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CAlignRangeCollectionList< TAlnRange > Class Template Reference

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

#include <util/align_range_coll.hpp>

+ Inheritance diagram for CAlignRangeCollectionList< TAlnRange >:
+ Collaboration diagram for CAlignRangeCollectionList< TAlnRange >:

Classes

class  const_iterator
 
class  iterator
 
struct  PIndexByFirstLess
 
struct  PIndexBySecondLess
 

Public Types

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
 

Public Member Functions

 CAlignRangeCollectionList (int flags=fDefaultPolicy)
 
 CAlignRangeCollectionList (const TAlignRangeVectorImpl &v, int flags)
 
 CAlignRangeCollectionList (const TAlignRangeList &v, int flags)
 
position_type GetFirstFrom () const
 
position_type GetFirstToOpen () const
 
position_type GetFirstTo () const
 
position_type GetFirstLength (void) const
 
CRange< position_type > GetFirstRange () const
 
int GetFlags () const
 
bool IsSet (int flags) const
 
int GetPolicyFlags () const
 
int GetStateFlags () const
 
TSignedSeqPos GetSecondPosByFirstPos (position_type pos, ESearchDirection dir=eNone) const
 
TSignedSeqPos GetFirstPosBySecondPos (position_type pos, ESearchDirection dir=eNone) const
 
void Sort ()
 
void SortInsertions (void)
 
void CombineAbutting ()
 merge adjacent segments together, merging changes collection size and invalidates iterators More...
 
void Validate ()
 analyses segements and updates flags More...
 
void Normalize ()
 ensures that segments are sorted, if fAllowAdjust is not set - merges adjacent segments More...
 
void AddInsertion (const TAlignRange &r)
 
void AddInsertions (const TInsertions &insertions)
 
void AddInsertions (const TThisType &collection)
 
const TInsertions & GetInsertions () const
 Each insertion shows where the 'first' sequence has a gap while the 'second' sequence has the insertion of the specified length. More...
 
void IntersectFirst (const CRange< position_type > &range)
 
void IntersectSecond (const CRange< position_type > &range)
 

Static Public Member Functions

static int ValidateRanges (const TAlignRange &r_1, const TAlignRange &r_2)
 determine conflicts between two ranges More...
 

Protected Member Functions

void x_SetFlags (int flags)
 
void x_ResetFlags (int flags)
 
void x_ValidateFlags ()
 
iterator begin_nc ()
 
iterator end_nc ()
 
bool x_Equals (const TThisType &c) const
 
TAlignRangeVectorImpl & x_GetAlignRangeVector () const
 
void x_Index (TIndexKey iter)
 
void x_UnindexByFirst (TIndexKey iter)
 
void x_UnindexBySecond (TIndexKey iter)
 
void x_Unindex (TIndexKey iter)
 
void x_IndexAll ()
 
void x_UnindexAll ()
 
TRawIterator x_Insert (TRawIterator where, const TAlignRange &r)
 
void x_Erase (TRawIterator iter)
 
const_iterator x_FindRangeContaining (position_type pos) const
 
pair< pair< const_iterator, const_iterator >, bool > x_FindRangesBySecondContaining (position_type pos) const
 
iterator x_FindInsertionPlace (const TAlignRange &r)
 
void x_MultiplyCoordsBy3 ()
 
template<class TRanges >
void x_IntersectFirst (TRanges &ranges, const CRange< position_type > &range)
 
template<class TRanges >
void x_IntersectSecond (TRanges &ranges, const CRange< position_type > &range)
 

Protected Attributes

TAlignRangeVectorImpl m_RangesVector
 
TAlignRangeList m_RangesList
 
TInsertions m_Insertions
 
int m_Flags
 
TIndexByFirst m_IndexByFirst
 combination of EFlags More...
 
