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BlockModel Class Reference

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

+ Collaboration diagram for BlockModel:

Public Member Functions

 BlockModel ()
 
 BlockModel (const CRef< CSeq_align > seqAlign, bool forSlave=true)
 
 BlockModel (CRef< CSeq_id > sedId, bool withOneBlock=true)
 
 BlockModel (const BlockModel &rhs)
 
void addBlock (Block &block)
 
bool isAlike (const BlockModel &rhs) const
 
bool operator== (const BlockModel &rhs) const
 
bool contain (const BlockModel &rhs) const
 
pair< DeltaBlockModel *, bool > operator- (const BlockModel &bm) const
 
pair< DeltaBlockModel *, bool > intersect (const BlockModel &bm) const
 
pair< BlockModel *, bool > operator+ (const DeltaBlockModel &delta) const
 
BlockModel & operator= (const BlockModel &rhs)
 
BlockModel * completeCastTo (const BlockModel &target) const
 
void findIntersectingBlocks (const Block &target, vector< int > &result) const
 
vector< Block > & getBlocks ()
 
Block & getBlock (int bn)
 
int getBlockNumber (int pos) const
 
const vector< Block > & getBlocks () const
 
CRef< CSeq_id > getSeqId () const
 
void setSeqId (CRef< CSeq_id > seqId)
 
CRef< CSeq_align > toSeqAlign (const BlockModel &master) const
 
bool blockMatch (const BlockModel &bm) const
 
bool completeModelExtendsIntoUnallowedGappedRegion (const BlockModel &completeModel, int sequenceLength, const vector< int > *commonBlockExt=NULL) const
 
int getLastAlignedPosition () const
 
int getFirstAlignedPosition () const
 
int getTotalBlockLength () const
 
int getGapToNTerminal (int bn) const
 
int getGapToCTerminal (int bn, int len=-1) const
 
bool isValid (int seqLen, int &errBlock) const
 
bool overlap (const BlockModel &bm) const
 
void addOffset (int nExt)
 
bool mask (const BlockModel &maskBlockModel)
 
bool mask (const vector< Block > &maskBlocks)
 
void clipToRange (unsigned int min, unsigned max)
 
string toString () const
 

Static Public Member Functions

static string toString (const BlockModel &bm)
 

Private Member Functions

bool intersectOneBlock (const Block &aBlock, DeltaBlockModel &delta) const
 
bool minusOneBlock (const Block &aBlock, DeltaBlockModel &delta) const
 

Private Attributes

vector< Block > m_blocks
 
CRef< CSeq_id > m_seqId
 

Detailed Description

Definition at line 67 of file cuBlock.hpp.

Constructor & Destructor Documentation

◆ BlockModel() [1/4]

BlockModel::BlockModel ( )

Definition at line 191 of file cuBlock.cpp.

Referenced by operator+().

◆ BlockModel() [2/4]

BlockModel::BlockModel ( const CRef< CSeq_align >  seqAlign,
bool  forSlave = true 
)

Definition at line 196 of file cuBlock.cpp.

References assert, GetBlockLengths(), GetBlockStarts(), GetSeqID(), i, m_blocks, and m_seqId.

◆ BlockModel() [3/4]

BlockModel::BlockModel ( CRef< CSeq_id >  sedId,
bool  withOneBlock = true 
)

Definition at line 210 of file cuBlock.cpp.

References m_blocks.

◆ BlockModel() [4/4]

BlockModel::BlockModel ( const BlockModel &  rhs)

Definition at line 220 of file cuBlock.cpp.

Member Function Documentation

◆ addBlock()

void BlockModel::addBlock ( Block &  block)

Definition at line 225 of file cuBlock.cpp.

References m_blocks, and Block::setId().

Referenced by IntersectByMaster().

◆ addOffset()

void BlockModel::addOffset ( int  nExt)

Definition at line 649 of file cuBlock.cpp.

References i, and m_blocks.

◆ blockMatch()

bool BlockModel::blockMatch ( const BlockModel &  bm) const

Definition at line 259 of file cuBlock.cpp.

References i, and m_blocks.

Referenced by BlockModelPair::degap(), MultipleAlignment::extractAlignedSubset(), MultipleAlignment::isBlockAligned(), BlockModelPair::isValid(), and toSeqAlign().

◆ clipToRange()

void BlockModel::clipToRange ( unsigned int  min,
unsigned  max 
)

Definition at line 808 of file cuBlock.cpp.

References getBlocks(), mask(), max(), and min().

◆ completeCastTo()

BlockModel * BlockModel::completeCastTo ( const BlockModel &  target) const

Definition at line 469 of file cuBlock.cpp.

References contain().

Referenced by MultipleAlignment::locateChildRow().

◆ completeModelExtendsIntoUnallowedGappedRegion()

bool BlockModel::completeModelExtendsIntoUnallowedGappedRegion ( const BlockModel &  completeModel,
int  sequenceLength,
const vector< int > *  commonBlockExt = NULL 
) const

Definition at line 271 of file cuBlock.cpp.

