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NCBI C++ ToolKit: CAlignRangeCollection< TAlnRange

Search Toolkit Book for CAlignRangeCollection

class CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange. More...

#include <util/align_range_coll.hpp>

enum   EFlags {
  fKeepNormalized = 0x0001 , fAllowMixedDir = 0x0002 , fAllowOverlap = 0x0004 , fAllowAbutting = 0x0008 ,
  fIgnoreInsertions = 0x0010 , fDefaultPolicy = fKeepNormalized , fDefaultPoicy = fDefaultPolicy , fPolicyMask = 0x001f ,
  fNotValidated = 0x0100 , fInvalid = 0x0200 , fUnsorted = 0x010000 , fDirect = 0x020000 ,
  fReversed = 0x040000 , fMixedDir = fDirect | fReversed , fOverlap = 0x080000 , fAbutting = 0x100000
}   enum   ESearchDirection {
  eNone , eForward , eBackwards , eLeft ,
  eRight
}   adding empty ranges is considered valid, they are simply ignored More...
  typedef TAlnRange  TAlignRange   typedef TAlignRange::position_type  position_type   typedef CAlignRangeCollection< TAlignRange >  TThisType   typedef vector< TAlignRange >  TAlignRangeVector   typedef TAlignRangeVector::const_iterator  const_iterator   typedef TAlignRangeVector::const_reverse_iterator  const_reverse_iterator   typedef TAlignRangeVector::size_type  size_type   template<class TAlnRange>
class CAlignRangeCollection< TAlnRange >

class CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange.

The collection has two coordinate spaces: "First" - primary, usually represents alignment or consensus space, "Second" - represents a coordinate space associated with the aligned sequence. policies - do not overlap on master

Definition at line 75 of file align_range_coll.hpp.

◆ const_iterator ◆ const_reverse_iterator ◆ iterator ◆ position_type ◆ reverse_iterator ◆ size_type ◆ TAlignRange ◆ TAlignRangeVector ◆ TThisType ◆ EFlags

template<class TAlnRange >

Enumerator fKeepNormalized 

Policies:

fAllowMixedDir 

enforce all policies after any modification

if normalization is not possible exception will be thrown

fAllowOverlap 

allow segments with different orientation

fAllowAbutting 

allow segments overlapping on the first sequence

fIgnoreInsertions 

allows segments not separated by gaps

fDefaultPolicy 

do not store insertions

fDefaultPoicy  fPolicyMask 

Keep compatible with SC-8.0.

fNotValidated 

State flags:

fInvalid 

collection was modified and not validated

fUnsorted 

one or more policies violated

fDirect  fReversed 

contains at least one direct range

fMixedDir 

contains at least one reversed range

fOverlap  fAbutting 

Definition at line 86 of file align_range_coll.hpp.

◆ ESearchDirection

template<class TAlnRange >

adding empty ranges is considered valid, they are simply ignored

Enumerator eNone  eForward  eBackwards  eLeft  eRight 

Definition at line 116 of file align_range_coll.hpp.

◆ CAlignRangeCollection() [1/2] ◆ CAlignRangeCollection() [2/2] ◆ AddInsertion() ◆ AddInsertions() [1/2] ◆ AddInsertions() [2/2] ◆ Assign()

template<class TAlnRange >

◆ begin()

template<class TAlnRange >

Definition at line 146 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< CAlignRange< TSeqPos > >::erase(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find_2(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find_insertion_point(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstFrom(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstLength(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstPosBySecondPos(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetSecondPosByFirstPos(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::lower_bound(), SubtractAlnRngCollections(), CAlignRangeCollection< CAlignRange< TSeqPos > >::upper_bound(), CSparseIterator::x_InitIterator(), CAlnMixMerger::x_Merge(), CRuler::x_RenderOriginAndMetric(), and CRuler::x_UpdateMappingByPane().

◆ begin_nc()

template<class TAlnRange >

◆ clear()

template<class TAlnRange >

◆ CombineAbutting()

template<class TAlnRange >

◆ empty()

template<class TAlnRange >

◆ end()

template<class TAlnRange >

Definition at line 151 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< CAlignRange< TSeqPos > >::erase(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find_2(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find_insertion_point(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstPosBySecondPos(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetSecondPosByFirstPos(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::lower_bound(), CAlignRangeCollection< CAlignRange< TSeqPos > >::pop_back(), CAlignRangeCollection< CAlignRange< TSeqPos > >::push_back(), SubtractOnFirst(), CAlignRangeCollection< CAlignRange< TSeqPos > >::upper_bound(), and CSparseIterator::x_InitIterator().

