multovl  1.3
Multiple overlaps of genomic regions
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multovl::AncestorRegion Class Reference

AncestorRegion objects represent the regions that give rise to overlaps. They are essentially Region-s, with the additional track ID attribute (an uint) that indicates which track they belong to. Track IDs are assigned by client programs and may indirectly refer to files or database objects. More...

#include "ancregion.hh"

Inheritance diagram for multovl::AncestorRegion:
multovl::Region

Public Member Functions

 AncestorRegion ()
 Init to empty.
 
 AncestorRegion (const Region &region, unsigned int trackid=0)
 Init with base class /region/ and /trackid/ (default 0)
 
 AncestorRegion (unsigned int f, unsigned int l, char s, const std::string &nm, unsigned int trackid=0)
 
const unsigned int & track_id () const
 Returns the current track ID.
 
unsigned int track_id (unsigned int trackid)
 Sets the track ID to /trackid/. Returns old track ID.
 
bool operator== (const AncestorRegion &rhs) const
 Equality. All fields must be equal.
 
bool operator< (const AncestorRegion &rhs) const
 
std::string to_attrstring () const
 
- Public Member Functions inherited from multovl::Region
 Region ()
 Inits to empty (makes sense when using as input buffer)
 
 Region (unsigned int f, unsigned int l, char s, const std::string &nm)
 
virtual ~Region ()
 empty virtual dtor
 
void set_coords (unsigned int f, unsigned int l)
 
void strand (char s)
 Sets the strand.
 
std::string name (const std::string &nm)
 
const unsigned int & first () const
 Returns the first coordinate.
 
const unsigned int & last () const
 Returns the last coordinate.
 
const unsigned int & length () const
 Returns the length.
 
bool is_empty () const
 Zero-length regions are considered empty.
 
const char & strand () const
 Returns the strand information.
 
const std::string & name () const
 Returns the name of the region.
 
bool equal_pos (const Region &rhs) const
 
bool operator== (const Region &rhs) const
 
bool operator< (const Region &rhs) const
 

Friends

class boost::serialization::access
 

Detailed Description

AncestorRegion objects represent the regions that give rise to overlaps. They are essentially Region-s, with the additional track ID attribute (an uint) that indicates which track they belong to. Track IDs are assigned by client programs and may indirectly refer to files or database objects.

Constructor & Destructor Documentation

multovl::AncestorRegion::AncestorRegion ( unsigned int  f,
unsigned int  l,
char  s,
const std::string &  nm,
unsigned int  trackid = 0 
)
inline

Inits to contain the genomic region with positions [f..l], strand /s/, name /nm/, track ID /trackid/.

Member Function Documentation

bool multovl::AncestorRegion::operator< ( const AncestorRegion rhs) const

Ordering. Sorted on the track ID, then on the coordinates and the name (lexicographically).

std::string multovl::AncestorRegion::to_attrstring ( ) const

Makes a string that describes the ancestor region so that it can be put in a GFF-style ANCESTORS attribute when Multovl prints the overlaps. The format is "<trackid>:<name>:<strand>:<first>-<last>"


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