References getBlock(), getBlockNumber(), getBlocks(), getGapToCTerminal(), Block::getLen(), Block::getStart(), i, and m_blocks.

◆ contain()

bool BlockModel::contain ( const BlockModel &  rhs) const

Definition at line 398 of file cuBlock.cpp.

References i, isAlike(), and m_blocks.

Referenced by completeCastTo(), and MultipleAlignment::findParentalEquivalent().

◆ findIntersectingBlocks()

void BlockModel::findIntersectingBlocks ( const Block &  target,
vector< int > &  result 
) const

Definition at line 524 of file cuBlock.cpp.

References i, Block::isIntersecting(), m_blocks, and result.

Referenced by intersectOneBlock(), and minusOneBlock().

◆ getBlock()

Block& BlockModel::getBlock ( int  bn)
inline

Definition at line 98 of file cuBlock.hpp.

References m_blocks.

Referenced by completeModelExtendsIntoUnallowedGappedRegion(), BlockModelPair::extendMidway(), IntersectByMaster(), BlockModelPair::mapToMaster(), and BlockModelPair::mapToSlave().

◆ getBlockNumber()

int BlockModel::getBlockNumber ( int  pos) const

Definition at line 703 of file cuBlock.cpp.

References i, int, and m_blocks.

Referenced by completeModelExtendsIntoUnallowedGappedRegion(), BlockModelPair::mapToMaster(), and BlockModelPair::mapToSlave().

◆ getBlocks() [1/2]

vector<Block>& BlockModel::getBlocks ( )
inline

Definition at line 97 of file cuBlock.hpp.

References m_blocks.

Referenced by ResidueProfiles::adjustConsensusAndGuide(), clipToRange(), completeModelExtendsIntoUnallowedGappedRegion(), BlockModelPair::degap(), BlockModelPair::extendMidway(), BlockExtender::extendOnePair(), BlockExtender::findCommonExtension(), IntersectByMaster(), CDUpdater::isFragmentedSeq(), ResidueProfiles::makeConsensus(), mask(), BlockModelPair::mask(), BlockExtender::optimizeBlockScore(), and PssmScorer::score().

◆ getBlocks() [2/2]

const vector<Block>& BlockModel::getBlocks ( ) const
inline

Definition at line 101 of file cuBlock.hpp.

References m_blocks.

◆ getFirstAlignedPosition()

int BlockModel::getFirstAlignedPosition ( ) const

Definition at line 602 of file cuBlock.cpp.

References Block::getStart(), and m_blocks.

Referenced by overlap().

◆ getGapToCTerminal()

int BlockModel::getGapToCTerminal ( int  bn,
int  len = -1 
) const

Definition at line 632 of file cuBlock.cpp.

References delta(), len, and m_blocks.

Referenced by completeModelExtendsIntoUnallowedGappedRegion(), BlockModelPair::extendMidway(), IntersectByMaster(), and CDUpdater::isFragmentedSeq().

◆ getGapToNTerminal()

int BlockModel::getGapToNTerminal ( int  bn) const

Definition at line 618 of file cuBlock.cpp.

References delta(), and m_blocks.

Referenced by BlockModelPair::extendMidway(), and CDUpdater::isFragmentedSeq().

◆ getLastAlignedPosition()

int BlockModel::getLastAlignedPosition ( ) const

Definition at line 596 of file cuBlock.cpp.

References Block::getEnd(), and m_blocks.

Referenced by isValid(), overlap(), and PssmScorer::score().

◆ getSeqId()

CRef< CSeq_id > BlockModel::getSeqId ( ) const
inline

Definition at line 102 of file cuBlock.hpp.

References m_seqId.

Referenced by ConsensusMaker::addRows(), MultipleAlignment::locateChildRow(), mask(), BlockModelPair::remaster(), remasterAlignannot(), and toSeqAlign().

◆ getTotalBlockLength()

int BlockModel::getTotalBlockLength ( ) const

Definition at line 608 of file cuBlock.cpp.

References i, len, and m_blocks.

Referenced by BlockExtender::findCommonExtension(), BlockFormater::findIntersectingBlocks(), BlockFormater::getOverlappingPercentages(), IntersectByMaster(), mask(), and BlockModelPair::remaster().

◆ intersect()

pair< DeltaBlockModel *, bool > BlockModel::intersect ( const BlockModel &  bm) const

Definition at line 431 of file cuBlock.cpp.

References delta(), i, intersectOneBlock(), and m_blocks.

Referenced by intersectOneBlock(), and BlockModelPair::remaster().

◆ intersectOneBlock()

bool BlockModel::intersectOneBlock ( const Block &  aBlock,
DeltaBlockModel &  delta 
) const
private

Definition at line 508 of file cuBlock.cpp.

References delta(), findIntersectingBlocks(), intersect(), and m_blocks.

