multovl  1.3
Multiple overlaps of genomic regions
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multovl::io::GffLinereader Class Reference

Linereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3. More...

#include "linereader.hh"

Inheritance diagram for multovl::io::GffLinereader:
multovl::io::BedLinereader multovl::io::Linereader

Public Member Functions

 GffLinereader ()
 Init to empty.
 
- Public Member Functions inherited from multovl::io::BedLinereader
 BedLinereader ()
 Sets up a BedLinereader object.
 
virtual bool read_into (Region &region) const
 
- Public Member Functions inherited from multovl::io::Linereader
 Linereader (const std::string &commentchars="#")
 
Status parse (const std::string &line)
 
Status status () const
 
const std::string & comment () const
 
size_t fieldcnt () const
 
const std::string & error_msg () const
 
const std::string & chrom () const
 
unsigned int first () const
 
unsigned int last () const
 
char strand () const
 
const std::string & name () const
 

Protected Member Functions

virtual void parse_data (const std::string &line)
 Parse a /line/ assuming it contains GFF-formatted data.
 
- Protected Member Functions inherited from multovl::io::BedLinereader
virtual void reset ()
 
- Protected Member Functions inherited from multovl::io::Linereader
void set_statusflag (Status flag)
 

Additional Inherited Members

- Public Types inherited from multovl::io::Linereader
enum  Status {
  CLEAN = 0, ERROR = 1, EMPTY = 2, COMMENT = 4,
  DATA = 8
}
 Symbolic constants to signify the result of a parsing operation. More...
 
- Static Protected Member Functions inherited from multovl::io::Linereader
static bool empty_white (const std::string &str)
 Returns /true/ if /str/ is empty or contains whitespace characters only.
 
static unsigned int str_to_uint (std::string &str) throw (Exception)
 
- Protected Attributes inherited from multovl::io::Linereader
Status _status
 the status after parsing
 
size_t _fieldcnt
 how many column fields have been seen
 
std::string _comment
 store a comment line
 
std::string _err
 stores parsing error messages
 
std::string _chrom
 
std::string _name
 
unsigned int _first
 
unsigned int _last
 
char _strand
 

Detailed Description

Linereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3.


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