TIndexBySecond m_IndexBySecond
 

Container Interface

immitating vector, but providing only "const" access to elements

typedef TRawIterator TIndexKey
 
typedef multiset< TIndexKey, PIndexByFirstLess > TIndexByFirst
 
typedef multiset< TIndexKey, PIndexBySecondLess > TIndexBySecond
 
void reserve (int count)
 
const_iterator begin () const
 
const_iterator end () const
 
const_reverse_iterator rbegin () const
 
const_reverse_iterator rend () const
 
size_type size () const
 
bool empty () const
 
const TIndexByFirst & GetIndexByFirst () const
 
const TIndexBySecond & GetIndexBySecond () const
 
const_iterator insert (const TAlignRange &r)
 
const_iterator insert (const_iterator it, const TAlignRange &arg_r)
 
const_iterator erase (const_iterator it_del)
 
void push_back (const TAlignRange &r)
 
void pop_back ()
 
const TAlignRange & operator[] (size_type pos) const
 Use iterator access. More...
 
void clear ()
 
const_iterator find (position_type pos) const
 
pair< const_iterator, bool > find_2 (position_type pos) const
 returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator points to a first range that has ToOpen > pos; the bool element of pair specifies whether the range contains the position. More...
 
const_iterator find_by_second (position_type pos) const
 
pair< pair< const_iterator, const_iterator >, bool > find_2_by_second (position_type pos) const
 returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator points to a first range that has ToOpen > pos; the bool element of pair specifies whether the range contains the position. More...
 
const_iterator find_insertion_point (const TAlignRange &range) const
 

Detailed Description

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.

Member Typedef Documentation

◆ const_reverse_iterator

template<class TAlnRange >
typedef TAlignRangeList::const_reverse_iterator CAlignRangeCollectionList< TAlnRange >::const_reverse_iterator

Definition at line 887 of file align_range_coll.hpp.

◆ position_type

template<class TAlnRange >
typedef TAlignRange::position_type CAlignRangeCollectionList< TAlnRange >::position_type

Definition at line 756 of file align_range_coll.hpp.

◆ size_type

template<class TAlnRange >
typedef TAlignRangeList::size_type CAlignRangeCollectionList< TAlnRange >::size_type

Definition at line 888 of file align_range_coll.hpp.

◆ TAlignRange

template<class TAlnRange >
typedef TAlnRange CAlignRangeCollectionList< TAlnRange >::TAlignRange

Definition at line 755 of file align_range_coll.hpp.

◆ TAlignRangeList

template<class TAlnRange >
typedef list<TAlignRange> CAlignRangeCollectionList< TAlnRange >::TAlignRangeList

Definition at line 758 of file align_range_coll.hpp.

◆ TAlignRangeVector

template<class TAlnRange >
typedef vector<TAlignRange> CAlignRangeCollectionList< TAlnRange >::TAlignRangeVector

Definition at line 762 of file align_range_coll.hpp.

◆ TAlignRangeVectorImpl

template<class TAlnRange >
typedef vector<TAlignRange> CAlignRangeCollectionList< TAlnRange >::TAlignRangeVectorImpl

Use iterators on TAlignRangeList or TInsertions for insertions.

Definition at line 761 of file align_range_coll.hpp.

◆ TIndexByFirst

template<class TAlnRange >
typedef multiset<TIndexKey, PIndexByFirstLess> CAlignRangeCollectionList< TAlnRange >::TIndexByFirst

Definition at line 1021 of file align_range_coll.hpp.

◆ TIndexBySecond

template<class TAlnRange >
typedef multiset<TIndexKey, PIndexBySecondLess> CAlignRangeCollectionList< TAlnRange >::TIndexBySecond

Definition at line 1022 of file align_range_coll.hpp.

◆ TIndexKey

template<class TAlnRange >
typedef TRawIterator CAlignRangeCollectionList< TAlnRange >::TIndexKey

Definition at line 990 of file align_range_coll.hpp.

◆ TInsertions

template<class TAlnRange >
typedef vector<TAlignRange> CAlignRangeCollectionList< TAlnRange >::TInsertions

Definition at line 759 of file align_range_coll.hpp.

◆ TRawIterator

template<class TAlnRange >
typedef TAlignRangeList::iterator CAlignRangeCollectionList< TAlnRange >::TRawIterator

Definition at line 764 of file align_range_coll.hpp.

◆ TThisType

template<class TAlnRange >
typedef CAlignRangeCollectionList<TAlignRange> CAlignRangeCollectionList< TAlnRange >::TThisType

Definition at line 757 of file align_range_coll.hpp.

