(void) const

Get e-value threshold for accepting RPS Blast hits.

TKMethods::EDistMeasures m_ClustDistMeasure

TKMethods::ECompressedAlphabet GetKmerAlphabet(void) const

Get alphabet used for creating word count vectors.

void SetInClustAlnMethod(EInClustAlnMethod method)

void SetIterate(bool use)

Set use of iterative alignment option.

ETreeMethod GetTreeMethod(void) const

Get method for creating tree that guides progressive alignment.

EMode

Mode of multi aligner setings. Values can be combined.

vector< SConstraint > TConstraints

void SetPseudocount(double pseudocount)

Set pseudocount for calculating column entropy.

bool GetUseQueryClusters(void) const

Check if query clustering option is on.

void SetRpsEvalue(double evalue)

Set e-value threshold for accepting RPS Blast hits.

void SetDomainResFreqBoost(double boost)

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

void SetUsePreRpsHits(bool use)

Set use of precomputed RPS Blast hits.

CMultiAlignerOptions(const CMultiAlignerOptions &)

Forbidding copy constructor.

CMultiAlignerOptions & operator=(const CMultiAlignerOptions &)

Forbidding assignment operator.

CNWAligner::TScore TScore

void SetRealign(bool r)

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

int GetKmerLength(void) const

Get word size for creating word count vectors.

TKMethods::ECompressedAlphabet m_KmerAlphabet

int GetUserConstraintsScore(void) const

Get score for user alignment constraints.

void SetGapExtendPenalty(TScore penalty)

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

void SetCentralSeq(int c)

Set central sequence.

double GetBlastpEvalue(void) const

Get e-value for accepting Blastp hits.

void SetEndGapExtendPenalty(TScore penalty)

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

bool GetVerbose(void) const

Get verbose mode.

double m_DomainResFreqBoost

double GetDomainResFreqBoost(void) const

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

Interface for computing and manipulating k-mer counts vectors that allows for different implementatio...

static const char * str(char *buf, int n)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_COBALT_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > & pointer

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Structure for representing single user constraint for pair-wise alignment.

SConstraint(int ind1, int start1, int end1, int ind2, int start2, int end2)

Create constraint for given sequences and locations.

SConstraint(void)

Create empty constraint.

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