RNA.h File Reference

#include <string>
#include <cstring>
#include "../src/defines.h"
#include "../src/rna_library.h"
#include "../src/pfunction.h"
#include "thermodynamics.h"
#include "../src/TProgressDialog.h"
#include "../src/phmm/utils/xmath/log/xlog_math.h"
#include "RsampleData.h"
#include "../src/algorithm.h"
#include "../src/draw.h"

Classes
class	RNA

Macros
#define	SEQUENCE_STRING   0
	A string containing the sequence – NOT a file name. More...
#define	FILE_CT   1
	CT Structure file. More...
#define	FILE_SEQ   2
	Sequence file (FASTA, SEQ or plain-text sequence) More...
#define	FILE_PFS   3
	Partition function save file (*.pfs) More...
#define	FILE_SAV   4
	Folding Save file (*.sav) More...
#define	FILE_DBN   5
	Dot-Bracket Notation Structure file (*.dbn, *.dot, *.bracket) More...
#define	FILE_MSA   6
	Multiple sequence alignemnt file FASTA format. More...

Typedefs
typedef int	RNAInputType
	RNA Class. More...

Macro Definition Documentation

FILE_CT

#define FILE_CT   1

CT Structure file.

FILE_DBN

#define FILE_DBN   5

Dot-Bracket Notation Structure file (*.dbn, *.dot, *.bracket)

FILE_MSA

#define FILE_MSA   6

Multiple sequence alignemnt file FASTA format.

FILE_PFS

#define FILE_PFS   3

Partition function save file (*.pfs)

FILE_SAV

#define FILE_SAV   4

Folding Save file (*.sav)

FILE_SEQ

#define FILE_SEQ   2

Sequence file (FASTA, SEQ or plain-text sequence)

SEQUENCE_STRING

#define SEQUENCE_STRING   0

A string containing the sequence – NOT a file name.

Typedef Documentation

RNAInputType

typedef int RNAInputType

RNA Class.

The RNA class provides an entry point for all the single sequence operations of RNAstructure.The following constants can be supplied to the RNA class constructor RNAInputType parameter to indicate the type of file represented by the filepathOrSequence parameter. 0 => A literal sequence (NOT a file) 1 => Structure File (CT, DBN/DOT/BRACKET) 2 => Sequence File (SEQ, FASTA, or text) 3 => Partition-Function-Save-File (PFS) 4 => Folding-Save-File (FSV or SAV) 5 => Bracket File (DBN/DOT/BRACKET) (1 will also work, but is slighly less efficient. 5 is more strict)