ConsensusMaker Class Reference

Search Toolkit Book for ConsensusMaker

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

Collaboration diagram for ConsensusMaker:

Public Member Functions
	ConsensusMaker (CCdCore *cd, double incl=0.5)
	~ConsensusMaker ()
void	makeConsensus ()
ResidueProfiles &	getResidueProfiles ()
const string &	getConsensus ()
CRef< CSeq_entry >	getConsensusSeqEntry ()
const BlockModelPair &	getGuideAlignment () const
BlockModelPair &	getGuideAlignment ()
CRef< CSeq_align >	getGuideSeqAlign ()
CRef< CSeq_align_set >	remasterWithConsensus () const
void	remasterWithConsensus (bool extended)
void	skipUnalignedSeg (int threshold)
double	GetInclusionRule () const

Static Public Member Functions
static CRef< CSeq_align_set >	degapAlignment (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
CCdCore *	m_cd
list< CRef< CSeq_align > >	m_seqAligns
CRef< CSeq_id >	m_masterSeqId
CRef< CSeq_id >	m_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

Definition at line 57 of file cuConsensusMaker.cpp.

References ResidueProfiles::addOneRow(), CSeq_id_Base::e_Local, CCdCore::FindConsensusInSequenceList(), BlockModelPair::getMaster(), BlockModel::getSeqId(), CCdCore::GetSeqIndex(), CCdCore::GetSequenceStringByIndex(), BlockModelPair::getSlave(), IsConsensus(), m_cd, m_conSeqId, m_masterSeqId, m_rp, and m_seqAligns.

degapAlignment() [1/2]

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

static

Definition at line 203 of file cuConsensusMaker.cpp.

References CSeq_align_set_Base::Set().

Referenced by degapCdAlignment(), degapCdAlignmentToPending(), and remasterWithConsensus().

degapAlignment() [2/2]

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

static

Definition at line 211 of file cuConsensusMaker.cpp.

References BlockModelPair::degap(), CCdCore::GetNumRows(), CCdCore::GetSeqAlign(), i, and BlockModelPair::toSeqAlign().

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

(

)

Definition at line 107 of file cuConsensusMaker.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, m_consensus, m_conSeqId, result, CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetMol(), CSeq_data_Base::SetNcbieaa(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by PssmMaker::make(), and remasterWithConsensus().

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

(

)

Definition at line 133 of file cuConsensusMaker.cpp.

References ResidueProfiles::getGuideAlignment(), m_rp, and BlockModelPair::toSeqAlign().

GetInclusionRule()

double ConsensusMaker::GetInclusionRule ( ) const

inline

Definition at line 68 of file cuConsensusMaker.hpp.

getResidueProfiles()

ResidueProfiles& ConsensusMaker::getResidueProfiles ( )

inline

Definition at line 56 of file cuConsensusMaker.hpp.

Referenced by PssmMaker::make(), PssmMaker::printAlignment(), and PssmMaker::printAlignmentByColumn().

makeConsensus()

void ConsensusMaker::makeConsensus

(

)

Definition at line 92 of file cuConsensusMaker.cpp.

References ResidueProfiles::calculateRowWeights(), ResidueProfiles::getGuideAlignment(), BlockModelPair::getMaster(), BlockModelPair::getSlave(), m_consensus, m_conSeqId, m_inclusionRule, m_masterSeqId, m_rp, ResidueProfiles::makeConsensus(), ResidueProfiles::setInclusionThreshold(), and BlockModel::setSeqId().

remasterWithConsensus() [1/2]

CRef< CSeq_align_set > ConsensusMaker::remasterWithConsensus

(

)

const

Definition at line 148 of file cuConsensusMaker.cpp.

References bmp, ResidueProfiles::getGuideAlignment(), BlockModelPair::getMaster(), BlockModelPair::getSlave(), m_rp, m_seqAligns, BlockModelPair::remaster(), result, and BlockModelPair::toSeqAlign().

remasterWithConsensus() [2/2]

void ConsensusMaker::remasterWithConsensus

(

bool

extended

)

Definition at line 170 of file cuConsensusMaker.cpp.

References CCdCore::AddSequence(), bmp, BlockModelPair::degap(), degapAlignment(), getConsensusSeqEntry(), ResidueProfiles::getGuideAlignment(), BlockModelPair::getMaster(), BlockModelPair::getSlave(), m_cd, m_rp, BlockModelPair::remaster(), CCdd_Base::SetSeqannot(), BlockModelPair::toSeqAlign(), and CCdCore::UsesConsensusSequenceAsMaster().

skipUnalignedSeg()

void ConsensusMaker::skipUnalignedSeg

(

int

threshold

)

Definition at line 139 of file cuConsensusMaker.cpp.

References ResidueProfiles::adjustConsensusAndGuide(), ResidueProfiles::countUnalignedConsensus(), ResidueProfiles::getConsensus(), m_consensus, m_rp, and ResidueProfiles::skipUnalignedSeg().

Referenced by PssmMaker::make().

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

Definition at line 78 of file cuConsensusMaker.hpp.

Referenced by getConsensus(), getConsensusSeqEntry(), makeConsensus(), and skipUnalignedSeg().

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

Definition at line 85 of file cuConsensusMaker.hpp.

Referenced by addRows(), getGuideAlignment(), getGuideSeqAlign(), makeConsensus(), remasterWithConsensus(), and skipUnalignedSeg().

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:

• include/algo/structure/cd_utils/cuConsensusMaker.hpp
• src/algo/structure/cd_utils/cuConsensusMaker.cpp