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ConsensusMaker Class Reference

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#include <algo/structure/cd_utils/cuConsensusMaker.hpp>

+ Collaboration diagram for ConsensusMaker:

Public Member Functions

 ConsensusMaker (CCdCore *cd, double incl=0.5)
 
 ~ConsensusMaker ()
 
void makeConsensus ()
 
ResidueProfilesgetResidueProfiles ()
 
const stringgetConsensus ()
 
CRef< CSeq_entrygetConsensusSeqEntry ()
 
const BlockModelPairgetGuideAlignment () const
 
BlockModelPairgetGuideAlignment ()
 
CRef< CSeq_aligngetGuideSeqAlign ()
 
CRef< CSeq_align_setremasterWithConsensus () const
 
void remasterWithConsensus (bool extended)
 
void skipUnalignedSeg (int threshold)
 
double GetInclusionRule () const
 

Static Public Member Functions

static CRef< CSeq_align_setdegapAlignment (CCdCore *cd)
 
static void degapAlignment (CCdCore *cd, list< CRef< CSeq_align > > &seqAligns)
 
static void degapCdAlignment (CCdCore *cd)
 
static void degapCdAlignmentToPending (CCdCore *cd)
 

Private Member Functions

void addRows ()
 

Private Attributes

string m_consensus
 
CCdCorem_cd
 
list< CRef< CSeq_align > > m_seqAligns
 
CRef< CSeq_idm_masterSeqId
 
CRef< CSeq_idm_conSeqId
 
bool m_made
 
double m_inclusionRule
 
ResidueProfiles m_rp
 

Detailed Description

Definition at line 47 of file cuConsensusMaker.hpp.

Constructor & Destructor Documentation

◆ ConsensusMaker()

ConsensusMaker::ConsensusMaker ( CCdCore cd,
double  incl = 0.5 
)

Definition at line 40 of file cuConsensusMaker.cpp.

References IsConsensus().

◆ ~ConsensusMaker()

ConsensusMaker::~ConsensusMaker ( )

Definition at line 53 of file cuConsensusMaker.cpp.

Member Function Documentation

◆ addRows()

void ConsensusMaker::addRows ( )
private

◆ degapAlignment() [1/2]

CRef< CSeq_align_set > ConsensusMaker::degapAlignment ( CCdCore cd)
static

◆ degapAlignment() [2/2]

void ConsensusMaker::degapAlignment ( CCdCore cd,
list< CRef< CSeq_align > > &  seqAligns 
)
static

◆ degapCdAlignment()

void ConsensusMaker::degapCdAlignment ( CCdCore cd)
static

Definition at line 223 of file cuConsensusMaker.cpp.

References degapAlignment(), and CCdd_Base::SetSeqannot().

◆ degapCdAlignmentToPending()

void ConsensusMaker::degapCdAlignmentToPending ( CCdCore cd)
static

Definition at line 231 of file cuConsensusMaker.cpp.

References CCdCore::AddPendingSeqAlign(), and degapAlignment().

◆ getConsensus()

const string & ConsensusMaker::getConsensus ( )

Definition at line 102 of file cuConsensusMaker.cpp.

References m_consensus.

Referenced by PssmMaker::getConsensus(), and PssmMaker::makeDefaultPssm().

◆ getConsensusSeqEntry()

CRef< CSeq_entry > ConsensusMaker::getConsensusSeqEntry ( )

◆ getGuideAlignment() [1/2]

BlockModelPair & ConsensusMaker::getGuideAlignment ( )

Definition at line 128 of file cuConsensusMaker.cpp.

References ResidueProfiles::getGuideAlignment(), and m_rp.

◆ getGuideAlignment() [2/2]

const BlockModelPair & ConsensusMaker::getGuideAlignment ( ) const

Definition at line 123 of file cuConsensusMaker.cpp.

References ResidueProfiles::getGuideAlignment(), and m_rp.

Referenced by PssmMaker::getGuideAlignment().

◆ getGuideSeqAlign()

CRef< CSeq_align > ConsensusMaker::getGuideSeqAlign ( )

◆ GetInclusionRule()

double ConsensusMaker::GetInclusionRule ( ) const
inline

Definition at line 68 of file cuConsensusMaker.hpp.

◆ getResidueProfiles()

ResidueProfiles& ConsensusMaker::getResidueProfiles ( )
inline

◆ makeConsensus()

void ConsensusMaker::makeConsensus ( )

◆ remasterWithConsensus() [1/2]

CRef< CSeq_align_set > ConsensusMaker::remasterWithConsensus ( ) const

◆ remasterWithConsensus() [2/2]

void ConsensusMaker::remasterWithConsensus ( bool  extended)

◆ skipUnalignedSeg()

void ConsensusMaker::skipUnalignedSeg ( int  threshold)

Member Data Documentation

◆ m_cd

CCdCore* ConsensusMaker::m_cd
private

Definition at line 79 of file cuConsensusMaker.hpp.

Referenced by addRows(), and remasterWithConsensus().

◆ m_consensus

string ConsensusMaker::m_consensus
private

◆ m_conSeqId

CRef< CSeq_id > ConsensusMaker::m_conSeqId
private

Definition at line 82 of file cuConsensusMaker.hpp.

Referenced by addRows(), getConsensusSeqEntry(), and makeConsensus().

◆ m_inclusionRule

double ConsensusMaker::m_inclusionRule
private

Definition at line 84 of file cuConsensusMaker.hpp.

Referenced by makeConsensus().

◆ m_made

bool ConsensusMaker::m_made
private

Definition at line 83 of file cuConsensusMaker.hpp.

◆ m_masterSeqId

CRef< CSeq_id > ConsensusMaker::m_masterSeqId
private

Definition at line 81 of file cuConsensusMaker.hpp.

Referenced by addRows(), and makeConsensus().

◆ m_rp

ResidueProfiles ConsensusMaker::m_rp
private

◆ m_seqAligns

list< CRef< CSeq_align > > ConsensusMaker::m_seqAligns
private

Definition at line 80 of file cuConsensusMaker.hpp.

Referenced by addRows(), and remasterWithConsensus().


The documentation for this class was generated from the following files:
Modified on Wed Feb 21 09:54:33 2024 by modify_doxy.py rev. 669887