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NCBI C++ ToolKit: BlockModel Class Reference

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

  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  

Definition at line 67 of file cuBlock.hpp.

◆ BlockModel() [1/4] BlockModel::BlockModel ( ) ◆ BlockModel() [2/4] ◆ BlockModel() [3/4] ◆ BlockModel() [4/4] ◆ addBlock() void BlockModel::addBlock ( Block &  block ) ◆ addOffset() void BlockModel::addOffset ( int  nExt ) ◆ blockMatch() ◆ clipToRange() void BlockModel::clipToRange ( unsigned int  min, unsigned  max  ) ◆ completeCastTo() ◆ completeModelExtendsIntoUnallowedGappedRegion() bool BlockModel::completeModelExtendsIntoUnallowedGappedRegion ( const BlockModel &  completeModel, int  sequenceLength, const vector< int > *  commonBlockExt = NULL  ) const ◆ contain() ◆ findIntersectingBlocks() void BlockModel::findIntersectingBlocks ( const Block &  target, vector< int > &  result  ) const ◆ getBlock() ◆ getBlockNumber() int BlockModel::getBlockNumber ( int  pos ) const ◆ 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 ◆ getFirstAlignedPosition() int BlockModel::getFirstAlignedPosition ( ) const ◆ getGapToCTerminal() int BlockModel::getGapToCTerminal ( int  bn, int  len = -1  ) const ◆ getGapToNTerminal() int BlockModel::getGapToNTerminal ( int  bn ) const ◆ getLastAlignedPosition() int BlockModel::getLastAlignedPosition ( ) const ◆ getSeqId() ◆ getTotalBlockLength() int BlockModel::getTotalBlockLength ( ) const ◆ intersect() ◆ intersectOneBlock() ◆ isAlike() ◆ isValid() bool BlockModel::isValid ( int  seqLen, int &  errBlock  ) const ◆ mask() [1/2] ◆ mask() [2/2]

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() ◆ operator+() ◆ operator-() ◆ operator=() ◆ operator==() ◆ overlap() ◆ setSeqId() ◆ toSeqAlign()

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 ◆ toString() [2/2] ◆ 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

The documentation for this class was generated from the following files:

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