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NCBI C++ ToolKit: CDiagRangeCollection Class Reference
Search Toolkit Book for CDiagRangeCollection
#include <objtools/alnmgr/alndiag.hpp>
CDiagRangeCollection (int first_width=1, int second_width=1) Constructor. More...
void Diff (const TAlnRngColl &substrahend, TAlnRngColl &difference) Calculate a difference. More...
void TrimFirstFrom (TAlnRng &rng, int trim) Trimming methods. More...
void TrimFirstTo (TAlnRng &rng, int trim) void TrimSecondFrom (TAlnRng &rng, int trim) void TrimSecondTo (TAlnRng &rng, int trim) CAlignRangeCollection (int flags=fDefaultPolicy) CAlignRangeCollection (const TAlignRangeVector &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 TAlignRangeVector &insertions) void AddInsertions (const TThisType &collection) const TAlignRangeVector & 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) void reserve (int count) void Assign (const CAlignRangeCollectionList< TAlignRange > &src) 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_iterator find_insertion_point (const TAlignRange &r) const_iterator insert (const TAlignRange &r) const_iterator insert (const_iterator where, const TAlignRange &r) const_iterator erase (const_iterator it) void push_back (const TAlignRange &r) void pop_back () const TAlignRange & operator[] (size_type pos) const TAlignRange & operator[] (size_type pos) 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 lower_bound (position_type pos) const const_iterator upper_bound (position_type pos) const
Definition at line 44 of file alndiag.hpp.
◆ TAlnRng ◆ TAlnRngColl ◆ TAlnRngCollExt ◆ CDiagRangeCollection() CDiagRangeCollection::CDiagRangeCollection ( int first_width = 1, int second_width = 1 ) ◆ Diff() ◆ TrimFirstFrom() void CDiagRangeCollection::TrimFirstFrom ( TAlnRng & rng, int trim ) inline ◆ TrimFirstTo() void CDiagRangeCollection::TrimFirstTo ( TAlnRng & rng, int trim ) inline ◆ TrimSecondFrom() void CDiagRangeCollection::TrimSecondFrom ( TAlnRng & rng, int trim ) inline ◆ TrimSecondTo() void CDiagRangeCollection::TrimSecondTo ( TAlnRng & rng, int trim ) inline ◆ x_Diff() ◆ x_DiffSecond() ◆ m_Extender ◆ m_FirstWidth int CDiagRangeCollection::m_FirstWidth private ◆ m_SecondWidth int CDiagRangeCollection::m_SecondWidth private
The documentation for this class was generated from the following files:
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