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NCBI C++ ToolKit: CAlignRangeCollectionList< TAlnRange

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class CAlignRangeCollectionList<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 CAlignRangeCollectionList< TAlignRange >  TThisType   typedef list< TAlignRange >  TAlignRangeList   typedef vector< TAlignRange >  TInsertions   typedef vector< TAlignRange >  TAlignRangeVectorImpl   Use iterators on TAlignRangeList or TInsertions for insertions. More...
  typedef vector< TAlignRange >  TAlignRangeVector   typedef TAlignRangeList::iterator  TRawIterator   typedef TAlignRangeList::const_reverse_iterator  const_reverse_iterator   typedef TAlignRangeList::size_type  size_type   template<class TAlnRange>
class CAlignRangeCollectionList< TAlnRange >

class CAlignRangeCollectionList<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 752 of file align_range_coll.hpp.

◆ const_reverse_iterator ◆ position_type ◆ size_type ◆ TAlignRange ◆ TAlignRangeList ◆ TAlignRangeVector ◆ TAlignRangeVectorImpl

template<class TAlnRange >

Use iterators on TAlignRangeList or TInsertions for insertions.

Definition at line 761 of file align_range_coll.hpp.

◆ TIndexByFirst ◆ TIndexBySecond ◆ TIndexKey ◆ TInsertions ◆ TRawIterator ◆ 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 890 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 920 of file align_range_coll.hpp.

◆ CAlignRangeCollectionList() [1/3] ◆ CAlignRangeCollectionList() [2/3] ◆ CAlignRangeCollectionList() [3/3] ◆ AddInsertion()

template<class TAlnRange >

◆ AddInsertions() [1/2]

template<class TAlnRange >

◆ AddInsertions() [2/2] ◆ begin()

template<class TAlnRange >

Definition at line 960 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< TAlnRange >::Assign(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::begin(), BOOST_AUTO_TEST_CASE(), CreateAnchoredAlnVec(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstFrom(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstLength(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstPosBySecondPos(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetSecondPosByFirstPos(), InitSplicedsegFromPairwiseAln(), CPairwise_CI::operator++(), CAlnTestApp::Run(), s_TranslateAnchorToAlnCoords(), s_TranslateToAlnCoords(), CSparseAln::x_Build(), and CPairwise_CI::x_Init().

◆ begin_nc()

template<class TAlnRange >

◆ clear() ◆ CombineAbutting()

template<class TAlnRange >

◆ empty()

template<class TAlnRange >

Definition at line 985 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), CSparseAln::GetAlnSeqString(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstFrom(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstLength(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstTo(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstToOpen(), s_TranslateAnchorToAlnCoords(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort(), SubtractAlnRngCollections(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate(), CSparseAln::x_Build(), and CPairwise_CI::x_Init().

◆ end()

template<class TAlnRange >

Definition at line 965 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< TAlnRange >::Assign(), CreateAnchoredAlnVec(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::end(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_2(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_by_second(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstPosBySecondPos(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetSecondPosByFirstPos(), InitSplicedsegFromPairwiseAln(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), CPairwise_CI::operator bool(), CPairwise_CI::operator++(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::pop_back(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::push_back(), s_TranslatePairwiseToAlnCoords(), CMergedPairwiseAln::x_AddPairwise(), CSparseAln::x_Build(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindRangeContaining(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindRangesBySecondContaining(), CPairwise_CI::x_Init(), and CPairwise_CI::x_InitSegment().

