#include <SeqLoc.h>
Inheritance diagram for SeqLoc:
Public Member Functions | |
SeqLoc (dsu::Strand_t, int, int) | |
a sequence location is made up of a strand, (positive or negative, or both) and the 5' 3' location. | |
SeqLoc (const SeqLoc &) | |
copy constructor | |
virtual | ~SeqLoc () |
object does not manage dynamic memory allocation | |
dsu::Strand_t | getStrnd () const |
return which strand this location refers to | |
int | getEnd5 () const |
get 5' end (always from positive perspective) | |
int | getEnd3 () const |
get 3' end (always from positive perspective) | |
bool | inRange (int) const |
unsigned | length () const |
sequence location length: 3'-5'+1 | |
bool | isEnd5Set () const |
if 5' == -1 returns false, true otherwise | |
bool | isEnd3Set () const |
if 3' == -1 returns false, true otherwise | |
bool | operator== (const SeqLoc &sl) const |
returns true if both sequence locations are on the same strand, and have the same 5' and 3' values | |
virtual const string & | getTypeStr () const |
object identifier, useful, for polymorophic applications of SeqLoc | |
virtual void | print (std::ostream &, const string &="") const |
print sequence location information | |
virtual int | getClosestEnd5 (int) const |
returns 5' (derived classes overide this behavior) | |
virtual int | getClosestEnd3 (int, int) const |
returns 3' (derived classes overide this behavior) | |
virtual bool | isActualOverlap (int, int) const |
Precondition, int,int are already within the boundaries of this sequence location this only applies to seqlocations broken into sub sequence elements, e.g. | |
void | setEnd5 (int) |
user can set 5' end | |
void | setEnd3 (int) |
user can set 3' end | |
void | setStrnd (dsu::Strand_t strnd) |
user can set 3' end | |
Friends | |
std::ostream & | operator<< (std::ostream &, const SeqLoc &) |
bool | operator< (const SeqLoc &, const SeqLoc &) |
bool | isOverlap (const SeqLoc &, const SeqLoc &) |
This means that 5' < 3' always, and that the sequence location may refer to exclusively to one strand or both depending on the constructor Collaborators:
None. SeqLoc is the Base Class of a hierarchy
|
a sequence location is made up of a strand, (positive or negative, or both) and the 5' 3' location. 5' is from the positive strand perspective always, so 5' < 3' always. The 5' and 3' coordinates are inclusive so that the length of the sequence is 3'-5'+1
|
|
|
|
Precondition, int,int are already within the boundaries of this sequence location this only applies to seqlocations broken into sub sequence elements, e.g. |
|
print sequence location information
Reimplemented in DataSetAbstractProduct, and Prediction. |