Referenced by intersect().

◆ isAlike()

bool BlockModel::isAlike ( const BlockModel &  rhs) const

Definition at line 238 of file cuBlock.cpp.

References m_blocks, m_seqId, and SeqIdsMatch().

Referenced by contain(), and operator==().

◆ isValid()

bool BlockModel::isValid ( int  seqLen,
int &  errBlock 
) const

Definition at line 657 of file cuBlock.cpp.

References getLastAlignedPosition(), i, int, and m_blocks.

Referenced by toSeqAlign().

◆ mask() [1/2]

bool BlockModel::mask ( const BlockModel &  maskBlockModel)

Definition at line 717 of file cuBlock.cpp.

References getBlocks(), getSeqId(), result, and SeqIdsMatch().

Referenced by clipToRange(), and BlockModelPair::mask().

◆ mask() [2/2]

bool BlockModel::mask ( const vector< Block > &  maskBlocks)

Definition at line 727 of file cuBlock.cpp.

References _ASSERT, set< Key, Compare >::end(), set< Key, Compare >::find(), getBlocks(), getTotalBlockLength(), i, set< Key, Compare >::insert(), and len.

◆ minusOneBlock()

bool BlockModel::minusOneBlock ( const Block &  aBlock,
DeltaBlockModel &  delta 
) const
private

Definition at line 493 of file cuBlock.cpp.

References delta(), findIntersectingBlocks(), and m_blocks.

Referenced by operator-().

◆ operator+()

pair< BlockModel *, bool > BlockModel::operator+ ( const DeltaBlockModel &  delta) const

Definition at line 444 of file cuBlock.cpp.

References BlockModel(), delta(), Block::getLen(), Block::getStart(), m_blocks, m_seqId, and result.

◆ operator-()

pair< DeltaBlockModel *, bool > BlockModel::operator- ( const BlockModel &  bm) const

Definition at line 413 of file cuBlock.cpp.

References set< Key, Compare >::begin(), delta(), set< Key, Compare >::end(), i, set< Key, Compare >::insert(), m_blocks, and minusOneBlock().

◆ operator=()

BlockModel & BlockModel::operator= ( const BlockModel &  rhs)

Definition at line 231 of file cuBlock.cpp.

References m_blocks, and m_seqId.

◆ operator==()

bool BlockModel::operator== ( const BlockModel &  rhs) const

Definition at line 247 of file cuBlock.cpp.

References i, isAlike(), and m_blocks.

◆ overlap()

bool BlockModel::overlap ( const BlockModel &  bm) const

Definition at line 688 of file cuBlock.cpp.

References getFirstAlignedPosition(), getLastAlignedPosition(), m_seqId, and SeqIdsMatch().

◆ setSeqId()

void BlockModel::setSeqId ( CRef< CSeq_id >  seqId)
inline

Definition at line 103 of file cuBlock.hpp.

References m_seqId.

Referenced by ConsensusMaker::makeConsensus().

◆ toSeqAlign()

CRef< CSeq_align > BlockModel::toSeqAlign ( const BlockModel &  master) const

Definition at line 557 of file cuBlock.cpp.

References CSeq_id::Assign(), blockMatch(), CSeq_align_Base::eType_partial, getSeqId(), i, isValid(), m_blocks, CSeq_align_Base::Reset(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

Referenced by MultipleAlignment::extractAlignedSubset(), IntersectByMaster(), and BlockModelPair::toSeqAlign().

◆ toString() [1/2]

string BlockModel::toString ( ) const

Definition at line 830 of file cuBlock.cpp.

References GetSeqIDStr(), i, NStr::IntToString(), m_blocks, m_seqId, CRef< C, Locker >::NotEmpty(), and tmp.

◆ toString() [2/2]

string BlockModel::toString ( const BlockModel &  bm)
static

Definition at line 865 of file cuBlock.cpp.

Member Data Documentation

◆ m_blocks

vector<Block> BlockModel::m_blocks
private

Definition at line 137 of file cuBlock.hpp.

Referenced by addBlock(), addOffset(), blockMatch(), BlockModel(), completeModelExtendsIntoUnallowedGappedRegion(), contain(), findIntersectingBlocks(), getBlock(), getBlockNumber(), getBlocks(), getFirstAlignedPosition(), getGapToCTerminal(), getGapToNTerminal(), getLastAlignedPosition(), getTotalBlockLength(), intersect(), intersectOneBlock(), isAlike(), isValid(), minusOneBlock(), operator+(), operator-(), operator=(), operator==(), toSeqAlign(), and toString().

◆ m_seqId

CRef< CSeq_id > BlockModel::m_seqId
private

Definition at line 138 of file cuBlock.hpp.

Referenced by BlockModel(), getSeqId(), isAlike(), operator+(), operator=(), overlap(), setSeqId(), and toString().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:57:44 2024 by modify_doxy.py rev. 669887