◆ end_nc()

template<class TAlnRange >

◆ erase()

template<class TAlnRange >

◆ find() ◆ find_2()

template<class TAlnRange >

◆ find_2_by_second()

template<class TAlnRange >

◆ find_by_second() ◆ find_insertion_point() ◆ GetFirstFrom()

template<class TAlnRange >

◆ GetFirstLength() ◆ GetFirstPosBySecondPos()

template<class TAlnRange >

◆ GetFirstRange()

template<class TAlnRange >

◆ GetFirstTo()

template<class TAlnRange >

◆ GetFirstToOpen() ◆ GetFlags()

template<class TAlnRange >

Definition at line 1264 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< TAlnRange >::Assign(), BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), CreateSeqAlignFromEachPairwiseAln(), DumpPairwiseAln(), InitSplicedsegFromPairwiseAln(), operator<<(), s_TranslateToAlnCoords(), x_AdjustAnchorDirection(), CSparseAln::x_Build(), CPairwise_CI::x_Init(), and CSparse_CI::x_InitIterator().

◆ GetIndexByFirst()

template<class TAlnRange >

◆ GetIndexBySecond()

template<class TAlnRange >

◆ GetInsertions()

template<class TAlnRange >

◆ GetPolicyFlags()

template<class TAlnRange >

◆ GetSecondPosByFirstPos()

template<class TAlnRange >

◆ GetStateFlags() ◆ insert() [1/2]

template<class TAlnRange >

Definition at line 1033 of file align_range_coll.hpp.

Referenced by ConvertDendiagToPairwiseAln(), ConvertDensegToPairwiseAln(), ConvertPackedsegToPairwiseAln(), ConvertSeqLocsToPairwiseAln(), ConvertSparseToPairwiseAln(), ConvertSplicedToPairwiseAln(), ConvertStdsegToPairwiseAln(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), MergePairwiseAlns(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::push_back(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), SubtractOnFirst(), and SubtractOnSecond().

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

template<class TAlnRange >

◆ Normalize()

template<class TAlnRange >

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

Definition at line 1473 of file align_range_coll.hpp.

◆ operator[]()

template<class TAlnRange >

◆ pop_back() ◆ push_back()

template<class TAlnRange >

◆ rbegin()

template<class TAlnRange >

◆ rend() ◆ reserve() ◆ size()

template<class TAlnRange >

◆ Sort()

template<class TAlnRange >

◆ SortInsertions()

template<class TAlnRange >

◆ Validate()

template<class TAlnRange >

◆ ValidateRanges()

template<class TAlnRange >

◆ x_Equals() ◆ x_Erase()

template<class TAlnRange >

◆ x_FindInsertionPlace()

template<class TAlnRange >

◆ x_FindRangeContaining()

template<class TAlnRange >

◆ x_FindRangesBySecondContaining()

template<class TAlnRange >

◆ x_GetAlignRangeVector()

template<class TAlnRange >

◆ x_Index()

template<class TAlnRange >

◆ x_IndexAll()

template<class TAlnRange >

◆ x_Insert()

template<class TAlnRange >

◆ x_IntersectFirst()

template<class TAlnRange >

template<class TRanges >

◆ x_IntersectSecond()

template<class TAlnRange >

template<class TRanges >

◆ x_MultiplyCoordsBy3() ◆ x_ResetFlags()

template<class TAlnRange >

◆ x_SetFlags()

template<class TAlnRange >

◆ x_Unindex()

template<class TAlnRange >

◆ x_UnindexAll()

template<class TAlnRange >

◆ x_UnindexByFirst()

template<class TAlnRange >

◆ x_UnindexBySecond()

template<class TAlnRange >

◆ x_ValidateFlags()

template<class TAlnRange >

◆ m_Flags

template<class TAlnRange >

◆ m_IndexByFirst

template<class TAlnRange >

◆ m_IndexBySecond

template<class TAlnRange >

◆ m_Insertions

template<class TAlnRange >

◆ m_RangesList

template<class TAlnRange >

Definition at line 1794 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::begin(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::begin_nc(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CAlignRangeCollectionList(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::clear(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::empty(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::end(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::end_nc(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectFirst(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectSecond(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::rbegin(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::rend(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::reserve(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::size(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Equals(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_GetAlignRangeVector(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_IndexAll(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Insert(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_MultiplyCoordsBy3().

◆ m_RangesVector

template<class TAlnRange >

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

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