◆ end_nc()

template<class TAlnRange >

◆ erase()

template<class TAlnRange >

◆ find() ◆ find_2()

template<class TAlnRange >

◆ find_insertion_point()

template<class TAlnRange >

◆ GetFirstFrom()

template<class TAlnRange >

◆ GetFirstLength() ◆ GetFirstPosBySecondPos()

template<class TAlnRange >

◆ GetFirstRange()

template<class TAlnRange >

◆ GetFirstTo()

template<class TAlnRange >

◆ GetFirstToOpen()

template<class TAlnRange >

◆ GetFlags()

template<class TAlnRange >

◆ GetInsertions()

template<class TAlnRange >

Each insertion shows where the 'first' sequence has a gap while the 'second' sequence has the insertion of the specified length.

Direction of the insertion is always 'direct'.

Definition at line 622 of file align_range_coll.hpp.

◆ GetPolicyFlags()

template<class TAlnRange >

◆ GetSecondPosByFirstPos()

template<class TAlnRange >

◆ GetStateFlags() ◆ insert() [1/2]

template<class TAlnRange >

Definition at line 182 of file align_range_coll.hpp.

Referenced by CreateAlignRow(), CDiagRangeCollection::Diff(), GetAlignColl(), CSparseAlignment::Init(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::push_back(), CRuler::SetRange(), SubtractOnFirst(), SubtractOnSecond(), CAlnMixMerger::x_Merge(), and CRuler::x_UpdateMappingByPane().

◆ insert() [2/2] ◆ IntersectFirst() ◆ IntersectSecond() ◆ IsSet()

template<class TAlnRange >

◆ lower_bound() ◆ Normalize()

template<class TAlnRange >

ensures that segments are sorted, if fAllowAdjust is not set - merges adjacent segments

Definition at line 557 of file align_range_coll.hpp.

◆ operator[]() [1/2] ◆ operator[]() [2/2] ◆ pop_back() ◆ push_back() ◆ rbegin()

template<class TAlnRange >

◆ rend() ◆ reserve() ◆ size()

template<class TAlnRange >

◆ Sort()

template<class TAlnRange >

◆ SortInsertions()

template<class TAlnRange >

◆ upper_bound() ◆ Validate()

template<class TAlnRange >

◆ ValidateRanges()

template<class TAlnRange >

◆ x_Equals() ◆ x_IntersectFirst()

template<class TAlnRange >

◆ x_IntersectSecond()

template<class TAlnRange >

◆ x_MultiplyCoordsBy3() ◆ x_ResetFlags()

template<class TAlnRange >

◆ x_SetFlags()

template<class TAlnRange >

◆ x_ValidateFlags()

template<class TAlnRange >

◆ m_Flags

template<class TAlnRange >

◆ m_Insertions

template<class TAlnRange >

◆ m_Ranges

template<class TAlnRange >

Definition at line 734 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< CAlignRange< TSeqPos > >::begin(), CAlignRangeCollection< CAlignRange< TSeqPos > >::begin_nc(), CAlignRangeCollection< CAlignRange< TSeqPos > >::CAlignRangeCollection(), CAlignRangeCollection< CAlignRange< TSeqPos > >::clear(), CAlignRangeCollection< CAlignRange< TSeqPos > >::CombineAbutting(), CAlignRangeCollection< CAlignRange< TSeqPos > >::empty(), CAlignRangeCollection< CAlignRange< TSeqPos > >::end(), CAlignRangeCollection< CAlignRange< TSeqPos > >::end_nc(), CAlignRangeCollection< CAlignRange< TSeqPos > >::erase(), CAlignRangeCollection< CAlignRange< TSeqPos > >::find(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstFrom(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstLength(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstTo(), CAlignRangeCollection< CAlignRange< TSeqPos > >::GetFirstToOpen(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::IntersectFirst(), CAlignRangeCollection< CAlignRange< TSeqPos > >::IntersectSecond(), CAlignRangeCollection< CAlignRange< TSeqPos > >::operator[](), CAlignRangeCollection< CAlignRange< TSeqPos > >::rbegin(), CAlignRangeCollection< CAlignRange< TSeqPos > >::rend(), CAlignRangeCollection< CAlignRange< TSeqPos > >::reserve(), CAlignRangeCollection< CAlignRange< TSeqPos > >::size(), CAlignRangeCollection< CAlignRange< TSeqPos > >::Sort(), CAlignRangeCollection< CAlignRange< TSeqPos > >::Validate(), CAlignRangeCollection< CAlignRange< TSeqPos > >::x_Equals(), and CAlignRangeCollection< CAlignRange< TSeqPos > >::x_MultiplyCoordsBy3().

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

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