Member Enumeration Documentation

◆ EFlags

template<class TAlnRange >
enum CAlignRangeCollectionList::EFlags
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 >
enum CAlignRangeCollectionList::ESearchDirection

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.

Constructor & Destructor Documentation

◆ CAlignRangeCollectionList() [1/3]

template<class TAlnRange >
CAlignRangeCollectionList< TAlnRange >::CAlignRangeCollectionList ( int  flags = fDefaultPolicy)
inline

Definition at line 928 of file align_range_coll.hpp.

◆ CAlignRangeCollectionList() [2/3]

template<class TAlnRange >
CAlignRangeCollectionList< TAlnRange >::CAlignRangeCollectionList ( const TAlignRangeVectorImpl &  v,
int  flags 
)
inline

Definition at line 933 of file align_range_coll.hpp.

◆ CAlignRangeCollectionList() [3/3]

template<class TAlnRange >
CAlignRangeCollectionList< TAlnRange >::CAlignRangeCollectionList ( const TAlignRangeList &  v,
int  flags 
)
inline

Definition at line 941 of file align_range_coll.hpp.

Member Function Documentation

◆ AddInsertion()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::AddInsertion ( const TAlignRange &  r)
inline

Definition at line 1505 of file align_range_coll.hpp.

Referenced by ConvertDensegToPairwiseAln(), ConvertPackedsegToPairwiseAln(), ConvertSplicedToPairwiseAln(), ConvertStdsegToPairwiseAln(), and s_TranslatePairwiseToAlnCoords().

◆ AddInsertions() [1/2]

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::AddInsertions ( const TInsertions &  insertions)
inline

Definition at line 1513 of file align_range_coll.hpp.

Referenced by MergePairwiseAlns().

◆ AddInsertions() [2/2]

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::AddInsertions ( const TThisType &  collection)
inline

Definition at line 1524 of file align_range_coll.hpp.

◆ begin()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::begin ( void  ) const
inline

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 >
iterator CAlignRangeCollectionList< TAlnRange >::begin_nc ( )
inlineprotected

Definition at line 1583 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert().

◆ clear()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::clear ( void  )
inline

Definition at line 1148 of file align_range_coll.hpp.

◆ CombineAbutting()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::CombineAbutting ( )
inline

merge adjacent segments together, merging changes collection size and invalidates iterators

Definition at line 1423 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Normalize().

◆ empty()

template<class TAlnRange >
bool CAlignRangeCollectionList< TAlnRange >::empty ( void  ) const
inline

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 >
const_iterator CAlignRangeCollectionList< TAlnRange >::end ( void  ) const
inline

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 >
iterator CAlignRangeCollectionList< TAlnRange >::end_nc ( )
inlineprotected

Definition at line 1587 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindInsertionPlace().

◆ erase()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::erase ( const_iterator  it_del)
inline

Definition at line 1104 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::pop_back().

◆ find()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::find ( position_type  pos) const
inline

Definition at line 1160 of file align_range_coll.hpp.

◆ find_2()

template<class TAlnRange >
pair<const_iterator, bool> CAlignRangeCollectionList< TAlnRange >::find_2 ( position_type  pos) const
inline

returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator points to a first range that has ToOpen > pos; the bool element of pair specifies whether the range contains the position.

Definition at line 1170 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetSecondPosByFirstPos(), and CPairwise_CI::x_Init().

◆ find_2_by_second()

template<class TAlnRange >
pair<pair<const_iterator, const_iterator>, bool> CAlignRangeCollectionList< TAlnRange >::find_2_by_second ( position_type  pos) const
inline

returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator points to a first range that has ToOpen > pos; the bool element of pair specifies whether the range contains the position.

Definition at line 1190 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstPosBySecondPos().

◆ find_by_second()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::find_by_second ( position_type  pos) const
inline

Definition at line 1180 of file align_range_coll.hpp.

◆ find_insertion_point()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::find_insertion_point ( const TAlignRange &  range) const
inline

Definition at line 1197 of file align_range_coll.hpp.

