multovl
1.3
Multiple overlaps of genomic regions
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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"
Public Member Functions | |
GffLinereader () | |
Init to empty. | |
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BedLinereader () | |
Sets up a BedLinereader object. | |
virtual bool | read_into (Region ®ion) const |
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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. | |
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virtual void | reset () |
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void | set_statusflag (Status flag) |
Additional Inherited Members | |
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enum | Status { CLEAN = 0, ERROR = 1, EMPTY = 2, COMMENT = 4, DATA = 8 } |
Symbolic constants to signify the result of a parsing operation. More... | |
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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) |
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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 |
Linereader for GFF-formatted lines. Only the columns containing coordinate information are parsed, the rest are ignored. No distinction between GFF2 and GFF3.