OpenStructure
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#include <aligned_region.hh>
Public Types | |
typedef AlignedColumnIterator | iterator |
Public Member Functions | |
AlignedRegion (const AlignmentHandle &aln, int start, int end, int master=-1) | |
int | GetEnd () const |
int | GetStart () const |
int | GetMaster () const |
void | SetMaster (int master) |
void | Delete () |
void | Replace (const AlignedRegion &aln_r) |
void | ShiftLeft (int n) |
void | ShiftRight (int n) |
int | GetLength () const |
AlignmentHandle | GetAlignmentHandle () const |
AlignedColumn | operator[] (int index) const |
AlignedColumnIterator | begin () |
AlignedColumnIterator | end () |
bool | operator== (const AlignedRegion &rhs) const |
bool | operator!= (const AlignedRegion &rhs) const |
represents a region in a sequence alignment
The region covers the half-closed interval start/stop.
You should never need to construct an aligned region manually. Use one of the helper methods of AlignmentHandle.
Definition at line 38 of file aligned_region.hh.
typedef AlignedColumnIterator iterator |
Definition at line 40 of file aligned_region.hh.
AlignedRegion | ( | const AlignmentHandle & | aln, |
int | start, | ||
int | end, | ||
int | master = -1 |
||
) |
AlignedColumnIterator begin | ( | ) |
iterator pointing at start of aligned region
void Delete | ( | ) |
delete interval and update length of AlignedRegion
AlignedColumnIterator end | ( | ) |
iterator pointing at end of aligned region.
AlignmentHandle GetAlignmentHandle | ( | ) | const |
retrieve alignment handle for aligned region
int GetEnd | ( | ) | const |
get end of aligned region
int GetLength | ( | ) | const |
length of the aligned region
int GetMaster | ( | ) | const |
int GetStart | ( | ) | const |
get start of aligned region
bool operator!= | ( | const AlignedRegion & | rhs | ) | const |
bool operator== | ( | const AlignedRegion & | rhs | ) | const |
AlignedColumn operator[] | ( | int | index | ) | const |
get aligned column at given index
The indices range from 0 to GetLength()-1.
void Replace | ( | const AlignedRegion & | aln_r | ) |
replace region with content of AlignedRegion and set length to length of aln_r
void SetMaster | ( | int | master | ) |
void ShiftLeft | ( | int | n | ) |
shift the aligned region of the master sequence to the left by n characters.
void ShiftRight | ( | int | n | ) |
shift the aligned region of the master sequence to the right by n characters.