◆ GetFirstFrom()

template<class TAlnRange >
position_type CAlignRangeCollectionList< TAlnRange >::GetFirstFrom ( void  ) const
inline

Definition at line 1218 of file align_range_coll.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), DumpPairwiseAln(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstRange().

◆ GetFirstLength()

template<class TAlnRange >
position_type CAlignRangeCollectionList< TAlnRange >::GetFirstLength ( void  ) const
inline

Definition at line 1248 of file align_range_coll.hpp.

◆ GetFirstPosBySecondPos()

template<class TAlnRange >
TSignedSeqPos CAlignRangeCollectionList< TAlnRange >::GetFirstPosBySecondPos ( position_type  pos,
ESearchDirection  dir = eNone 
) const
inline

Definition at line 1305 of file align_range_coll.hpp.

Referenced by s_TranslatePairwiseToAlnCoords().

◆ GetFirstRange()

template<class TAlnRange >
CRange<position_type> CAlignRangeCollectionList< TAlnRange >::GetFirstRange ( ) const
inline

Definition at line 1259 of file align_range_coll.hpp.

Referenced by DumpPairwiseAln().

◆ GetFirstTo()

template<class TAlnRange >
position_type CAlignRangeCollectionList< TAlnRange >::GetFirstTo ( void  ) const
inline

Definition at line 1238 of file align_range_coll.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstRange().

◆ GetFirstToOpen()

template<class TAlnRange >
position_type CAlignRangeCollectionList< TAlnRange >::GetFirstToOpen ( void  ) const
inline

Definition at line 1228 of file align_range_coll.hpp.

◆ GetFlags()

template<class TAlnRange >
int CAlignRangeCollectionList< TAlnRange >::GetFlags ( void  ) const
inline

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 >
const TIndexByFirst& CAlignRangeCollectionList< TAlnRange >::GetIndexByFirst ( ) const
inline

Definition at line 1024 of file align_range_coll.hpp.

Referenced by SubtractAlnRngCollections(), and SubtractOnFirst().

◆ GetIndexBySecond()

template<class TAlnRange >
const TIndexBySecond& CAlignRangeCollectionList< TAlnRange >::GetIndexBySecond ( ) const
inline

Definition at line 1028 of file align_range_coll.hpp.

Referenced by SubtractOnSecond().

◆ GetInsertions()

template<class TAlnRange >
const TInsertions& CAlignRangeCollectionList< TAlnRange >::GetInsertions ( void  ) const
inline

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 1538 of file align_range_coll.hpp.

Referenced by CAlignRangeCollection< TAlnRange >::Assign(), CheckPairwiseAln(), DumpPairwiseAln(), MergePairwiseAlns(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwiseToAlnCoords(), CMergedPairwiseAln::x_AddPairwise(), and CSparseAln::x_Build().

◆ GetPolicyFlags()

template<class TAlnRange >
int CAlignRangeCollectionList< TAlnRange >::GetPolicyFlags ( ) const
inline

Definition at line 1272 of file align_range_coll.hpp.

Referenced by CreateAnchoredAlnVec(), MergePairwiseAlns(), CAnchoredAln::SplitStrands(), SubtractAlnRngCollections(), and CMergedPairwiseAln::x_AddPairwise().

◆ GetSecondPosByFirstPos()

template<class TAlnRange >
TSignedSeqPos CAlignRangeCollectionList< TAlnRange >::GetSecondPosByFirstPos ( position_type  pos,
ESearchDirection  dir = eNone 
) const
inline

Definition at line 1280 of file align_range_coll.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CheckPairwiseAln(), DumpPairwiseAln(), and s_TranslatePairwise().

◆ GetStateFlags()

template<class TAlnRange >
int CAlignRangeCollectionList< TAlnRange >::GetStateFlags ( ) const
inline

Definition at line 1276 of file align_range_coll.hpp.

◆ insert() [1/2]

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::insert ( const TAlignRange &  r)
inline

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]

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::insert ( const_iterator  it,
const TAlignRange &  arg_r 
)
inline

Definition at line 1050 of file align_range_coll.hpp.

◆ IntersectFirst()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::IntersectFirst ( const CRange< position_type > &  range)
inline

Definition at line 1543 of file align_range_coll.hpp.

◆ IntersectSecond()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::IntersectSecond ( const CRange< position_type > &  range)
inline

Definition at line 1548 of file align_range_coll.hpp.

◆ IsSet()

template<class TAlnRange >
bool CAlignRangeCollectionList< TAlnRange >::IsSet ( int  flags) const
inline

Definition at line 1268 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertion(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertions(), BuildAlignDataSource(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CreateAnchoredAlnVec(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), CAnchoredAln::SplitStrands(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_ValidateFlags().

◆ Normalize()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::Normalize ( void  )
inline

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 >
const TAlignRange& CAlignRangeCollectionList< TAlnRange >::operator[] ( size_type  pos) const
inline

Use iterator access.

Definition at line 1137 of file align_range_coll.hpp.

◆ pop_back()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::pop_back ( void  )
inline

Definition at line 1131 of file align_range_coll.hpp.

◆ push_back()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::push_back ( const TAlignRange &  r)
inline

Definition at line 1126 of file align_range_coll.hpp.

Referenced by CAnchoredAln::SplitStrands().

◆ rbegin()

template<class TAlnRange >
const_reverse_iterator CAlignRangeCollectionList< TAlnRange >::rbegin ( void  ) const
inline

Definition at line 970 of file align_range_coll.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstLength(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstTo(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFirstToOpen().

◆ rend()

template<class TAlnRange >
const_reverse_iterator CAlignRangeCollectionList< TAlnRange >::rend ( void  ) const
inline

Definition at line 975 of file align_range_coll.hpp.

◆ reserve()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::reserve ( int  count)
inline

Definition at line 952 of file align_range_coll.hpp.

◆ size()

template<class TAlnRange >
size_type CAlignRangeCollectionList< TAlnRange >::size ( void  ) const
inline

Definition at line 980 of file align_range_coll.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CDiagHit::CDiagHit(), CreateAlignSetFromPairwiseAln(), CreateDensegFromPairwiseAln(), and CreatePackedsegFromPairwiseAln().

◆ Sort()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::Sort ( void  )
inline

Definition at line 1394 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Normalize().

◆ SortInsertions()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::SortInsertions ( void  )
inline

Definition at line 1415 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertions(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort().

◆ Validate()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::Validate ( void  )
inline

analyses segements and updates flags

Definition at line 1447 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Normalize().

◆ ValidateRanges()

template<class TAlnRange >
static int CAlignRangeCollectionList< TAlnRange >::ValidateRanges ( const TAlignRange &  r_1,
const TAlignRange &  r_2 
)
inlinestatic

determine conflicts between two ranges

Definition at line 1481 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate().

◆ x_Equals()

template<class TAlnRange >
bool CAlignRangeCollectionList< TAlnRange >::x_Equals ( const TThisType &  c) const
inlineprotected

Definition at line 1591 of file align_range_coll.hpp.

◆ x_Erase()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_Erase ( TRawIterator  iter)
inlineprotected

Definition at line 1661 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert().

◆ x_FindInsertionPlace()

template<class TAlnRange >
iterator CAlignRangeCollectionList< TAlnRange >::x_FindInsertionPlace ( const TAlignRange &  r)
inlineprotected

Definition at line 1728 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_insertion_point(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert().

◆ x_FindRangeContaining()

template<class TAlnRange >
const_iterator CAlignRangeCollectionList< TAlnRange >::x_FindRangeContaining ( position_type  pos) const
inlineprotected

Definition at line 1675 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_2().

◆ x_FindRangesBySecondContaining()

template<class TAlnRange >
pair<pair<const_iterator, const_iterator>, bool> CAlignRangeCollectionList< TAlnRange >::x_FindRangesBySecondContaining ( position_type  pos) const
inlineprotected

Definition at line 1701 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_2_by_second(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::find_by_second().

◆ x_GetAlignRangeVector()

template<class TAlnRange >
TAlignRangeVectorImpl& CAlignRangeCollectionList< TAlnRange >::x_GetAlignRangeVector ( ) const
inlineprotected

Definition at line 1596 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::operator[]().

◆ x_Index()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_Index ( TIndexKey  iter)
inlineprotected

Definition at line 1605 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_IndexAll(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Insert().

◆ x_IndexAll()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_IndexAll ( )
inlineprotected

Definition at line 1637 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CAlignRangeCollectionList().

◆ x_Insert()

template<class TAlnRange >
TRawIterator CAlignRangeCollectionList< TAlnRange >::x_Insert ( TRawIterator  where,
const TAlignRange &  r 
)
inlineprotected

Definition at line 1648 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert().

◆ x_IntersectFirst()

template<class TAlnRange >
template<class TRanges >
void CAlignRangeCollectionList< TAlnRange >::x_IntersectFirst ( TRanges &  ranges,
const CRange< position_type > &  range 
)
inlineprotected

Definition at line 1760 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectFirst().

◆ x_IntersectSecond()

template<class TAlnRange >
template<class TRanges >
void CAlignRangeCollectionList< TAlnRange >::x_IntersectSecond ( TRanges &  ranges,
const CRange< position_type > &  range 
)
inlineprotected

Definition at line 1777 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectSecond().

◆ x_MultiplyCoordsBy3()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_MultiplyCoordsBy3 ( )
inlineprotected

Definition at line 1740 of file align_range_coll.hpp.

◆ x_ResetFlags()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_ResetFlags ( int  flags)
inlineprotected

Definition at line 1558 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::clear(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate().

◆ x_SetFlags()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_SetFlags ( int  flags)
inlineprotected

Definition at line 1554 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_ValidateFlags().

◆ x_Unindex()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_Unindex ( TIndexKey  iter)
inlineprotected

Definition at line 1632 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Erase().

◆ x_UnindexAll()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_UnindexAll ( )
inlineprotected

Definition at line 1643 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::clear().

◆ x_UnindexByFirst()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_UnindexByFirst ( TIndexKey  iter)
inlineprotected

Definition at line 1610 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Unindex().

◆ x_UnindexBySecond()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_UnindexBySecond ( TIndexKey  iter)
inlineprotected

Definition at line 1621 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Unindex().

◆ x_ValidateFlags()

template<class TAlnRange >
void CAlignRangeCollectionList< TAlnRange >::x_ValidateFlags ( )
inlineprotected

Definition at line 1562 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert().

Member Data Documentation

◆ m_Flags

template<class TAlnRange >
int CAlignRangeCollectionList< TAlnRange >::m_Flags
protected

Definition at line 1796 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetPolicyFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetStateFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IsSet(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_ResetFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_SetFlags(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_ValidateFlags().

◆ m_IndexByFirst

template<class TAlnRange >
TIndexByFirst CAlignRangeCollectionList< TAlnRange >::m_IndexByFirst
protected

combination of EFlags

Definition at line 1798 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetIndexByFirst(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::reserve(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Sort(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindInsertionPlace(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindRangeContaining(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Index(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_UnindexAll(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_UnindexByFirst().

◆ m_IndexBySecond

template<class TAlnRange >
TIndexBySecond CAlignRangeCollectionList< TAlnRange >::m_IndexBySecond
protected

Definition at line 1799 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetIndexBySecond(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::reserve(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_FindRangesBySecondContaining(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Index(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_UnindexAll(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_UnindexBySecond().

◆ m_Insertions

template<class TAlnRange >
TInsertions CAlignRangeCollectionList< TAlnRange >::m_Insertions
protected

Definition at line 1795 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertion(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertions(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::GetInsertions(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectFirst(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IntersectSecond(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::SortInsertions(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_MultiplyCoordsBy3().

◆ m_RangesList

template<class TAlnRange >
TAlignRangeList CAlignRangeCollectionList< TAlnRange >::m_RangesList
protected

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 >
TAlignRangeVectorImpl CAlignRangeCollectionList< TAlnRange >::m_RangesVector
mutableprotected

Definition at line 1793 of file align_range_coll.hpp.

Referenced by CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::clear(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::reserve(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Erase(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_GetAlignRangeVector(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_Insert(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_MultiplyCoordsBy3().

The documentation for this class was generated from the following file:
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Modified on Fri Sep 20 14:57:21 2024 by modify_doxy.py rev. 669887